Draft genome sequence of the pulse crop blackgram [Vigna mungo (L.) Hepper] reveals potential R-genes

Souframanien, J.; Raizada, Avi; Dhanasekar, P.; Suprasanna, Penna

doi:10.1038/s41598-021-90683-9

Cited by 29 publications

(10 citation statements)

References 49 publications

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“…Among the different R gene classes, Kinases (KIN) (33%), NBS (N) (14.5%) and Receptor Like Proteins (RLP) (13%) were dominant (Supplementary Table S5 ). These results are similar to the R genes predicted in other plants genomes 67 , 68 .…”

Section: Resultssupporting

confidence: 90%

De novo assembly and characterization of the draft genome of the cashew (Anacardium occidentale L.)

Savadi

Muralidhara

Godwin³

et al. 2022

Sci Rep

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Cashew is the second most important tree nut crop in the global market. Cashew is a diploid and heterozygous species closely related to the mango and pistachio. Its improvement by conventional breeding is slow due to the long juvenile phase. Despite the economic importance, very little genomics/transcriptomics information is available for cashew. In this study, the Oxford nanopore reads and Illumina reads were used for de novo assembly of the cashew genome. The hybrid assembly yielded a 356.6 Mb genome corresponding to 85% of the estimated genome size (419 Mb). The BUSCO analysis showed 91.8% of genome completeness. Transcriptome mapping showed 92.75% transcripts aligned with the assembled genome. Gene predictions resulted in the identification of 31,263 genes coding for a total of 35,000 gene isoforms. About 46% (165 Mb) of the cashew genome comprised of repetitive sequences. Phylogenetic analyses of the cashew with nine species showed that it was closely related to Mangifera indica. Analysis of cashew genome revealed 3104 putative R-genes. The first draft assembly of the genome, transcriptome and R gene information generated in this study would be the foundation for understanding the molecular basis of economic traits and genomics-assisted breeding in cashew.

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Section: Resultssupporting

confidence: 90%

De novo assembly and characterization of the draft genome of the cashew (Anacardium occidentale L.)

Savadi

Muralidhara

Godwin³

et al. 2022

Sci Rep

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show abstract

“…In genomes of eukaryotes, retrotransposons (Class I) are the most abundant transposable elements. Within the legume family, their composition can vary in different species due to the predominant number of Ty1 Copia (Istvánek et al, 2014;Jegadeesan et al, 2021) or Ty3-Gypsy elements (Kreplak et al, 2019;Lonardi et al, 2019). In the studied species of the sect.…”

Section: Discussionmentioning

confidence: 99%

Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae)

et al. 2022

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The section Multicaulia is the largest clade in the genus Hedysarum L. (Fabaceae). Representatives of the sect. Multicaulia are valuable plants used for medicinal and fodder purposes. The taxonomy and phylogeny of the sect. Multicaulia are still ambiguous. To clarify the species relationships within sect. Multicaulia, we, for the first time, explored repeatomes of H. grandiflorum Pall., H. zundukii Peschkova, and H. dahuricum Turcz. using next-generation sequencing technologies and a subsequent bioinformatic analysis by RepeatExplorer/TAREAN pipelines. The comparative repeatome analysis showed that mobile elements made up 20–24% (Class I) and about 2–2.5% (Class II) of their repetitive DNAs. The amount of ribosomal DNA varied from 1 to 2.6%, and the content of satellite DNA ranged from 2.7 to 5.1%. For each species, five high confident putative tandem DNA repeats and 5–10 low confident putative DNA repeats were identified. According to BLAST, these repeats demonstrated high sequence similarity within the studied species. FISH-based mapping of 35S rDNA, 5S rDNA, and satDNAs made it possible to detect new effective molecular chromosome markers for Hedysarum species and construct the species karyograms. Comparison of the patterns of satDNA localization on chromosomes of the studied species allowed us to assess genome diversity within the sect. Multicaulia. In all studied species, we revealed intra- and interspecific variabilities in patterns of the chromosomal distribution of molecular chromosome markers. In H. gmelinii Ledeb. and H. setigerum Turcz. ex Fisch. et Meyer, similar subgenomes were detected, which confirmed the polyploid status of their genomes. Our findings demonstrated a close genomic relationship among six studied species indicating their common origin and confirmed the taxonomic status of H. setigerum as a subspecies of H. gmelinii as well as the validity of combining the sect. Multicaulia and Subacaulia into one sect. Multicaulia.

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“…The increased availability of mung bean genome sequences resulted in more conveniently mung bean genomic analysis [ 15 – 17 ]. To explore the inner mechanism of drought resistance in mung bean, leaf samples at 4 stages were obtained from control and drought-treated mung bean, also the morphological and physiological changes were detected in this study.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic and biochemical analyses of drought response mechanism in mung bean (Vignaradiata (L.) Wilczek) leaves

Guo

Zhang

et al. 2023

PLoS ONE

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Drought is a major factor that limiting mung bean development. To clarify the molecular mechanism of mung bean in response to drought stress, 2 mung bean groups were established, the experimental group (drought-treated) and the control group (normal water management). With prominent difference of 2 groups in stomatal conductance, relative water content and phenotype, leaf samples were collected at 4 stages, and the physiological index of MDA, POD, chlorophyll, and soluble proteins were estimated. RNA-seq was used to obtain high quality data of samples, and differentially expressed genes were identified by DESeq2. With GO and KEGG analysis, DEGs were enriched into different classifications and pathways. WGCNA was used to detect the relationship between physiological traits and genes, and qPCR was performed to confirm the accuracy of the data. We obtained 169.49 Gb of clean data from 24 samples, and the Q30 of each date all exceeded 94%. In total, 8963 DEGs were identified at 4 stages between the control and treated samples, and the DEGs were involved in most biological processes. 1270 TFs screened from DEGs were clustered into 158 TF families, such as AP2, RLK-Pelle-DLSVA, and NAC TF families. Genes related to physiological traits were closely related to plant hormone signaling, carotenoid biosynthesis, chlorophyll metabolism, and protein processing. This paper provides a large amount of data for drought research in mung bean.

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Draft genome sequence of the pulse crop blackgram [Vigna mungo (L.) Hepper] reveals potential R-genes

Cited by 29 publications

References 49 publications

De novo assembly and characterization of the draft genome of the cashew (Anacardium occidentale L.)

De novo assembly and characterization of the draft genome of the cashew (Anacardium occidentale L.)

Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae)

Transcriptomic and biochemical analyses of drought response mechanism in mung bean (Vignaradiata (L.) Wilczek) leaves

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