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Open AccessArticle

Comparison of Recombination Rate, Reference Bias, and Unique Pangenomic Haplotypes in Cannabis sativa Using Seven De Novo Genome Assemblies

by George M. Stack, Michael A. Quade, Dustin G. Wilkerson, Luis A. Monserrate, Philip C. Bentz, Sarah B. Carey, Jane Grimwood, Jacob A. Toth, Seth Crawford, Alex Harkess and Lawrence B. Smart

Int. J. Mol. Sci. 2025, 26(3), 1165; https://doi.org/10.3390/ijms26031165 - 29 Jan 2025

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Abstract

Genomic characterization of Cannabis sativa has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Here, we present seven new chromosome-level haplotype-phased genomes of C. sativa. All of these genotypes [...] Read more.

Genomic characterization of Cannabis sativa has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Here, we present seven new chromosome-level haplotype-phased genomes of C. sativa. All of these genotypes were alive at the time of publication, and several have numerous years of associated phenotype data. We performed a k-mer-based pangenome analysis to contextualize these assemblies within over 200 existing assemblies. This allowed us to identify unique haplotypes and genomic diversity among Cannabis sativa genotypes. We leveraged linkage maps constructed from F₂ progeny of two of the assembled genotypes to characterize the recombination rate across the genome showing strong periphery-biased recombination. Lastly, we re-aligned a bulk segregant analysis dataset for the major-effect flowering locus Early1 to several of the new assemblies to evaluate the impact of reference bias on the mapping results and narrow the locus to a smaller region of the chromosome. These new assemblies, combined with the continued propagation of the genotypes, will contribute to the growing body of genomic resources for C. sativa to accelerate future research efforts. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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20 pages, 4091 KiB

Open AccessArticle

Multi-Omics Analysis Decodes Biosynthesis of Specialized Metabolites Constituting the Therapeutic Terrains of Magnolia obovata

by Megha Rai, Amit Rai, Towa Yokosaka, Tetsuya Mori, Ryo Nakabayashi, Michimi Nakamura, Hideyuki Suzuki, Kazuki Saito and Mami Yamazaki

Int. J. Mol. Sci. 2025, 26(3), 1068; https://doi.org/10.3390/ijms26031068 - 26 Jan 2025

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Abstract

Magnolia obovata is renowned for its unique bioactive constituents with medicinal properties traditionally used to treat digestive disorders, anxiety, and respiratory conditions. This study aimed to establish a comprehensive omics resource through untargeted metabolome and transcriptome profiling to explore biosynthesis of pharmacologically active [...] Read more.

Magnolia obovata is renowned for its unique bioactive constituents with medicinal properties traditionally used to treat digestive disorders, anxiety, and respiratory conditions. This study aimed to establish a comprehensive omics resource through untargeted metabolome and transcriptome profiling to explore biosynthesis of pharmacologically active compounds of M. obovata using seven tissues: young leaf, mature leaf, stem, bark, central cylinder, floral bud, and pistil. Untargeted metabolomic analysis identified 6733 mass features across seven tissues and captured chemo-diversity and its tissue-specificity in M. obovata. Through a combination of cheminformatics and manual screening approach, we confirmed the identities of 105 metabolites, including neolignans, such as honokiol and magnolol, which were found to be spatially accumulated in the bark tissue. RNA sequencing generated a comprehensive transcriptome resource, and expression analysis revealed significant tissue-specific expression patterns. Omics dataset integration identified T12 transcript module from WGCNA being correlated with the biosynthesis of magnolol and honokiol in M. obovata. Notably, phylogenetic analysis using transcripts from T12 module identified two laccase (Mo_LAC1 and Mo_LAC2) and three dirigent proteins from the DIR-b/d subfamily as potential candidate genes involved in neolignan biosynthesis. This research established omics resources of M. obovata and laid the groundwork for future studies aimed at optimizing and further understanding the biosynthesis of metabolites of therapeutic potential. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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15 pages, 5245 KiB

Open AccessArticle

Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14

by Dingkun Jiang, Xinfeng Zhang, Lin Luo, Tian Li, Hao Chen, Nana Ma, Lufeng Fu, Peng Tian, Fei Mao, Peitao Lü, Honghong Guo and Fangjie Zhu

Int. J. Mol. Sci. 2025, 26(2), 763; https://doi.org/10.3390/ijms26020763 - 17 Jan 2025

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Abstract

The Arabidopsis transcription factor WUSCHEL-related homeobox 14 (AtWOX14) plays versatile roles in plant growth and development. However, its biochemical specificity of DNA binding, its genome-wide regulatory targets, and how these are affected by DNA methylation remain uncharacterized. To clarify the biochemistry underlying the [...] Read more.

