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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 16599

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Dr. Frank M. You

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Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
Interests: plant bioinformatics; comparative genomics; genome evolution; quantitative genetics and statistical genomics; genetics and breeding; software tool and database development
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Special Issue Information

Dear Colleagues,

Genomics is a fast-evolving comprehensive field combining multiple disciplines, such as genetics, molecular biology, biostatistics, and bioinformatics. Genomics is becoming an essential tool for plant breeding. Recent advances of sequencing technologies, biotechnologies, and bioinformatics tools have substantially enhanced our ability to analyse and understand genomes and the relationship between genotype and phenotype. The purpose of this Collection is to report the recent progress achieved in all fields of genomics studies in plants. This includes, but is not limited to, genetic and physical mapping, genome sequencing, exome sequencing, RNA sequencing, genome structure and organization, genome assembly, gene prediction, comparative genomics, genome evolution, genome/gene editing, expression profiling, the functions of specific genes, protein–protein interaction, pathways, and epigenomics, SNP identification, genome-wide association studies, and genomic prediction, bioinformatics tools and database development. Applications of various integrated genomic and bioinformatics tools in plant breeding are also welcome. Both original research reports and review articles are encouraged.

Dr. Frank M. You
Collection Editor

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Keywords

structural genomics
functional genomics
epigenomics
gene expression
genome sequencing
genome organization
genome evolution
marker development
quantitative trait loci (QTL)
QTL mapping
genome-wide association study
genomic selection
genomic prediction
genomics-assisted selection
genome/gene editing
database development
bioinformatics tool

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Published Papers (6 papers)

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Research

16 pages, 12293 KiB

Open AccessArticle

Genome-Wide Identification of BES1 Gene Family in Six Cucurbitaceae Species and Its Expression Analysis in Cucurbita moschata

by Minyan Xu, Yanping Wang, Mengting Zhang, Meng Chen, Ying Ni, Xuewei Xu, Shengkai Xu, Yuting Li and Xin Zhang

Int. J. Mol. Sci. 2023, 24(3), 2287; https://doi.org/10.3390/ijms24032287 - 24 Jan 2023

Cited by 5 | Viewed by 2299

Abstract

The BES1 (BRI1-EMSSUPPRESSOR1) gene family play a vital role in the BR (brassinosteroid) signaling pathway, which is involved in the growth and development, biotic, abiotic, and hormone stress response in many plants. However, there are few reports of BES1 in Cucurbita moschata. In this study, 50 BES1 genes were identified in six Cucurbitaceae species by genome-wide analysis, which could be classified into 3 groups according to their gene structural features and motif compositions, and 13 CmoBES1 genes in Cucurbita moschata were mapped on 10 chromosomes. Quantitative real-time PCR analysis showed that the CmoBES1 genes displayed differential expression under different abiotic stress and hormone treatments. Subcellular localization showed that the most of CmoBES1 proteins localized in nucleus and cytoplasm, and transactivation assay indicated 9 CmoBES1 proteins played roles as transcription factors. Our analysis of BES1s diversity, localization, and expression in Curcubitaceae contributes to the better understanding of the essential roles of these transcription factors in plants. Full article

(This article belongs to the Special Issue Plant Genomics and Bioinformatics)

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16 pages, 7647 KiB

Open AccessArticle

Genetic Variants Associated with Long-Terminal Repeats Can Diagnostically Classify Cannabis Varieties

by Jackson M. J. Oultram, Joseph L. Pegler, Greg M. Symons, Timothy A. Bowser, Andrew L. Eamens, Christopher P. L. Grof and Darren J. Korbie

Int. J. Mol. Sci. 2022, 23(23), 14531; https://doi.org/10.3390/ijms232314531 - 22 Nov 2022

