International Journal of Molecular Sciences

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4 pages, 201 KiB

Open AccessEditorial

Comparative Genomics and Functional Genomics Analysis in Plants

by Jiacheng Wang, Yaojia Chen and Quan Zou

Int. J. Mol. Sci. 2023, 24(7), 6539; https://doi.org/10.3390/ijms24076539 - 31 Mar 2023

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Abstract

Comparative genomics and functional genomics are two basic branches of plant genomics [...] Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

Research

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23 pages, 5439 KiB

Open AccessArticle

De Novo Transcriptome Profiling for the Generation and Validation of Microsatellite Markers, Transcription Factors, and Database Development for Andrographis paniculata

by Rakesh Singh, Akshay Singh, Ajay Kumar Mahato, Ritu Paliwal, Gunjan Tiwari and Ashok Kumar

Int. J. Mol. Sci. 2023, 24(11), 9212; https://doi.org/10.3390/ijms24119212 - 24 May 2023

Cited by 4 | Viewed by 1986

Abstract

Andrographis paniculata belongs to the family Acanthaceae and is known for its medicinal properties owing to the presence of unique constituents belonging to the lactones, diterpenoids, diterpene glycosides, flavonoids, and flavonoid glycosides groups of chemicals. Andrographolide, a major therapeutic constituent of A. paniculata, [...] Read more.

Andrographis paniculata belongs to the family Acanthaceae and is known for its medicinal properties owing to the presence of unique constituents belonging to the lactones, diterpenoids, diterpene glycosides, flavonoids, and flavonoid glycosides groups of chemicals. Andrographolide, a major therapeutic constituent of A. paniculata, is extracted primarily from the leaves of this plant and exhibits antimicrobial and anti-inflammatory activities. Using 454 GS-FLX pyrosequencing, we have generated a whole transcriptome profile of entire leaves of A. paniculata. A total of 22,402 high-quality transcripts were generated, with an average transcript length and N50 of 884 bp and 1007 bp, respectively. Functional annotation revealed that 19,264 (86%) of the total transcripts showed significant similarity with the NCBI-Nr database and were successfully annotated. Out of the 19,264 BLAST hits, 17,623 transcripts were assigned GO terms and distributed into three major functional categories: molecular function (44.62%), biological processes (29.19%), and cellular component (26.18%) based on BLAST2GO. Transcription factor analysis showed 6669 transcripts, belonging to 57 different transcription factor families. Fifteen TF genes that belong to the NAC, MYB, and bHLH TF categories were validated by RT PCR amplification. In silico analysis of gene families involved in the synthesis of biochemical compounds having medicinal values, such as cytochrome p450, protein kinases, heat shock proteins, and transporters, was completed and a total of 102 different transcripts encoding enzymes involved in the biosynthesis of terpenoids were predicted. Out of these, 33 transcripts belonged to terpenoid backbone biosynthesis. This study also identified 4254 EST-SSRs from 3661 transcripts, representing 16.34% of the total transcripts. Fifty-three novel EST-SSR markers generated from our EST dataset were used to assess the genetic diversity among eighteen A. paniculata accessions. The genetic diversity analysis revealed two distinct sub-clusters and all accessions based on the genetic similarity index were distinct from each other. A database based on EST transcripts, EST-SSR markers, and transcription factors has been developed using data generated from the present study combined with available transcriptomic resources from a public database using Meta transcriptome analysis to make genomic resources available in one place to the researchers working on this medicinal plant. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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29 pages, 1584 KiB

Open AccessArticle

Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

by Dmitry I. Karetnikov, Gennady V. Vasiliev, Stepan V. Toshchakov, Nikolay A. Shmakov, Mikhail A. Genaev, Mikhail A. Nesterov, Salmaz M. Ibragimova, Daniil A. Rybakov, Tatjana A. Gavrilenko, Elena A. Salina, Maxim V. Patrushev, Alex V. Kochetov and Dmitry A. Afonnikov

Int. J. Mol. Sci. 2023, 24(6), 5713; https://doi.org/10.3390/ijms24065713 - 16 Mar 2023

Cited by 3 | Viewed by 3054

Abstract

Solanum tuberosum L. (common potato) is one of the most important crops produced almost all over the world. Genomic sequences of potato opens the way for studying the molecular variations related to diversification. We performed a reconstruction of genomic sequences for 15 tetraploid [...] Read more.

Solanum tuberosum L. (common potato) is one of the most important crops produced almost all over the world. Genomic sequences of potato opens the way for studying the molecular variations related to diversification. We performed a reconstruction of genomic sequences for 15 tetraploid potato cultivars grown in Russia using short reads. Protein-coding genes were identified; conserved and variable parts of pan-genome and the repertoire of the NBS-LRR genes were characterized. For comparison, we used additional genomic sequences for twelve South American potato accessions, performed analysis of genetic diversity, and identified the copy number variations (CNVs) in two these groups of potato. Genomes of Russian potato cultivars were more homogeneous by CNV characteristics and have smaller maximum deletion size in comparison with South American ones. Genes with different CNV occurrences in two these groups of potato accessions were identified. We revealed genes of immune/abiotic stress response, transport and five genes related to tuberization and photoperiod control among them. Four genes related to tuberization and photoperiod were investigated in potatoes previously (phytochrome A among them). A novel gene, homologous to the poly(ADP-ribose) glycohydrolase (PARG) of Arabidopsis, was identified that may be involved in circadian rhythm control and contribute to the acclimatization processes of Russian potato cultivars. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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16 pages, 2768 KiB

Open AccessArticle

Insight into the Organization of the B10v3 Cucumber Genome by Integration of Biological and Bioinformatic Data

by Szymon Turek, Wojciech Pląder, Yoshikazu Hoshi, Agnieszka Skarzyńska and Magdalena Pawełkowicz

Int. J. Mol. Sci. 2023, 24(4), 4011; https://doi.org/10.3390/ijms24044011 - 16 Feb 2023

Cited by 6 | Viewed by 1969

Abstract

The availability of a well-organized and annotated reference genome is essential for genome research and the analysis of re-sequencing approaches. The B10v3 cucumber (Cucumis sativus L.) reference genome has been sequenced and assembled into 8035 contigs, a small fraction of which have [...] Read more.