The Arabidopsis transcription factor WUSCHEL-related homeobox 14 (AtWOX14) plays versatile roles in plant growth and development. However, its biochemical specificity of DNA binding, its genome-wide regulatory targets, and how these are affected by DNA methylation remain uncharacterized. To clarify the biochemistry underlying the regulatory function of AtWOX14, using the recently developed 5mC-incorporation strategy, this study performed SELEX and DAP-seq for AtWOX14 both in the presence and absence of cytosine methylation, systematically curated 65 motif models and identified 51,039 genomic binding sites for AtWOX14, and examined how 5mC affects DNA binding of AtWOX14 through bioinformatic analyses. Overall, 5mC represses the DNA binding of AtWOX14 monomers but facilitates the binding of its dimers, and the methylation effect on a cytosine’s affinity to AtWOX14 is position-dependent. Notably, we found that the most preferred homodimeric configuration of AtWOX14 has changed from ER1 to ER0 upon methylation. This change has the potential to rewire the regulatory network downstream of AtWOX14, as suggested by the GO analyses and the strength changes in the DAP-seq peaks upon methylation. Therefore, this work comprehensively illustrates the specificity and targets of AtWOX14 and reports a previously unrecognized effect of DNA methylation on transcription factor binding. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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15 pages, 10249 KiB

Open AccessArticle

Deciphering the Proteome and Phosphoproteome of Peanut (Arachis hypogaea L.) Pegs Penetrating into the Soil

by Sha Yang, Mei He, Zhaohui Tang, Keke Liu, Jianguo Wang, Li Cui, Feng Guo, Ping Liu, Jialei Zhang and Shubo Wan

Int. J. Mol. Sci. 2025, 26(2), 634; https://doi.org/10.3390/ijms26020634 - 14 Jan 2025

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Abstract

Peanut (Arachis hypogaea L.) is one of the most important crops for oil and protein production. The unique characteristic of peanut is geocarpy, which means that it blooms aerially and the peanut gynophores (pegs) penetrate into the soil, driving the fruit underground. [...] Read more.

Peanut (Arachis hypogaea L.) is one of the most important crops for oil and protein production. The unique characteristic of peanut is geocarpy, which means that it blooms aerially and the peanut gynophores (pegs) penetrate into the soil, driving the fruit underground. In order to fully understand this phenomenon, we investigated the dynamic proteomic and phosphoproteomic profiling of the pegs aerially and underground in this study. A total of 6859 proteins and 4142 unique phosphoproteins with 10,070 phosphosites were identified. The data were validated and quantified using samples randomly selected from arial pegs (APs) and underground pegs (UPs) by parallel reaction monitoring (PRM). Function analyses of differentially abundant proteins (DAPs) and differentially regulated phosphoproteins (DRPPs) exhibited that they were mainly related to stress response, photosynthesis, and substance metabolism. Once the pegs successfully entered the soil, disease-resistant and stress response proteins, such as glutathione S-transferase, peroxidase, and cytochrome P450, significantly increased in the UP samples in order to adapt to the new soil environment. The increased abundance of photosynthesis-associated proteins in the UP samples provided more abundant photosynthetic products, which provided the preparation for subsequent pod development. Phosphoproteomics reveals the regulatory network of the synthesis of nutrients such as starch, protein, and fatty acid (FA). These results provide new insights into the mechanism, indicating that after the pegs are inserted into the soil, phosphorylation is involved in the rapid elongation of the pegs, accompanied by supplying energy for pod development and preparing for the synthesis of metabolites during pod development following mechanical stimulation and darkness. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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16 pages, 5330 KiB

Open AccessArticle

Mitochondrial Genome Characteristics Reveal Evolution of Danxiaorchis yangii and Phylogenetic Relationships

by Xuedie Liu, Huolin Luo, Zhong-Jian Liu and Bo-Yun Yang

Int. J. Mol. Sci. 2025, 26(2), 562; https://doi.org/10.3390/ijms26020562 - 10 Jan 2025

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Abstract

Danxiaorchis yangii is a fully mycoheterotrophic orchid that lacks both leaves and roots, belonging to the genus Danxiaorchis in the subtribe Calypsoinae. In this study, we assembled and annotated its mitochondrial genome (397,867 bp, GC content: 42.70%), identifying 55 genes, including 37 protein-coding [...] Read more.