Cited by 1 | Viewed by 1967

Abstract

Cannabis sativa (Cannabis) has recently been legalized in multiple countries globally for either its recreational or medicinal use. This, in turn, has led to a marked increase in the number of Cannabis varieties available for use in either market. However, little information currently exists on the genetic distinction between adopted varieties. Such fundamental knowledge is of considerable value and underpins the accelerated development of both a nascent pharmaceutical industry and the commercial recreational market. Therefore, in this study, we sought to assess genetic diversity across 10 Cannabis varieties by undertaking a reduced representation shotgun sequencing approach on 83 individual plants to identify variations which could be used to resolve the genetic structure of the assessed population. Such an approach also allowed for the identification of the genetic features putatively associated with the production of secondary metabolites in Cannabis. Initial analysis identified 3608 variants across the assessed population with phylogenetic analysis of this data subsequently enabling the confident grouping of each variety into distinct subpopulations. Within our dataset, the most diagnostically informative single nucleotide polymorphisms (SNPs) were determined to be associated with the long-terminal repeat (LTRs) class of retroelements, with 172 such SNPs used to fully resolve the genetic structure of the assessed population. These 172 SNPs could be used to design a targeted resequencing panel, which we propose could be used to rapidly screen different Cannabis plants to determine genetic relationships, as well as to provide a more robust, scientific classification of Cannabis varieties as the field moves into the pharmaceutical sphere. Full article

(This article belongs to the Special Issue Plant Genomics and Bioinformatics)

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17 pages, 2190 KiB

Open AccessArticle

Fine Mapping and Candidate Gene Analysis of Pm36, a Wild Emmer-Derived Powdery Mildew Resistance Locus in Durum Wheat

by Domenica Nigro, Antonio Blanco, Luciana Piarulli, Massimo Antonio Signorile, Pasqualina Colasuonno, Emanuela Blanco and Rosanna Simeone

Int. J. Mol. Sci. 2022, 23(21), 13659; https://doi.org/10.3390/ijms232113659 - 7 Nov 2022

Cited by 5 | Viewed by 2441

Abstract

Powdery mildew (PM) is an economically important foliar disease of cultivated cereals worldwide. The cultivation of disease-resistant varieties is considered the most efficient, sustainable and economical strategy for disease management. The objectives of the current study were to fine map the chromosomal region harboring the wild emmer PM resistance locus Pm36 and to identify candidate genes by exploiting the improved tetraploid wheat genomic resources. A set of backcross inbred lines (BILs) of durum wheat were genotyped with the SNP 25K chip array and comparison of the PM-resistant and susceptible lines defined a 1.5 cM region (physical interval of 1.08 Mb) harboring Pm36. The genetic map constructed with F_2:3 progenies derived by crossing the PM resistant line 5BIL-42 and the durum parent Latino, restricted to 0.3 cM the genetic distance between Pm36 and the SNP marker IWB22904 (physical distance 0.515 Mb). The distribution of the marker interval including Pm36 in a tetraploid wheat collection indicated that the positive allele was largely present in the domesticated and wild emmer Triticum turgidum spp. dicoccum and ssp. dicoccoides. Ten high-confidence protein coding genes were identified in the Pm36 region of the emmer, durum and bread wheat reference genomes, while three added genes showed no homologous in the emmer genome. The tightly linked markers can be used for marker-assisted selection in wheat breeding programs, and as starting point for the Pm36 map-based cloning. Full article

(This article belongs to the Special Issue Plant Genomics and Bioinformatics)

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24 pages, 3826 KiB

Open AccessArticle

Comparative Genomics and Phylogenetic Analysis of the Chloroplast Genomes in Three Medicinal Salvia Species for Bioexploration

by Qing Du, Heyu Yang, Jing Zeng, Zhuoer Chen, Junchen Zhou, Sihui Sun, Bin Wang and Chang Liu

Int. J. Mol. Sci. 2022, 23(20), 12080; https://doi.org/10.3390/ijms232012080 - 11 Oct 2022

Cited by 6 | Viewed by 2178

Abstract

To systematically determine their phylogenetic relationships and develop molecular markers for species discrimination of Salvia bowleyana, S. splendens, and S. officinalis, we sequenced their chloroplast genomes using the Illumina Hiseq 2500 platform. The chloroplast genomes length of S. bowleyana, S. splendens, and S. officinalis were 151,387 bp, 150,604 bp, and 151,163 bp, respectively. The six genes ndhB, rpl2, rpl23, rps7, rps12, and ycf2 were present in the IR regions. The chloroplast genomes of S. bowleyana, S. splendens, and S. officinalis contain 29 tandem repeats; 35, 29, 24 simple-sequence repeats, and 47, 49, 40 interspersed repeats, respectively. The three specific intergenic sequences (IGS) of rps16-trnQ-UUG, trnL-UAA-trnF-GAA, and trnM-CAU-atpE were found to discriminate the 23 Salvia species. A total of 91 intergenic spacer sequences were identified through genetic distance analysis. The two specific IGS regions (trnG-GCC-trnM-CAU and ycf3-trnS-GGA) have the highest K2p value identified in the three studied Salvia species. Furthermore, the phylogenetic tree showed that the 23 Salvia species formed a monophyletic group. Two pairs of genus-specific DNA barcode primers were found. The results will provide a solid foundation to understand the phylogenetic classification of the three Salvia species. Moreover, the specific intergenic regions can provide the probability to discriminate the Salvia species between the phenotype and the distinction of gene fragments. Full article