The availability of a well-organized and annotated reference genome is essential for genome research and the analysis of re-sequencing approaches. The B10v3 cucumber (Cucumis sativus L.) reference genome has been sequenced and assembled into 8035 contigs, a small fraction of which have been mapped to individual chromosomes. Currently, bioinformatics methods based on comparative homology have made it possible to re-order the sequenced contigs by mapping them to the reference genomes. The B10v3 genome (North-European, Borszczagowski line) was rearranged against the genomes of cucumber 9930 (‘Chinese Long’ line) and Gy14 (North American line). Furthermore, a better insight into the organization of the B10v3 genome was obtained by integrating the data available in the literature on the assignment of contigs to chromosomes in the B10v3 genome with the results of the bioinformatic analysis. The combination of information on the markers used in the assembly of the B10v3 genome and the results of FISH and DArT-seq experiments confirmed the reliability of the in silico assignment. Approximately 98% of the protein-coding genes within the chromosomes were assigned and a significant proportion of the repetitive fragments in the sequenced B10v3 genome were identified using the RagTag programme. In addition, BLAST analyses provided comparative information between the B10v3 genome and the 9930 and Gy14 data sets. This revealed both similarities and differences in the functional proteins found between the coding sequences region in the genomes. This study contributes to better knowledge and understanding of cucumber genome line B10v3. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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12 pages, 299 KiB

Open AccessArticle

De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions

by Brennan Hyden, Kai Feng, Timothy B. Yates, Sara Jawdy, Chelsea Cereghino, Lawrence B. Smart and Wellington Muchero

Int. J. Mol. Sci. 2023, 24(3), 2904; https://doi.org/10.3390/ijms24032904 - 2 Feb 2023

Cited by 2 | Viewed by 2682

Abstract

Poplar and willow species in the Salicaceae are dioecious, yet have been shown to use different sex determination systems located on different chromosomes. Willows in the subgenus Vetrix are interesting for comparative studies of sex determination systems, yet genomic resources for these species [...] Read more.

Poplar and willow species in the Salicaceae are dioecious, yet have been shown to use different sex determination systems located on different chromosomes. Willows in the subgenus Vetrix are interesting for comparative studies of sex determination systems, yet genomic resources for these species are still quite limited. Only a few annotated reference genome assemblies are available, despite many species in use in breeding programs. Here we present de novo assemblies and annotations of 11 shrub willow genomes from six species. Copy number variation of candidate sex determination genes within each genome was characterized and revealed remarkable differences in putative master regulator gene duplication and deletion. We also analyzed copy number and expression of candidate genes involved in floral secondary metabolism, and identified substantial variation across genotypes, which can be used for parental selection in breeding programs. Lastly, we report on a genotype that produces only female descendants and identified gene presence/absence variation in the mitochondrial genome that may be responsible for this unusual inheritance. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

16 pages, 3510 KiB

Open AccessArticle

Genome-Wide Association Studies of Seven Root Traits in Soybean (Glycine max L.) Landraces

by Seong-Hoon Kim, Rupesh Tayade, Byeong-Hee Kang, Bum-Soo Hahn, Bo-Keun Ha and Yoon-Ha Kim

Int. J. Mol. Sci. 2023, 24(1), 873; https://doi.org/10.3390/ijms24010873 - 3 Jan 2023

Cited by 7 | Viewed by 4042

Abstract

Soybean [Glycine max (L.) Merr.], an important oilseed crop, is a low-cost source of protein and oil. In Southeast Asia and Africa, soybeans are widely cultivated for use as traditional food and feed and industrial purposes. Given the ongoing changes in global [...] Read more.

Soybean [Glycine max (L.) Merr.], an important oilseed crop, is a low-cost source of protein and oil. In Southeast Asia and Africa, soybeans are widely cultivated for use as traditional food and feed and industrial purposes. Given the ongoing changes in global climate, developing crops that are resistant to climatic extremes and produce viable yields under predicted climatic conditions will be essential in the coming decades. To develop such crops, it will be necessary to gain a thorough understanding of the genetic basis of agronomic and plant root traits. As plant roots generally lie beneath the soil surface, detailed observations and phenotyping throughout plant development present several challenges, and thus the associated traits have tended to be ignored in genomics studies. In this study, we phenotyped 357 soybean landraces at the early vegetative (V2) growth stages and used a 180 K single-nucleotide polymorphism (SNP) soybean array in a genome-wide association study (GWAS) conducted to determine the phenotypic relationships among root traits, elucidate the genetic bases, and identify significant SNPs associated with root trait-controlling genomic regions/loci. A total of 112 significant SNP loci/regions were detected for seven root traits, and we identified 55 putative candidate genes considered to be the most promising. Our findings in this study indicate that a combined approach based on SNP array and GWAS analyses can be applied to unravel the genetic basis of complex root traits in soybean, and may provide an alternative high-resolution marker strategy to traditional bi-parental mapping. In addition, the identified SNPs, candidate genes, and diverse variations in the root traits of soybean landraces will serve as a valuable basis for further application in genetic studies and the breeding of climate-resilient soybeans characterized by improved root traits. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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18 pages, 856 KiB

Open AccessArticle

Gain or Loss? Evidence for Legume Predisposition to Symbiotic Interactions with Rhizobia via Loss of Pathogen-Resistance-Related Gene Families

by Katarzyna B. Czyż, Candy M. Taylor, Michał Kawaliło and Grzegorz Koczyk

Int. J. Mol. Sci. 2022, 23(24), 16003; https://doi.org/10.3390/ijms232416003 - 15 Dec 2022

Cited by 1 | Viewed by 1752

Abstract

Nodulation is a hallmark yet non-universal characteristic of legumes. It is unknown whether the mechanisms underlying nitrogen-fixing symbioses evolved within legumes and the broader nitrogen-fixing clade (NFC) repeatedly de novo or based on common ancestral pathways. Ten new transcriptomes representing members from the [...] Read more.