Danxiaorchis yangii is a fully mycoheterotrophic orchid that lacks both leaves and roots, belonging to the genus Danxiaorchis in the subtribe Calypsoinae. In this study, we assembled and annotated its mitochondrial genome (397,867 bp, GC content: 42.70%), identifying 55 genes, including 37 protein-coding genes (PCGs), 16 tRNAs, and 2 rRNAs, and conducted analyses of relative synonymous codon usage (RSCU), repeat sequences, horizontal gene transfers (HGTs), and gene selective pressure (dN/dS). Additionally, we sequenced and assembled its plastome, which has a reduced size of 110,364 bp (GC content: 36.60%), comprising 48 PCGs, 26 tRNAs, and 4 rRNAs. We identified 64 potential chloroplast DNA fragments transferred to the mitogenome. Phylogenomic analysis focusing on 33 mitogenomes, with Vitis vinifera as the outgroup, indicated that D. yangii is grouped as follows: D. yangii + ((Dendrobium wilsonii + Dendrobium wilsonii henanense) + Phalaenopsis aphrodite). Phylogenetic analysis based on 83 plastid PCGs from these species showed that D. yangii is grouped as follows: (D. yangii + Pha. aphrodite) + (Den. wilsonii + Den. henanense). Gene selective pressure analysis revealed that most mitochondrial and plastid genes in D. yangii are under purifying selection, ensuring functional stability, and certain genes may have undergone positive selection or adaptive evolution, reflecting the species’ adaptation to specific ecological environments. Our study provides valuable data on the plastomes and mitogenomes of D. yangii and lays the groundwork for future research on genetic variation, evolutionary relationships, and the breeding of orchids. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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21 pages, 9347 KiB

Open AccessArticle

Complete Chloroplast Genomes of 9 Impatiens Species: Genome Structure, Comparative Analysis, and Phylogenetic Relationships

by Hui Ma, Zhiqiang Liu, Wenxiang Lan, Mengqing Yang, Qing Mo, Xi Huang, Peiqing Wu, Haiquan Huang and Meijuan Huang

Int. J. Mol. Sci. 2025, 26(2), 536; https://doi.org/10.3390/ijms26020536 - 10 Jan 2025

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Abstract

Impatiens is a genus of functional herbaceous plants in the Balsaminaceae, which are not only of great ornamental value and one of the world’s top three flower bedding plants but also have a wide range of medicinal and edible uses. Currently, the taxonomy [...] Read more.

Impatiens is a genus of functional herbaceous plants in the Balsaminaceae, which are not only of great ornamental value and one of the world’s top three flower bedding plants but also have a wide range of medicinal and edible uses. Currently, the taxonomy and phylogenetic relationships of Impatiens species are still controversial. In order to better understand their chloroplast properties and phylogenetic evolution, nine Impatiens plants (Impatiens repens, Impatiens rectirostrata, Impatiens baishaensis, Impatiens rostellata, Impatiens faberi, Impatiens oxyanthera, Impatiens tienchuanensis, Impatiens blepharosepala, Impatiens distracta) were sequenced, and their complete chloroplast genomes were analysed. Nine species of Impatiens chloroplast genomes ranged in length from 150,810 bp (I. rectirostrata) to 152,345 bp (I. blepharosepala). The chloroplast genomes were all typical circular DNA molecules, and the GC content in each region was consistent with the published chloroplast genomes of Impatiens plants. The results showed that the seven mutational hotspots (trnL-UAG, ndhG, ycf1, ccsA, rrn23, trnA-UGC, and ycf2) could be used as supporting data for further analyses of the phylogenetic tree and species identification. In addition, the results of the phylogenetic tree support that Balsaminaceae is a monophyletic taxon, and that Hydrocera triflora is at the base of the branch, is the original species of Balsaminaceae, and is in a sister group relationship with Impatiens species. The results of this paper enrich the data of Impatiens chloroplast genomes, and the availability of these chloroplast genomes will provide rich genetic information for species identification, thus enhancing the taxonomic accuracy and phylogenetic resolution of Impatiens, and further promoting the investigation and rational use of Impatiens plant resources. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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19 pages, 3347 KiB

