{"doi":"10.1111/1755-0998.13243","title":"A chromosome‐scale assembly of the black gram (<i>Vigna mungo</i>) genome","abstract":"<jats:title>Abstract</jats:title><jats:p>Black gram (<jats:italic>Vigna mungo</jats:italic>) is an important short duration grain legume crop. Black gram seeds provide an inexpensive source of dietary protein. Here, we applied the 10X Genomics linked‐read technology to obtain a de novo whole genome assembly of <jats:italic>V. mungo</jats:italic> cultivated variety Chai Nat 80 (CN80). The preliminary assembly contained 12,228 contigs and had an N50 length of 5.2 Mb. Subsequent scaffolding using the long‐range Chicago and HiC techniques yielded the first high‐quality, chromosome‐level assembly of 499 Mb comprising 11 pseudomolecules. Comparative genomics analyses based on sequence information from single‐copy orthologous genes revealed that black gram and mungbean (<jats:italic>Vigna radiata</jats:italic>) diverged about 2.7 million years ago . The transversion rate (4DTv) analysis in <jats:italic>V. mungo</jats:italic> revealed no evidence supporting a recent genome‐wide duplication event observed in the tetraploid créole bean (<jats:italic>Vigna reflexo‐pilosa</jats:italic>). The proportion of repetitive elements in the black gram genome is slightly lower than the numbers reported for related <jats:italic>Vigna</jats:italic> species. The majority of long terminal repeat retrotransposons appeared to integrate into the genome within the last five million years. We also examined alternative splicing events in <jats:italic>V. mungo</jats:italic> using full‐length transcript sequences. While intron retention was the most prevalent mode of alternative splicing in several plant species, alternative 3' acceptor site selection represented the majority of events in black gram. Our high‐quality genome assembly along with the genomic variation information from the germplasm provides valuable resources for accelerating the development of elite varieties through marker‐assisted breeding and for future comparative genomics and phylogenetic studies in legume species.</jats:p>","journal":"Molecular Ecology Resources","year":2021,"id":640155,"datarank":0.611630616585858,"base_score":4.07753744390572,"endowment":4.07753744390572,"self_citation_contribution":0.611630616585858,"citation_network_contribution":0.0,"self_endowment_contribution":0.611630616585858,"citer_contribution":0.0,"corpus_percentile":68.1,"corpus_rank":4315,"citation_count":58,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1663647,"name":"Wanapinun Nawae","orcid":"0000-0001-9228-6963","position":1,"is_corresponding":false},{"id":1663648,"name":"Chaiwat Naktang","orcid":null,"position":2,"is_corresponding":false},{"id":1663649,"name":"Chutima Sonthirod","orcid":null,"position":3,"is_corresponding":false},{"id":1663650,"name":"Thippawan Yoocha","orcid":null,"position":4,"is_corresponding":false},{"id":1663651,"name":"Wasitthee Kongkachana","orcid":null,"position":5,"is_corresponding":false},{"id":1663652,"name":"Duangjai Sangsrakru","orcid":null,"position":6,"is_corresponding":false},{"id":1663653,"name":"Nukoon Jomchai","orcid":null,"position":7,"is_corresponding":false},{"id":1663654,"name":"Sonicha U‐thoomporn","orcid":null,"position":8,"is_corresponding":false},{"id":1663655,"name":"Prakit Somta","orcid":"0000-0002-1002-8360","position":9,"is_corresponding":false},{"id":1663656,"name":"Kularb Laosatit","orcid":null,"position":10,"is_corresponding":false},{"id":1663657,"name":"Sithichoke Tangphatsornruang","orcid":"0000-0003-2673-0012","position":11,"is_corresponding":false},{"id":1663646,"name":"Wirulda Pootakham","orcid":"0000-0001-6721-6453","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"A chromosome‐scale assembly of the black gram (<i>Vigna mungo</i>) genome","abstract":"<jats:title>Abstract</jats:title><jats:p>Black gram (<jats:italic>Vigna mungo</jats:italic>) is an important short duration grain legume crop. Black gram seeds provide an inexpensive source of dietary protein. Here, we applied the 10X Genomics linked‐read technology to obtain a de novo whole genome assembly of <jats:italic>V. mungo</jats:italic> cultivated variety Chai Nat 80 (CN80). The preliminary assembly contained 12,228 contigs and had an N50 length of 5.2 Mb. Subsequent scaffolding using the long‐range Chicago and HiC techniques yielded the first high‐quality, chromosome‐level assembly of 499 Mb comprising 11 pseudomolecules. Comparative genomics analyses based on sequence information from single‐copy orthologous genes revealed that black gram and mungbean (<jats:italic>Vigna radiata</jats:italic>) diverged about 2.7 million years ago . The transversion rate (4DTv) analysis in <jats:italic>V. mungo</jats:italic> revealed no evidence supporting a recent genome‐wide duplication event observed in the tetraploid créole bean (<jats:italic>Vigna reflexo‐pilosa</jats:italic>). The proportion of repetitive elements in the black gram genome is slightly lower than the numbers reported for related <jats:italic>Vigna</jats:italic> species. The majority of long terminal repeat retrotransposons appeared to integrate into the genome within the last five million years. We also examined alternative splicing events in <jats:italic>V. mungo</jats:italic> using full‐length transcript sequences. While intron retention was the most prevalent mode of alternative splicing in several plant species, alternative 3' acceptor site selection represented the majority of events in black gram. Our high‐quality genome assembly along with the genomic variation information from the germplasm provides valuable resources for accelerating the development of elite varieties through marker‐assisted breeding and for future comparative genomics and phylogenetic studies in legume species.</jats:p>","is_dataset_classified":null,"base_score":4.07753744390572,"endowment":4.07753744390572,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"32794377","pmcid":null,"openalex_id":"https://openalex.org/W3049081103","authors":[],"funders":[{"funder_name":"National Science and Technology Development Agency","grant_id":"1000221","title":null}],"total_grants":1,"fwci":7.7647,"citation_percentile":0.97145663,"influential_citations":0,"citation_trend":[{"year":2021,"count":3},{"year":2022,"count":20},{"year":2023,"count":12},{"year":2024,"count":10},{"year":2025,"count":8},{"year":2026,"count":5}],"oa_status":"closed","license":"http://onlinelibrary.wiley.com/termsAndConditions#vor","oa_locations":[{"url":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.13243","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13243","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13243","host_type":"publisher"},{"url":"https://doi.org/10.1111/1755-0998.13243","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/32794377","host_type":"repository"}],"fields_of_study":["Agricultural pest management studies","Legume Nitrogen Fixing Symbiosis","Genetic and Environmental Crop Studies","Chromosomes, Plant","Crops, Agricultural","Genome, Plant","Phylogeny","Plant Breeding","Retroelements","Vigna"],"mesh_terms":["Plant Breeding","Vigna","Phylogeny","Crops, Agricultural","Retroelements","Genome, Plant","Chromosomes, Plant"],"keywords":["Biology","Vigna","Genome","Sequence assembly","Genetics","Contig","Illumina dye sequencing","Genomics","Gram","Whole genome sequencing","Genome size","Botany","Gene","Transcriptome","Alternative splicing","Vigna Mungo","Hic","Black Gram","10X Genomics","Chromosome-scale Genome Assembly"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-07T07:07:41.237098Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}