Nodulation is a hallmark yet non-universal characteristic of legumes. It is unknown whether the mechanisms underlying nitrogen-fixing symbioses evolved within legumes and the broader nitrogen-fixing clade (NFC) repeatedly de novo or based on common ancestral pathways. Ten new transcriptomes representing members from the Cercidoideae and Caesalpinioideae subfamilies were supplemented with published omics data from 65 angiosperms, to investigate how gene content correlates with nodulation capacity within Fabaceae and the NFC. Orthogroup analysis categorized annotated genes into 64150 orthogroups, of which 19 were significantly differentially represented between nodulating versus non-nodulating NFC species and were most commonly absent in nodulating taxa. The distribution of six over-represented orthogroups within Viridiplantae representatives suggested that genomic evolution events causing gene family expansions, including whole-genome duplications (WGDs), were unlikely to have facilitated the development of stable symbioses within Fabaceae as a whole. Instead, an absence of representation of 13 orthogroups indicated that losses of genes involved in trichome development, defense and wounding responses were strongly associated with rhizobial symbiosis in legumes. This finding provides novel evidence of a lineage-specific predisposition for the evolution and/or stabilization of nodulation in Fabaceae, in which a loss of pathogen resistance genes may have allowed for stable mutualistic interactions with rhizobia. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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22 pages, 41104 KiB

Open AccessArticle

Genome-Wide Identification of Wheat KNOX Gene Family and Functional Characterization of TaKNOX14-D in Plants

by Song Li, Yaxin Yao, Wenjie Ye, Shaoyu Wang, Chao Zhang, Shudong Liu, Fengli Sun and Yajun Xi

Int. J. Mol. Sci. 2022, 23(24), 15918; https://doi.org/10.3390/ijms232415918 - 14 Dec 2022

Cited by 6 | Viewed by 3172

Abstract

The KNOX genes play important roles in maintaining SAM and regulating the development of plant leaves. However, the TaKNOX genes in wheat are still not well understood, especially their role in abiotic stress. In this study, a total of 36 KNOX genes were [...] Read more.

The KNOX genes play important roles in maintaining SAM and regulating the development of plant leaves. However, the TaKNOX genes in wheat are still not well understood, especially their role in abiotic stress. In this study, a total of 36 KNOX genes were identified, and we demonstrated the function of the TaKNOX14-D gene under mechanical injury and cold stress. Thirty-six TaKNOX genes were divided into two groups, and thirty-four TaKNOX genes were predicted to be located in the nucleus by Cell-PLoc. These genes contained five tandem duplications. Fifteen collinear gene pairs were exhibited in wheat and rice, one collinear gene pair was exhibited in wheat and Arabidopsis. The phylogenetic tree and motif analysis suggested that the TaKNOX gene appeared before C3 and C4 diverged. Gene structure showed that the numbers of exons and introns in TaKNOX gene are different. Wheat TaKNOX genes showed different expression patterns during the wheat growth phase, with seven TaKNOX genes being highly expressed in the whole growth period. These seven genes were also highly expressed in most tissues, and also responded to most abiotic stress. Eleven TaKNOX genes were up-regulated in the tillering node during the leaf regeneration period after mechanical damage. When treating the wheat with different hormones, the expression patterns of TaKNOX were changed, and results showed that ABA promoted TaKNOX expression and seven TaKNOX genes were up-regulated under cytokinin and auxin treatment. Overexpression of the TaKNOX14-D gene in Arabidopsis could increase the leaf size, plant height and seed size. This gene overexpression in Arabidopsis also increased the compensatory growth capacity after mechanical damage. Overexpression lines also showed high resistance to cold stress. This study provides a better understanding of the TaKNOX genes. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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21 pages, 5063 KiB

Open AccessArticle

Comparative Genomics and Functional Studies of Putative m⁶A Methyltransferase (METTL) Genes in Cotton

by Junfeng Cao, Chaochen Huang, Jun’e Liu, Chenyi Li, Xia Liu, Zishou Zheng, Lipan Hou, Jinquan Huang, Lingjian Wang, Yugao Zhang, Xiaoxia Shangguan and Zhiwen Chen

Int. J. Mol. Sci. 2022, 23(22), 14111; https://doi.org/10.3390/ijms232214111 - 15 Nov 2022

Cited by 7 | Viewed by 2357

Abstract

N6-methyladenosine (m⁶A) RNA modification plays important regulatory roles in plant development and adapting to the environment, which requires methyltransferases to achieve the methylation process. However, there has been no research regarding m⁶A RNA methyltransferases in cotton. Here, a systematic [...] Read more.

N6-methyladenosine (m⁶A) RNA modification plays important regulatory roles in plant development and adapting to the environment, which requires methyltransferases to achieve the methylation process. However, there has been no research regarding m⁶A RNA methyltransferases in cotton. Here, a systematic analysis of the m⁶A methyltransferase (METTL) gene family was performed on twelve cotton species, resulting in six METTLs identified in five allotetraploid cottons, respectively, and three to four METTLs in the seven diploid species. Phylogenetic analysis of protein-coding sequences revealed that METTL genes from cottons, Arabidopsis thaliana, and Homo sapiens could be classified into three clades (METTL3, METTL14, and METTL-like clades). Cis-element analysis predicated the possible functions of METTL genes in G. hirsutum. RNA-seq data revealed that GhMETTL14 (GH_A07G0817/GH_D07G0819) and GhMETTL3 (GH_A12G2586/GH_D12G2605) had high expressions in root, stem, leaf, torus, petal, stamen, pistil, and calycle tissues. GhMETTL14 also had the highest expression in 20 and 25 dpa fiber cells, implying a potential role at the cell wall thickening stage. Suppressing GhMETTL3 and GhMETTL14 by VIGS caused growth arrest and even death in G. hirsutum, along with decreased m⁶A abundance from the leaf tissues of VIGS plants. Overexpression of GhMETTL3 and GhMETTL14 produced distinct differentially expressed genes (DEGs) in A. thaliana, indicating their possible divergent functions after gene duplication. Overall, GhMETTLs play indispensable but divergent roles during the growth of cotton plants, which provides the basis for the systematic investigation of m⁶A in subsequent studies to improve the agronomic traits in cotton. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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17 pages, 3075 KiB

Open AccessArticle

Integrated Genomic and Transcriptomic Elucidation of Flowering in Garlic

by Einat Shemesh-Mayer, Adi Faigenboim, Tomer E. Ben Michael and Rina Kamenetsky-Goldstein

Int. J. Mol. Sci. 2022, 23(22), 13876; https://doi.org/10.3390/ijms232213876 - 10 Nov 2022

Cited by 4 | Viewed by 2223

Abstract

Commercial cultivars of garlic are sterile, and therefore efficient breeding of this crop is impossible. Recent restoration of garlic fertility has opened new options for seed production and hybridization. Transcriptome catalogs were employed as a basis for garlic genetic studies, and in 2020 [...] Read more.