Open AccessArticle

Comparative Analysis of Active LTR Retrotransposons in Sunflower (Helianthus annuus L.): From Extrachromosomal Circular DNA Detection to Protein Structure Prediction

by Mikhail Kazancev, Pavel Merkulov, Kirill Tiurin, Yakov Demurin, Alexander Soloviev and Ilya Kirov

Int. J. Mol. Sci. 2024, 25(24), 13615; https://doi.org/10.3390/ijms252413615 - 19 Dec 2024

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Abstract

Plant genomes possess numerous transposable element (TE) insertions that have occurred during evolution. Most TEs are silenced or diverged; therefore, they lose their ability to encode proteins and are transposed in the genome. Knowledge of active plant TEs and TE-encoded proteins essential for [...] Read more.

Plant genomes possess numerous transposable element (TE) insertions that have occurred during evolution. Most TEs are silenced or diverged; therefore, they lose their ability to encode proteins and are transposed in the genome. Knowledge of active plant TEs and TE-encoded proteins essential for transposition and evasion of plant cell transposon silencing mechanisms remains limited. This study investigated active long terminal repeat (LTR) retrotransposons (RTEs) in sunflowers (Helianthus annuus), revealing heterogeneous and phylogenetically distinct RTEs triggered by epigenetic changes and heat stress. Many of these RTEs belong to three distinct groups within the Tekay clade, showing significant variations in chromosomal insertion distribution. Through protein analysis of these active RTEs, it was found that Athila RTEs and Tekay group 2 elements possess additional open reading frames (aORFs). The aORF-encoded proteins feature a transposase domain, a transmembrane domain, and nuclear localization signals. The aORF proteins of the Tekay subgroup exhibited remarkable conservation among over 500 Tekay members, suggesting their functional importance in RTE mobility. The predicted 3D structure of the sunflower Tekay aORF protein showed significant homology with Tekay proteins in rice, maize, and sorghum. Additionally, the structural features of aORF proteins resemble those of plant DRBM-containing proteins, suggesting their potential role in RNA-silencing modulation. These findings offer insights into the diversity and activity of sunflower RTEs, emphasizing the conservation and structural characteristics of aORF-encoded proteins. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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21 pages, 3237 KiB

Open AccessArticle

Analysis of Plant Physiological Parameters and Gene Transcriptional Changes Under the Influence of Humic Acid and Humic Acid-Amino Acid Combinations in Maize

by Kincső Decsi, Mostafa Ahmed, Roquia Rizk, Donia Abdul-Hamid and Zoltán Tóth

Int. J. Mol. Sci. 2024, 25(24), 13280; https://doi.org/10.3390/ijms252413280 - 11 Dec 2024

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Abstract

The study investigated the application of humic acids (HAs) and a combination of humic acids and amino acids (HA+AA) in maize under field conditions. Based on preliminary data in the literature, the aim was to investigate the effects of the two plant conditioning [...] Read more.

The study investigated the application of humic acids (HAs) and a combination of humic acids and amino acids (HA+AA) in maize under field conditions. Based on preliminary data in the literature, the aim was to investigate the effects of the two plant conditioning compounds on plant physiological parameters. In addition to measuring plant physiological parameters in the field, a complete transcriptome analysis was performed to determine exactly which genes were expressed after the treatments and in which physiological processes they play a role. Maize plants showed significant positive yield changes after two priming treatments. Genome-wide transcriptomic analysis revealed the activation of photosynthetic and cellular respiration processes, as well as protein synthesis pathways, which explains the increased yield even under extreme precipitation conditions. The results show that the HA treatment helped in water management and increased the chlorophyll content, while the HA+AA treatment led to higher protein and dry matter contents. The post-harvest tests also show that the HA+AA treatment resulted in the highest yield parameters. Functional annotation of the maize super transcriptome revealed genes related to translation processes, photosynthesis, and cellular respiration. The combined pathway analysis showed that the HA and combined treatments activated genes related to photosynthesis, carbon fixation, and cellular respiration, providing valuable in-depth insight into the usefulness of the HA and HA+AA treatments in priming. Based on the studies, we believe that the use of natural-based humic acid plant conditioners may provide a beneficial opportunity to promote renewable, regenerative agriculture. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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11 pages, 3100 KiB

Open AccessArticle

A 2.9 Mb Chromosomal Segment Deletion Is Responsible for Early Ripening and Deep Red Fruit in Citrus sinensis

by Jianmei Chen, Zhenmin Chen, Quming Xie, Xiaotong Wu, Qingyu Pei, Yi Lin, Qiong Chen and Shubei Wan

Int. J. Mol. Sci. 2024, 25(23), 12931; https://doi.org/10.3390/ijms252312931 - 2 Dec 2024

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Abstract

Sweet orange (Citrus sinensis) is an economically important fruit crop worldwide. Mining for genes associated with ripening periods and fruit color traits is crucial for plant genetics and for the improvement of external fruit quality traits. The present study identified a [...] Read more.