(This article belongs to the Special Issue Plant Genomics and Bioinformatics)

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16 pages, 5943 KiB

Open AccessArticle

Ectopic Overexpression of Histone H3K4 Methyltransferase CsSDG36 from Tea Plant Decreases Hyperosmotic Stress Tolerance in Arabidopsis thaliana

by Qinghua Chen, Linghui Guo, Yanwen Yuan, Shuangling Hu, Fei Guo, Hua Zhao, Zhenyu Yun, Yu Wang, Mingle Wang, Dejiang Ni, Lin Zhao and Pu Wang

Int. J. Mol. Sci. 2021, 22(10), 5064; https://doi.org/10.3390/ijms22105064 - 11 May 2021

Cited by 7 | Viewed by 2900

Abstract

Histone methylation plays an important regulatory role in the drought response of many plants, but its regulatory mechanism in the drought response of the tea plant remains poorly understood. Here, drought stress was shown to induce lower relative water content and significantly downregulate the methylations of histone H3K4 in the tea plant. Based on our previous analysis of the SET Domain Group (SDG) gene family, the full-length coding sequence (CDS) of CsSDG36 was cloned from the tea cultivar ‘Fuding Dabaicha’. Bioinformatics analysis showed that the open reading frame (ORF) of the CsSDG36 gene was 3138 bp, encoding 1045 amino acids and containing the conserved structural domains of PWWP, PHD, SET and PostSET. The CsSDG36 protein showed a close relationship to AtATX4 of the TRX subfamily, with a molecular weight of 118,249.89 Da, and a theoretical isoelectric point of 8.87, belonging to a hydrophilic protein without a transmembrane domain, probably located on the nucleus. The expression of CsSDG36 was not detected in the wild type, while it was clearly detected in the over-expression lines of Arabidopsis. Compared with the wild type, the over-expression lines exhibited lower hyperosmotic resistance by accelerating plant water loss, increasing reactive oxygen species (ROS) pressure, and increasing leaf stomatal density. RNA-seq analysis suggested that the CsSDG36 overexpression caused the differential expression of genes related to chromatin assembly, microtubule assembly, and leaf stomatal development pathways. qRT-PCR analysis revealed the significant down-regulation of stomatal development-related genes (BASL, SBT1.2(SDD1), EPF2, TCX3, CHAL, TMM, SPCH, ERL1, and EPFL9) in the overexpression lines. This study provides a novel sight on the function of histone methyltransferase CsSDG36 under drought stress. Full article

(This article belongs to the Special Issue Plant Genomics and Bioinformatics)

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19 pages, 2470 KiB

Open AccessArticle

Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection of Solanum tuberosum

by Venura Herath and Jeanmarie Verchot

Int. J. Mol. Sci. 2021, 22(6), 2837; https://doi.org/10.3390/ijms22062837 - 11 Mar 2021

Cited by 4 | Viewed by 3446

Abstract

Potato virus X (PVX) belongs to genus Potexvirus. This study characterizes the cellular transcriptome responses to PVX infection in Russet potato at 2 and 3 days post infection (dpi). Among the 1242 differentially expressed genes (DEGs), 268 genes were upregulated, and 37 genes were downregulated at 2 dpi while 677 genes were upregulated, and 265 genes were downregulated at 3 dpi. DEGs related to signal transduction, stress response, and redox processes. Key stress related transcription factors were identified. Twenty-five pathogen resistance gene analogs linked to effector triggered immunity or pathogen-associated molecular pattern (PAMP)-triggered immunity were identified. Comparative analysis with Arabidopsis unfolded protein response (UPR) induced DEGs revealed genes associated with UPR and plasmodesmata transport that are likely needed to establish infection. In conclusion, this study provides an insight on major transcriptional regulatory networked involved in early response to PVX infection and establishment. Full article

(This article belongs to the Special Issue Plant Genomics and Bioinformatics)

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