Commercial cultivars of garlic are sterile, and therefore efficient breeding of this crop is impossible. Recent restoration of garlic fertility has opened new options for seed production and hybridization. Transcriptome catalogs were employed as a basis for garlic genetic studies, and in 2020 the huge genome of garlic was fully sequenced. We provide conjoint genomic and transcriptome analysis of the regulatory network in flowering garlic genotypes. The genome analysis revealed phosphatidylethanolamine-binding proteins (PEBP) and LEAFY (LFY) genes that were not found at the transcriptome level. Functions of TFL-like genes were reduced and replaced by FT-like homologs, whereas homologs of MFT-like genes were not found. The discovery of three sequences of LFY-like genes in the garlic genome and confirmation of their alternative splicing suggest their role in garlic florogenesis. It is not yet clear whether AsLFY1 acts alone as the “pioneer transcription factor” or AsLFY2 also provides these functions. The presence of several orthologs of flowering genes that differ in their expression and co-expression network advocates ongoing evolution in the garlic genome and diversification of gene functions. We propose that the process of fertility deprivation in garlic cultivars is based on the loss of transcriptional functions of the specific genes. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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12 pages, 3669 KiB

Open AccessArticle

MnASI1 Mediates Resistance to Botrytis cinerea in Mulberry (Morus notabilis)

by Donghao Wang, Na Gong, Chaorui Liu, Suxia Li, Zhaocheng Guo, Gefan Wang, Qiqi Shang, Dongming Wang, Xianling Ji and Youchao Xin

Int. J. Mol. Sci. 2022, 23(21), 13372; https://doi.org/10.3390/ijms232113372 - 2 Nov 2022

Cited by 7 | Viewed by 1794

Abstract

Six α-amylase/subtilisin inhibitor genes (MnASIs) were identified from mulberry (Morus notabilis). In this study, bioinformatics and expression pattern analysis of six MnASIs were performed to determine their roles in resistance to B. cinerea. The expression of all six [...] Read more.

Six α-amylase/subtilisin inhibitor genes (MnASIs) were identified from mulberry (Morus notabilis). In this study, bioinformatics and expression pattern analysis of six MnASIs were performed to determine their roles in resistance to B. cinerea. The expression of all six MnASIs was significantly increased under Botrytis cinerea infection. MnASI1, which responded strongly to B. cinerea, was overexpressed in Arabidopsis and mulberry. The resistance of Arabidopsis and mulberry overexpressing MnASI1 gene to B. cinerea was significantly improved, the catalase (CAT) activity was increased, and the malondialdehyde (MDA) content was decreased after inoculation with B. cinerea. At the same time, H₂O₂ and O₂⁻ levels were reduced in MnASI1 transgenic Arabidopsis, reducing the damage of ROS accumulation to plants. In addition, MnASI1 transgenic Arabidopsis increased the expression of the salicylic acid (SA) pathway-related gene AtPR1. This study provides an important reference for further revealing the function of α-amylase/subtilisin inhibitors. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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12 pages, 1106 KiB

Open AccessArticle

A Novel RHS1 Locus in Rice Attributes Seed-Pod Shattering by the Regulation of Endogenous S-Nitrosothiols

by Bong-Gyu Mun, Muhammad Shahid, Gang Sub Lee, Adil Hussain and Byung-Wook Yun

Int. J. Mol. Sci. 2022, 23(21), 13225; https://doi.org/10.3390/ijms232113225 - 30 Oct 2022

Cited by 3 | Viewed by 2026

Abstract

Seed or pod shattering in rice (Oryza sativa) is considered to be one of the major factors involved in the domestication of rice as a crop. High seed shattering results in significant yield losses. In this study, we characterize the RICEHIGH [...] Read more.

Seed or pod shattering in rice (Oryza sativa) is considered to be one of the major factors involved in the domestication of rice as a crop. High seed shattering results in significant yield losses. In this study, we characterize the RICEHIGHSHATTERING 1 (RHS1) that corresponds to the locus LOC_Os04g41250 from a greenhouse screen, involving 145 Ac/Ds transposon mutant rice lines. The knockout mutant line rhs1 exhibited a significantly high shattering of grains in comparison to the wild-type plants. The exogenous application of nitric oxide (NO) resulted in a significant reduction in the expression of RHS1 in wild-type rice plants. The absence of RHS1, which encodes a putative armadillo/beta-catenin repeat family protein, resulted in high sensitivity of the rhs1 plants to nitrosative stress. Interestingly, the basal expression levels of QSH1 and SHAT1 genes (transcription factors that regulate seed-pod shattering in rice) were significantly lower in these plants than in wild-type plants; however, nitrosative stress negatively regulated the expression of QSH1 and SHAT1 in both WT and rhs1 plants, but positively regulated QSH4 expression in rhs1 plants alone. The expression levels of genes responsible for NO production (OsNIA1, OsNIA2, and OsNOA1) were lower in rhs1 plants than in WT plants under normal conditions. However, under nitrosative stress, the expression of OsNIA2 significantly increased in rhs1 plants. The expression of CPL1 (a negative regulator of seed shattering in rice) was significantly lower in rhs1 plants, and we found that CPL1 expression was correlated with S-nitrosothiol (SNO) alteration in rhs1. Interestingly noe1, a rice mutant with high SNO levels, exhibited low seed shattering, whereas rhs1 resulted in low SNO levels with high seed shattering. Therefore, RHS1 is a novel gene that negatively regulates the shattering trait in rice via regulation of endogenous SNO levels. However, the molecular mechanisms involved in the control of RHS1-mediated regulation of seed shattering and its interaction with nitric oxide and involvement in plant defense need to be investigated further. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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17 pages, 7537 KiB

Open AccessArticle

Comprehensive Identification and Analyses of the GRF Gene Family in the Whole-Genome of Four Juglandaceae Species

by Zhongrong Zhang, Shaowen Quan, Jianxin Niu, Caihua Guo, Chao Kang, Jinming Liu and Xing Yuan

Int. J. Mol. Sci. 2022, 23(20), 12663; https://doi.org/10.3390/ijms232012663 - 21 Oct 2022

Cited by 4 | Viewed by 2218

Abstract

The GRF gene family plays an important role in plant growth and development as regulators involved in plant hormone signaling and metabolism. However, the Juglandaceae GRF gene family remains to be studied. Here, we identified 15, 15, 19, and 20 GRF genes in [...] Read more.