Sweet orange (Citrus sinensis) is an economically important fruit crop worldwide. Mining for genes associated with ripening periods and fruit color traits is crucial for plant genetics and for the improvement of external fruit quality traits. The present study identified a novel navel orange accession, designated as Ganhong, with early ripening and deep red fruit traits. DNA sequence analysis showed a 2.9 Mb deletion in one copy of chromosome 7 in Ganhong navel orange. Flesh samples from Ganhong and its parental variety, Newhall navel orange, were sampled for RNA sequence analysis 200 days after flowering; 958 differentially expressed genes (DEGs) were identified between the two varieties. Functional enrichment analysis indicated that these DEGs were mainly enriched in phytohormones, particularly abscisic acid (ABA), related to fruit ripening. The deletion interval has 343 annotated genes, among which 4 genes (Cs_ont_7g018990, Cs_ont_7g019400, Cs_ont_7g019650, and Cs_ont_7g019820) were inferred to be candidate causal genes for early ripening and deep red fruit traits based on gene functionality and gene expression analysis. The present study laid a foundation for further elucidation of the mechanisms underlying the early ripening and deep red fruit trait in Ganhong navel orange. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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15 pages, 10071 KiB

Open AccessArticle

Genome-Wide Analysis of BURP Domain-Containing Gene Family in Solanum lycopersicum and Functional Analysis of SlRD1 Under Drought and Salt Stresses

by Huiru Sun, Jinyu Yang, Bei Fan, Min Ren, Yanfeng Wang, Guoliang Chen and Guoting Cheng

Int. J. Mol. Sci. 2024, 25(23), 12539; https://doi.org/10.3390/ijms252312539 - 22 Nov 2024

Cited by 1 | Viewed by 533

Abstract

The BURP domain-containing (BURP) genes belong to plant-specific families and are known as essential for various biological processes in plants. However, knowledge of the functions of BURP genes in tomato (Solanum lycopersicum) is lacking. In our study, bioinformatics analysis [...] Read more.

The BURP domain-containing (BURP) genes belong to plant-specific families and are known as essential for various biological processes in plants. However, knowledge of the functions of BURP genes in tomato (Solanum lycopersicum) is lacking. In our study, bioinformatics analysis was performed for the SlBURP gene family, including phylogeny, chromosomal localization, gene structure, cis-acting elements and expression. In addition, the function of SlRD1 in drought and salt stresses was explored. In tomato, fourteen BURP family members were identified, located on five chromosomes, including two tandem duplication clusters. These BURP members were classified into four subfamilies. The promoter regions of SlBURPs harbored numerous hormone- and stress-response elements. Tissue expression analysis showed that several SlBURPs were highly expressed in roots, flowers or fruits. Meanwhile, the expressions of most SlBURPs could be regulated by drought, salt and cold treatments, and some of them also responded to ABA treatment. Moreover, the ectopic expression of SlRD1 in Arabidopsis enhanced tolerances to drought and salt stresses and increased the sensitivity of seed germination to ABA. In conclusion, the comprehensive analysis of the SlBURP family in tomato and the functional exploration of SlRD1 in drought and salt stresses provide a basis for further dissecting the roles of tomato BURP genes. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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21 pages, 4811 KiB

Open AccessArticle

Genome-Wide Identification of GATA Family Genes in Potato and Characterization of StGATA12 in Response to Salinity and Osmotic Stress

by Xi Zhu, Huimin Duan, Ning Zhang, Yasir Majeed, Hui Jin, Wei Li, Zhuo Chen, Shu Chen, Jinghua Tang, Yu Zhang and Huaijun Si

Int. J. Mol. Sci. 2024, 25(22), 12423; https://doi.org/10.3390/ijms252212423 - 19 Nov 2024

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Abstract

GATA factors are evolutionarily conserved transcription regulators that are implicated in the regulation of physiological changes under abiotic stress. Unfortunately, there are few studies investigating the potential role of GATA genes in potato plants responding to salt and osmotic stresses. The physicochemical properties, [...] Read more.

GATA factors are evolutionarily conserved transcription regulators that are implicated in the regulation of physiological changes under abiotic stress. Unfortunately, there are few studies investigating the potential role of GATA genes in potato plants responding to salt and osmotic stresses. The physicochemical properties, chromosomal distribution, gene duplication, evolutionary relationships and classification, conserved motifs, gene structure, interspecific collinearity relationship, and cis-regulatory elements were analyzed. Potato plants were treated with NaCl and PEG to induce salinity and osmotic stress responses. qRT-PCR was carried out to characterize the expression pattern of StGATA family genes in potato plants subjected to salinity and osmotic stress. StGATA12 loss-of-function and gain-of-function plants were established. Morphological phenotypes and growth were indicated. Photosynthetic gas exchange was suggested by the net photosynthetic rate, transpiration rate, and stomatal conductance. Physiological indicators and the corresponding genes were indicated by enzyme activity and mRNA expression of genes encoding CAT, SOD, POD, and P5CS, and contents of H₂O₂, MDA, and proline. The expression patterns of StGATA family genes were altered in response to salinity and osmotic stress. StGATA12 protein is located in the nucleus. StGATA12 is involved in the regulation of potato plant growth in response to salinity and osmotic stress. Overexpression of StGATA12 promoted photosynthesis, transpiration, and stomatal conductance under salinity and osmotic stress. StGATA12 overexpression induced biochemical responses of potato plants to salinity and osmotic stress by regulating the levels of H₂O₂, MDA, and proline and the activity of CAT, SOD, and POD. StGATA12 overexpression induced the up-regulation of StCAT, StSOD, StPOD, and StP5CS against salinity and osmotic stress. StGATA12 could reinforce the ability of potato plants to resist salinity and osmosis-induced damages, which may provide an effective strategy to engineer potato plants for better adaptability to adverse salinity and osmotic conditions. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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18 pages, 4385 KiB

Open AccessArticle

Comparative Analyses of the Complete Mitogenomes of Two Oxyria Species (Polygonaceae) Provide Insights into Understanding the Mitogenome Evolution Within the Family

by Lijuan Li, Zhuo Jiang, Ye Xiong, Caleb Onoja Akogwu, Olutayo Mary Tolulope, Hao Zhou, Yanxia Sun, Hengchang Wang and Huajie Zhang

Int. J. Mol. Sci. 2024, 25(22), 11930; https://doi.org/10.3390/ijms252211930 - 6 Nov 2024

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Abstract

Oxyria (Polygonaceae) is a small genus only comprising two species, Oxyria digyna and O. sinensis. Both species have well-documented usage in Chinese herbal medicine. We sequenced and assembled the complete mitogenomes of these two species and conducted a comparative analysis of the [...] Read more.

Oxyria (Polygonaceae) is a small genus only comprising two species, Oxyria digyna and O. sinensis. Both species have well-documented usage in Chinese herbal medicine. We sequenced and assembled the complete mitogenomes of these two species and conducted a comparative analysis of the mitogenomes within Polygonaceae. Both O. digyna and O. sinensis displayed distinctive multi-branched conformations, consisting of one linear and one circular molecule. These two species shared similar gene compositions and exhibited distinct codon preferences, with mononucleotides as the most abundant type of simple sequence repeats. In the mitogenome of O. sinensis, a pair of long forward repeat sequences can mediate the division of molecule 1 into two sub-genomic circular molecules. Homologous sequence analysis revealed the occurrence of gene transfer between the chloroplast and mitochondrial genomes within Oxyria species. Additionally, a substantial number of homologous collinear blocks with varied arrangements were observed across different Polygonaceae species. Phylogenetic analysis suggested that mitogenome genes can serve as reliable markers for constructing phylogenetic relationships within Polygonaceae. Comparative analysis of eight species revealed Polygonaceae mitogenomes exhibited variability in gene presence, and most protein-coding genes (PCGs) have undergone negative selection. Overall, our study provided a comprehensive overview of the structural, functional, and evolutionary characteristics of the Polygonaceae mitogenomes. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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12 pages, 2301 KiB

Open AccessArticle

Developing Adventitious Root Meristems Induced by Layering for Plant Chromosome Preparation

by Xu Yan, Zizhou Wu, Honglin Wang, Yanchun Zuo and Zhouhe Du

Int. J. Mol. Sci. 2024, 25(21), 11723; https://doi.org/10.3390/ijms252111723 - 31 Oct 2024

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Abstract

Chromosome numbers and morphology are important characteristics of a species and its evolution. Root tips are the most commonly used tissue as a source of actively dividing cells for chromosome visualization in plants. Previously, rapidly growing root tips were collected from germinating kernels [...] Read more.