The GRF gene family plays an important role in plant growth and development as regulators involved in plant hormone signaling and metabolism. However, the Juglandaceae GRF gene family remains to be studied. Here, we identified 15, 15, 19, and 20 GRF genes in J. regia, C. illinoinensis, J. sigillata, and J. mandshurica, respectively. The phylogeny shows that the Juglandaceae family GRF is divided into two subfamilies, the ε-group and the non-ε-group, and that selection pressure analysis did not detect amino acid loci subject to positive selection pressure. In addition, we found that the duplications of the Juglandaceae family GRF genes were all segmental duplication events, and a total of 79 orthologous gene pairs and one paralogous homologous gene pair were identified in four Juglandaceae families. The Ka/KS ratios between these homologous gene pairs were further analyzed, and the Ka/KS values were all less than 1, indicating that purifying selection plays an important role in the evolution of the Juglandaceae family GRF genes. The codon bias of genes in the GRF family of Juglandaceae species is weak, and is affected by both natural selection pressure and base mutation, and translation selection plays a dominant role in the mutation pressure in codon usage. Finally, expression analysis showed that GRF genes play important roles in pecan embryo development and walnut male and female flower bud development, but with different expression patterns. In conclusion, this study will serve as a rich genetic resource for exploring the molecular mechanisms of flower bud differentiation and embryo development in Juglandaceae. In addition, this is the first study to report the GRF gene family in the Juglandaceae family; therefore, our study will provide guidance for future comparative and functional genomic studies of the GRF gene family in the Juglandaceae specie. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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14 pages, 1902 KiB

Open AccessArticle

Transcriptome Analysis of Developing Grains from Wheat Cultivars TAM 111 and TAM 112 Reveal Cultivar-Specific Regulatory Networks

by Ze-Tian Fang, Rajan Kapoor, Aniruddha Datta, Shuyu Liu, Matthew A. Stull, Paige G. Seitz, Charles D. Johnson and Sakiko Okumoto

Int. J. Mol. Sci. 2022, 23(20), 12660; https://doi.org/10.3390/ijms232012660 - 21 Oct 2022

Cited by 2 | Viewed by 2251

Abstract

Wheat flour’s end-use quality is tightly linked to the quantity and composition of storage proteins in the endosperm. TAM 111 and TAM 112 are two popular cultivars grown in the Southern US Great Plains with significantly different protein content. To investigate regulatory differences, [...] Read more.

Wheat flour’s end-use quality is tightly linked to the quantity and composition of storage proteins in the endosperm. TAM 111 and TAM 112 are two popular cultivars grown in the Southern US Great Plains with significantly different protein content. To investigate regulatory differences, transcriptome data were analyzed from developing grains at early- and mid-filling stages. At the mid-filling stage, TAM 111 preferentially upregulated starch metabolism-related pathways compared to TAM 112, whereas amino acid metabolism and transporter-related pathways were over-represented in TAM 112. Elemental analyses also indicated a higher N percentage in TAM 112 at the mid-filling stage. To explore the regulatory variation, weighted correlation gene network was constructed from publicly available RNAseq datasets to identify the modules differentially regulated in TAM 111 and TAM 112. Further, the potential transcription factors (TFs) regulating those modules were identified using graphical least absolute shrinkage and selection operator (GLASSO). Homologs of the OsNF-Y family members with known starch metabolism-related functions showed higher connectivities in TAM 111. Multiple TFs with high connectivity in TAM 112 had predicted functions associated with ABA response in grain. These results will provide novel targets for breeders to explore and further our understanding in mechanisms regulating grain development. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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19 pages, 6931 KiB

Open AccessArticle

Comparative Genomic and Expression Analysis Insight into Evolutionary Characteristics of PEBP Genes in Cultivated Peanuts and Their Roles in Floral Induction

by Chao Zhong, Zhao Li, Yunlian Cheng, Haina Zhang, Yu Liu, Xiaoguang Wang, Chunji Jiang, Xinhua Zhao, Shuli Zhao, Jing Wang, He Zhang, Xibo Liu and Haiqiu Yu

Int. J. Mol. Sci. 2022, 23(20), 12429; https://doi.org/10.3390/ijms232012429 - 17 Oct 2022

Cited by 4 | Viewed by 2048

Abstract

Phosphatidyl ethanolamine-binding proteins (PEBPs) are involved in regulating flowering time and various developmental processes. Functions and expression patterns in cultivated peanuts (Arachis hypogaea L.) remain unknown. In this study, 33 PEBP genes in cultivated peanuts were identified and divided into four subgroups: [...] Read more.

Phosphatidyl ethanolamine-binding proteins (PEBPs) are involved in regulating flowering time and various developmental processes. Functions and expression patterns in cultivated peanuts (Arachis hypogaea L.) remain unknown. In this study, 33 PEBP genes in cultivated peanuts were identified and divided into four subgroups: FT, TFL, MFT and FT-like. Gene structure analysis showed that orthologs from A and B genomes in cultivated peanuts had highly similar structures, but some orthologous genes have subgenomic dominance. Gene collinearity and phylogenetic analysis explain that some PEBP genes play key roles in evolution. Cis-element analysis revealed that PEBP genes are mainly regulated by hormones, light signals and stress-related pathways. Multiple PEPB genes had different expression patterns between early and late-flowering genotypes. Further detection of its response to temperature and photoperiod revealed that PEBPs ArahyM2THPA, ArahyEM6VH3, Arahy4GAQ4U, ArahyIZ8FG5, ArahyG6F3P2, ArahyLUT2QN, ArahyDYRS20 and ArahyBBG51B were the key genes controlling the flowering response to different flowering time genotypes, photoperiods and temperature. This study laid the foundation for the functional study of the PEBP gene in cultivated peanuts and the adaptation of peanuts to different environments. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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19 pages, 3204 KiB

Open AccessArticle

Genome-Wide Classification and Phylogenetic Analyses of the GDSL-Type Esterase/Lipase (GELP) Family in Flowering Plants

by Alberto Cenci, Mairenys Concepción-Hernández, Valentin Guignon, Geert Angenon and Mathieu Rouard

Int. J. Mol. Sci. 2022, 23(20), 12114; https://doi.org/10.3390/ijms232012114 - 11 Oct 2022

Cited by 6 | Viewed by 2770

Abstract

GDSL-type esterase/lipase (GELP) enzymes have key functions in plants, such as developmental processes, anther and pollen development, and responses to biotic and abiotic stresses. Genes that encode GELP belong to a complex and large gene family, ranging from tens to more than hundreds [...] Read more.

GDSL-type esterase/lipase (GELP) enzymes have key functions in plants, such as developmental processes, anther and pollen development, and responses to biotic and abiotic stresses. Genes that encode GELP belong to a complex and large gene family, ranging from tens to more than hundreds of members per plant species. To facilitate functional transfer between them, we conducted a genome-wide classification of GELP in 46 plant species. First, we applied an iterative phylogenetic method using a selected set of representative angiosperm genomes (three monocots and five dicots) and identified 10 main clusters, subdivided into 44 orthogroups (OGs). An expert curation for gene structures, orthogroup composition, and functional annotation was made based on a literature review. Then, using the HMM profiles as seeds, we expanded the classification to 46 plant species. Our results revealed the variable evolutionary dynamics between OGs in which some expanded, mostly through tandem duplications, while others were maintained as single copies. Among these, dicot-specific clusters and specific amplifications in monocots and wheat were characterized. This approach, by combining manual curation and automatic identification, was effective in characterizing a large gene family, allowing the establishment of a classification framework for gene function transfer and a better understanding of the evolutionary history of GELP. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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13 pages, 3180 KiB

Open AccessArticle

A Novel Beta-Glucosidase Gene for Plant Type Was Identified by Genome-Wide Association Study and Gene Co-Expression Analysis in Widespread Bermudagrass

by Lu Gan, Minghui Chen, Jingxue Zhang, Jibiao Fan and Xuebing Yan

Int. J. Mol. Sci. 2022, 23(19), 11432; https://doi.org/10.3390/ijms231911432 - 28 Sep 2022

Cited by 6 | Viewed by 2147

Abstract

Bermudagrass (Cynodon spp.) is one of the most widely distributed warm-season grasses globally. The growth habits and plant type of bermudagrass are strongly associated with the applied purpose of the landscape, livestock, and eco-remediation. Therefore, persistent efforts are made to investigate the [...] Read more.

Bermudagrass (Cynodon spp.) is one of the most widely distributed warm-season grasses globally. The growth habits and plant type of bermudagrass are strongly associated with the applied purpose of the landscape, livestock, and eco-remediation. Therefore, persistent efforts are made to investigate the genetic basis of plant type and growth habits of bermudagrass. Here, we dissect the genetic diversity of 91 wild bermudagrass resources by genome-wide association studies (GWAS) combined with weighted gene co-expression analysis (WGCNA). This work is based on the RNA-seq data and the genome of African bermudagrass (Cynodon transvaalensis Burtt Davy). Sixteen reliable single-nucleotide polymorphisms (SNPs) in transcribed regions were identified to be associated with the plant height and IAA content in diverse bermudagrass by GWAS. The integration of the results from WGCNA indicates that beta-glucosidase 31 (CdBGLU31) is a candidate gene underlying a G/A SNP signal. Furthermore, both qRT-PCR and correlation coefficient analyses indicate that CdBGLU31 might play a comprehensive role in plant height and IAA biosynthesis and signal. In addition, we observe lower plant height in Arabidopsis bglu11 mutants (homologs of CdBGLU31). It uncovers the breeding selection history of different plant types from diverse bermudagrass and provides new insights into the molecular function of CdBGLU31 both in plant types and in IAA biosynthetic pathways. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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14 pages, 3015 KiB

Open AccessArticle

GhBOP1 as a Key Factor of Ribosomal Biogenesis: Development of Wrinkled Leaves in Upland Cotton

by Yanwen Wang, Zhimao Sun, Long Wang, Lingling Chen, Lina Ma, Jiaoyan Lv, Kaikai Qiao, Shuli Fan and Qifeng Ma

Int. J. Mol. Sci. 2022, 23(17), 9942; https://doi.org/10.3390/ijms23179942 - 1 Sep 2022

Cited by 4 | Viewed by 1841

Abstract

Block of proliferation 1 (BOP1) is a key protein that helps in the maturation of ribosomes and promotes the progression of the cell cycle. However, its role in the leaf morphogenesis of cotton remains unknown. Herein, we report and study the function of [...] Read more.