Chromosome numbers and morphology are important characteristics of a species and its evolution. Root tips are the most commonly used tissue as a source of actively dividing cells for chromosome visualization in plants. Previously, rapidly growing root tips were collected from germinating kernels or from seedlings growing in pots or fields. However, the use of adventitious roots (ARs) derived from aerial tissue as meristems for chromosome visualization has always been overlooked. Here, we successfully induced ARs in 12 materials that were investigated, with the exception of Sorghum nitidum. Using ARs meristem we obtained high-quality chromosome spreads for Morus alba, Broussonetia papyrifera, Lolium multiflorum, Sorghum sudanense, S. propinquum, S. bicolor × S. sudanense, Zea mays, Z. mexicana, Glycine max, Medicago sativa, and Brassica napus. The results reported here demonstrate that layering is an alternative and effective method for producing meristematic cells for high-quality chromosome preparation in plant species producing ARs. For species that produce ARs by layering, this protocol is particularly valuable for the development of cost-effective and high-throughput non-invasive cytogenetic studies. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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15 pages, 5348 KiB

Open AccessArticle

Identification of Potato StPIN Gene Family and Regulation of Root Development by StPIN4

by Qian Zhang, Qing Liu, Jiangwei Yang, Ning Zhang and Huaijun Si

Int. J. Mol. Sci. 2024, 25(21), 11517; https://doi.org/10.3390/ijms252111517 - 26 Oct 2024

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Abstract

The growth hormone export PIN-FORMED (PIN) is an important carrier for regulating the polar transport of plant growth hormones and plays an important role in plant growth and development. However, little is known about the characteristics and functions of PINs in potatoes. In [...] Read more.

The growth hormone export PIN-FORMED (PIN) is an important carrier for regulating the polar transport of plant growth hormones and plays an important role in plant growth and development. However, little is known about the characteristics and functions of PINs in potatoes. In this study, 10 PIN members were identified from potatoes and named StPIN1, StPIN2, StPIN3, StPIN4, StPIN5, StPIN6, StPIN7, StPIN8, StPIN9, and StPIN10 according to their positions in the potato chromosome In addition, the expression of 10 StPINs was analyzed by qRT-PCR during potato root development. The results showed that the StPIN4 gene plays an important regulatory role in potato root development, and its tissue expression varied greatly. Several cis-regulatory elements related to growth factors were also detected in the promoter region of the StPIN gene. The transgenic overexpressing StPIN4 in potato showed suppressed growth in root length and lateral root number, and StPIN4-interfering plants showed the opposite. These results suggested that StPIN4 plays a key role in the regulation of the potato root architecture. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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19 pages, 3437 KiB

Open AccessArticle

Genome Analysis of BnCNGC Gene Family and Function Exploration of BnCNGC57 in Brassica napus L.

by Yue Wang, Qing Chi, Wenjing Jia, Tiantian Zheng, Binghua Li, Lin Li, Ting Li, Rui Gao, Wenzhe Liu, Shenglin Ye, Ruqiang Xu and Hanfeng Zhang

Int. J. Mol. Sci. 2024, 25(21), 11359; https://doi.org/10.3390/ijms252111359 - 22 Oct 2024

Viewed by 1034

Abstract

The cyclic nucleotide-gated ion channel (CNGC), as a non-selective cation channel, plays a pivotal role in plant growth and stress response. A systematic analysis and identification of the BnCNGC gene family in Brassica napus is crucial for uncovering its biological functions and potential [...] Read more.