Block of proliferation 1 (BOP1) is a key protein that helps in the maturation of ribosomes and promotes the progression of the cell cycle. However, its role in the leaf morphogenesis of cotton remains unknown. Herein, we report and study the function of GhBOP1 isolated from Gossypium hirsutum. The sequence alignment revealed that BOP1 protein was highly conserved among different species. The yeast two-hybrid experiments, bimolecular fluorescence complementation, and luciferase complementation techniques revealed that GhBOP1 interact with GhPES and GhWDR12. Subcellular localization experiments revealed that GhBOP1, GhPES and GhWDR12 were localized at the nucleolus. Suppression of GhBOP1 transcripts resulted in the uneven bending of leaf margins and the presence of young wrinkled leaves by virus-induced gene silencing assay. Abnormal palisade arrangements and the presence of large upper epidermal cells were observed in the paraffin sections of the wrinkled leaves. Meanwhile, a jasmonic acid-related gene, GhOPR3, expression was increased. In addition, a negative effect was exerted on the cell cycle and the downregulation of the auxin-related genes was also observed. These results suggest that GhBOP1 plays a critical role in the development of wrinkled cotton leaves, and the process is potentially modulated through phytohormone signaling. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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18 pages, 34668 KiB

Open AccessArticle

Changes of Sensory Quality, Flavor-Related Metabolites and Gene Expression in Peach Fruit Treated by Controlled Atmosphere (CA) under Cold Storage

by Hongru Liu, Hui He, Chenxia Liu, Chunfang Wang, Yongjin Qiao and Bo Zhang

Int. J. Mol. Sci. 2022, 23(13), 7141; https://doi.org/10.3390/ijms23137141 - 27 Jun 2022

Cited by 16 | Viewed by 2712

Abstract

Controlled atmosphere (CA) has been used to alleviate chilling injury (CI) of horticultural crops caused by cold storage. However, the effects of CA treatment on peach fruit sensory quality and flavor-related chemicals suffering from CI remain largely unknown. Here, we stored peach fruit [...] Read more.

Controlled atmosphere (CA) has been used to alleviate chilling injury (CI) of horticultural crops caused by cold storage. However, the effects of CA treatment on peach fruit sensory quality and flavor-related chemicals suffering from CI remain largely unknown. Here, we stored peach fruit under CA with 5% O₂ and 10% CO₂ at 0 °C up to 28 d followed by a subsequent 3 d shelf-life at 20 °C (28S3). CA significantly reduced flesh browning and improved sensory quality at 28S3. Though total volatiles declined during extended cold storage, CA accumulated higher content of volatile esters and lactones than control at 28S3. A total of 14 volatiles were positively correlated with consumer acceptability, mainly including three C6 compounds, three esters and four lactones derived from the fatty acid lipoxygenase (LOX) pathway. Correspondingly, the expression levels of genes including PpLOX1, hyperoxide lyase PpHPL1 and alcohol acyltransferase PpAAT1 were positively correlated with the change of esters and lactones. CA elevated the sucrose content and the degree of fatty acids unsaturation under cold storage, which gave us clues to clarify the mechanism of resistance to cold stress. The results suggested that CA treatment improved sensory quality by alleviating CI of peach fruits under cold storage. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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17 pages, 4518 KiB

Open AccessArticle

Genome-Wide Identification of the LHC Gene Family in Kiwifruit and Regulatory Role of AcLhcb3.1/3.2 for Chlorophyll a Content

by Juan Luo, Muhammad Abid, Jing Tu, Puxing Gao, Zupeng Wang and Hongwen Huang

Int. J. Mol. Sci. 2022, 23(12), 6528; https://doi.org/10.3390/ijms23126528 - 10 Jun 2022

Cited by 18 | Viewed by 2696

Abstract

Light-harvesting chlorophyll a/b-binding (LHC) protein is a superfamily that plays a vital role in photosynthesis. However, the reported knowledge of LHCs in kiwifruit is inadequate and poorly understood. In this study, we identified 42 and 45 LHC genes in Actinidia chinensis (Ac) and [...] Read more.

Light-harvesting chlorophyll a/b-binding (LHC) protein is a superfamily that plays a vital role in photosynthesis. However, the reported knowledge of LHCs in kiwifruit is inadequate and poorly understood. In this study, we identified 42 and 45 LHC genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes. Phylogenetic analysis showed that the kiwifruit LHCs of both species were grouped into four subfamilies (Lhc, Lil, PsbS, and FCII). Expression profiles and qRT-PCR results revealed expression levels of LHC genes closely related to the light, temperature fluctuations, color changes during fruit ripening, and kiwifruit responses to Pseudomonas syringae pv. actinidiae (Psa). Subcellular localization analysis showed that AcLhcb1.5/3.1/3.2 were localized in the chloroplast while transient overexpression of AcLhcb3.1/3.2 in tobacco leaves confirmed a significantly increased content of chlorophyll a. Our findings provide evidence of the characters and evolution patterns of kiwifruit LHCs genes in kiwifruit and verify the AcLhcb3.1/3.2 genes controlling the chlorophyll a content. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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19 pages, 8036 KiB

Open AccessArticle

HDACs Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in Prunus mume

by Juan Meng, Zhenying Wen, Mingyu Li, Tangren Cheng, Qixiang Zhang and Lidan Sun

Int. J. Mol. Sci. 2022, 23(11), 5957; https://doi.org/10.3390/ijms23115957 - 25 May 2022

Cited by 9 | Viewed by 2899

Abstract

Histone deacetylases (HDACs) play important roles in plant growth, development, and stress response. However, the pattern of how they are expressed in response to cold stress in the ornamental woody plant Prunus mume is poorly understood. Here, we identify 121 RoHDACs from eight [...] Read more.

Histone deacetylases (HDACs) play important roles in plant growth, development, and stress response. However, the pattern of how they are expressed in response to cold stress in the ornamental woody plant Prunus mume is poorly understood. Here, we identify 121 RoHDACs from eight Rosaceae plants of which 13 PmHDACs genes are from P. mume. A phylogenetic analysis suggests that the RoHDACs family is classified into three subfamilies, HDA1/RPD3, HD2, and SIR2. We identify 11 segmental duplication gene pairs of RoHDACs and find, via a sequence alignment, that the HDACs gene family, especially the plant-specific HD2 family, has experienced gene expansion and contraction at a recent genome evolution history. Each of the three HDACs subfamilies has its own conserved domains. The expression of PmHDACs in mei is found to be tissue-specific or tissue-wide. RNA-seq data and qRT-PCR experiments in cold treatments suggest that almost all PmHDACs genes—especially PmHDA1/6/14, PmHDT1, and PmSRT1/2—significantly respond to cold stress. Our analysis provides a fundamental insight into the phylogenetic relationship of the HDACs family in Rosaceae plants. Expression profiles of PmHDACs in response to cold stress could provide an important clue to improve the cold hardiness of mei. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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20 pages, 6610 KiB