The cyclic nucleotide-gated ion channel (CNGC), as a non-selective cation channel, plays a pivotal role in plant growth and stress response. A systematic analysis and identification of the BnCNGC gene family in Brassica napus is crucial for uncovering its biological functions and potential applications in plant science. In this study, we identified 61 BnCNGC members in the B. napus genome, which are phylogenetically similar to Arabidopsis and can be classified into Groups I-IV (with Group IV further subdivided into IV-a and IV-b). Collinearity analysis with other species provided insights into the evolution of BnCNGC. By homology modeling, we predicted the three-dimensional structure of BnCNGC proteins and analyzed cis-acting elements in their promoters, revealing diverse roles in hormone regulation, growth, and stress response. Notably, overexpression of BnCNGC57 (BnaC09g42460D) significantly increased seed size, possibly through regulating cell proliferation via the MAPK signaling pathway. Our findings contribute to a better understanding of the BnCNGC gene family and highlight the potential regulatory role of BnCNGC57 in the seed development of B. napus. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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14 pages, 4449 KiB

Open AccessArticle

Downregulation of the GhROD1 Gene Improves Cotton Fiber Fineness by Decreasing Acyl Pool Saturation, Stimulating Small Heat Shock Proteins (sHSPs), and Reducing H₂O₂ Production

by Bo Ding, Bi Liu, Xi Zhu, Huiming Zhang, Rongyu Hu, Silu Li, Liuqin Zhang, Linzhu Jiang, Yang Yang, Mi Zhang, Juan Zhao, Yan Pei and Lei Hou

Int. J. Mol. Sci. 2024, 25(20), 11242; https://doi.org/10.3390/ijms252011242 - 19 Oct 2024

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Abstract

Cotton fiber is one of the most important natural fiber sources in the world, and lipid metabolism plays a critical role in its development. However, the specific role of lipid molecules in fiber development and the impact of fatty acid alterations on fiber [...] Read more.

Cotton fiber is one of the most important natural fiber sources in the world, and lipid metabolism plays a critical role in its development. However, the specific role of lipid molecules in fiber development and the impact of fatty acid alterations on fiber quality remain largely unknown. In this study, we demonstrate that the downregulation of GhROD1, a gene encoding phosphatidylcholine diacylglycerol cholinephosphotransferase (PDCT), results in an improvement of fiber fineness. We found that GhROD1 downregulation significantly increases the proportion of linoleic acid (18:2) in cotton fibers, which subsequently upregulates genes encoding small heat shock proteins (sHSPs). This, in turn, reduces H₂O₂ production, thus delaying secondary wall deposition and leading to finer fibers. Our findings reveal how alterations in linoleic acid influence cellulose synthesis and suggest a potential strategy to improve cotton fiber quality by regulating lipid metabolism pathways. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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Review

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22 pages, 2008 KiB

Open AccessReview

Enhancing Crop Resilience: The Role of Plant Genetics, Transcription Factors, and Next-Generation Sequencing in Addressing Salt Stress

by Akhilesh Kumar Singh, Priti Pal, Uttam Kumar Sahoo, Laxuman Sharma, Brijesh Pandey, Anand Prakash, Prakash Kumar Sarangi, Piotr Prus, Raul Pașcalău and Florin Imbrea

Int. J. Mol. Sci. 2024, 25(23), 12537; https://doi.org/10.3390/ijms252312537 - 22 Nov 2024

Viewed by 1237

Abstract

Salt stress is a major abiotic stressor that limits plant growth, development, and agricultural productivity, especially in regions with high soil salinity. With the increasing salinization of soils due to climate change, developing salt-tolerant crops has become essential for ensuring food security. This [...] Read more.

Salt stress is a major abiotic stressor that limits plant growth, development, and agricultural productivity, especially in regions with high soil salinity. With the increasing salinization of soils due to climate change, developing salt-tolerant crops has become essential for ensuring food security. This review consolidates recent advances in plant genetics, transcription factors (TFs), and next-generation sequencing (NGS) technologies that are pivotal for enhancing salt stress tolerance in crops. It highlights critical genes involved in ion homeostasis, osmotic adjustment, and stress signaling pathways, which contribute to plant resilience under saline conditions. Additionally, specific TF families, such as DREB, NAC (NAM, ATAF, and CUC), and WRKY, are explored for their roles in activating salt-responsive gene networks. By leveraging NGS technologies—including genome-wide association studies (GWASs) and RNA sequencing (RNA-seq)—this review provides insights into the complex genetic basis of salt tolerance, identifying novel genes and regulatory networks that underpin adaptive responses. Emphasizing the integration of genetic tools, TF research, and NGS, this review presents a comprehensive framework for accelerating the development of salt-tolerant crops, contributing to sustainable agriculture in saline-prone areas. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genetics: 2nd Edition)

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