Open AccessArticle

Identification, In Silico Characterization, and Differential Expression Profiles of Carotenoid, Xanthophyll, Apocarotenoid Biosynthetic Pathways Genes, and Analysis of Carotenoid and Xanthophyll Accumulation in Heracleum moellendorffii Hance

by Ramaraj Sathasivam, Nam Su Kim, Minsol Choi, Haejin Kwon, Bao Van Nguyen, Jae Kwang Kim, Dae Hui Jeong, Eung Jun Park, Hong Woo Park and Sang Un Park

Int. J. Mol. Sci. 2022, 23(9), 4845; https://doi.org/10.3390/ijms23094845 - 27 Apr 2022

Cited by 3 | Viewed by 2531

Abstract

Heracleum moellendorffii Hance is a non-woody forest plant widely used in China, Korea, and Japan because of its various therapeutic properties. However, the genetic details of the carotenoid pathway (CP), xanthophyll pathway (XP), and apocarotenoid pathway (AP) genes have not been studied. Thus, [...] Read more.

Heracleum moellendorffii Hance is a non-woody forest plant widely used in China, Korea, and Japan because of its various therapeutic properties. However, the genetic details of the carotenoid pathway (CP), xanthophyll pathway (XP), and apocarotenoid pathway (AP) genes have not been studied. Thus, the CP, XP, and AP genes of H. moellendorffii were detected and analyzed. A total of fifteen genes were identified, of which eight, four, and three belonged to CP, XP, and AP, respectively. All identified genes possessed full open reading frames. Phylogenetic characterization of the identified gene sequences showed the highest similarity with other higher plants. Multiple alignments and 3D dimensional structures showed several diverse conserved motifs, such as the carotene-binding motif, dinucleotide-binding motif, and aspartate or glutamate residues. The results of real-time PCR showed that the CP, XP, and AP genes were highly expressed in leaves, followed by the stems and roots. In total, eight different individual carotenoids were identified using HPLC analysis. The highest individual and total carotenoid content were achieved in the leaves, followed by the stems and roots. This study will provide more information on the gene structure of the CP, XP, and AP genes, which may help to increase the accumulation of carotenoids in H. moellendorffii through genetic engineering. These results could be helpful for further molecular and functional studies of CP, XP, and AP genes. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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18 pages, 8398 KiB

Open AccessArticle

A Comprehensive Identification and Function Analysis of Serine/Arginine-Rich (SR) Proteins in Cotton (Gossypium spp.)

by Fei Wei, Pengyun Chen, Hongliang Jian, Lu Sun, Xiaoyan Lv, Hengling Wei, Hantao Wang, Tingli Hu, Liang Ma, Xiaokang Fu, Jianhua Lu, Shiyun Li and Shuxun Yu

Int. J. Mol. Sci. 2022, 23(9), 4566; https://doi.org/10.3390/ijms23094566 - 20 Apr 2022

Cited by 6 | Viewed by 2576

Abstract

As one of the most important factors in alternative splicing (AS) events, serine/arginine-rich (SR) proteins not only participate in the growth and development of plants but also play pivotal roles in abiotic stresses. However, the research about SR proteins in cotton is still [...] Read more.

As one of the most important factors in alternative splicing (AS) events, serine/arginine-rich (SR) proteins not only participate in the growth and development of plants but also play pivotal roles in abiotic stresses. However, the research about SR proteins in cotton is still lacking. In this study, we performed an extensive comparative analysis of SR proteins and determined their phylogeny in the plant lineage. A total of 169 SR family members were identified from four Gossypium species, and these genes could be divided into eight distinct subfamilies. The domain, motif distribution and gene structure of cotton SR proteins are conserved within each subfamily. The expansion of SR genes is mainly contributed by WGD and allopolyploidization events in cotton. The selection pressure analysis showed that all the paralogous gene pairs were under purifying selection pressure. Many cis-elements responding to abiotic stress and phytohormones were identified in the upstream sequences of the GhSR genes. Expression profiling suggested that some GhSR genes may involve in the pathways of plant resistance to abiotic stresses. The WGCNA analysis showed that GhSCL-8 co-expressed with many abiotic responding related genes in a salt-responding network. The Y2H assays showed that GhSCL-8 could interact with GhSRs in other subfamilies. The subcellular location analysis showed that GhSCL-8 is expressed in the nucleus. The further VIGS assays showed that the silencing of GhSCL-8 could decrease salt tolerance in cotton. These results expand our knowledge of the evolution of the SR gene family in plants, and they will also contribute to the elucidation of the biological functions of SR genes in the future. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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11 pages, 747 KiB

Open AccessArticle

Comparative Genomics of Seasonal Senescence in Forest Trees

by Anastasia Y. Batalova, Yuliya A. Putintseva, Michael G. Sadovsky and Konstantin V. Krutovsky

Int. J. Mol. Sci. 2022, 23(7), 3761; https://doi.org/10.3390/ijms23073761 - 29 Mar 2022

Cited by 4 | Viewed by 3320

Abstract

In the course of evolution, both flowering plants and some gymnosperms have developed such an adaptation to winter and unfavorable living conditions as deciduousness. Of particular interest is Siberian larch (Larix sibirica Ledeb.), which is the only species in the pine family [...] Read more.

In the course of evolution, both flowering plants and some gymnosperms have developed such an adaptation to winter and unfavorable living conditions as deciduousness. Of particular interest is Siberian larch (Larix sibirica Ledeb.), which is the only species in the pine family (Pinaceae) with a seasonal deciduousness. New generation sequencing technologies make it possible to study this phenomenon at the genomic level and to reveal the genetic mechanisms of leaf and needle aging in angiosperms and gymnosperms. Using a comparative analysis of the genomes of evergreen and deciduous trees, it was found that the genes that control EXORDIUM LIKE 2 (EXL2) and DORMANCY-ASSOCIATED PROTEIN 1 (DRM1) proteins are most represented in Siberian larch, while an excess of genes that control proteins acting as immune receptors were found in evergreens. Orthologs from the family of genes that control leucine-rich repeat receptor-like kinases (LRR-RLK) contributed mostly to the distinction between evergreens and deciduous plants. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants)

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