Long‐read‐based draft genome sequence of Indian black gram IPU‐94‐1 ‘Uttara’: Insights into disease resistance and seed storage protein genes
Abstract Black gram [Vigna mungo (L.) Hepper var. mungo] is a warm‐season legume highly prized for its protein content along with significant folate and iron proportions. To expedite the genetic enhancement of black gram, a high‐quality draft genome from the center of origin of the crop is indispens...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2022-09-01
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| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.20234 |
| _version_ | 1818022994291720192 |
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| author | Heena Ambreen Praveen Kumar Oraon Daniel Regie Wahlang Rama Rao Satyawada Surekha Katiyar‐Agarwal Manu Agarwal Arun Jagannath Amar Kumar Roli Budhwar Rohit Nandan Shukla Shailendra Goel |
| author_facet | Heena Ambreen Praveen Kumar Oraon Daniel Regie Wahlang Rama Rao Satyawada Surekha Katiyar‐Agarwal Manu Agarwal Arun Jagannath Amar Kumar Roli Budhwar Rohit Nandan Shukla Shailendra Goel |
| author_sort | Heena Ambreen |
| collection | DOAJ |
| description | Abstract Black gram [Vigna mungo (L.) Hepper var. mungo] is a warm‐season legume highly prized for its protein content along with significant folate and iron proportions. To expedite the genetic enhancement of black gram, a high‐quality draft genome from the center of origin of the crop is indispensable. Here, we established a draft genome sequence of an Indian black gram cultivar, ‘Uttara’ (IPU 94‐1), known for its high resistance to mungbean yellow mosaic virus. Pacific Biosciences of California, Inc. (PacBio) single‐molecule real‐time (SMRT) and Illumina sequencing assembled a draft reference‐guided assembly with a cumulative size of ∼454.4 Mb, of which, 444.4 Mb was anchored on 11 pseudomolecules corresponding to 11 chromosomes. Uttara assembly denotes features of a high‐quality draft genome illustrated through high N50 value (42.88 Mb), gene completeness (benchmarking universal single‐copy ortholog [BUSCO] score 94.17%) and low levels of ambiguous nucleotides (N) percent (0.0005%). Gene discovery using transcript evidence predicted 28,881 protein‐coding genes, from which, ∼95% were functionally annotated. A global survey of genes associated with disease resistance revealed 119 nucleotide binding site–leucine rich repeat (NBS‐LRR) proteins, while 23 genes encoding seed storage proteins (SSPs) were discovered in black gram. A large set of microsatellite loci were discovered for marker development in the crop. Our draft genome of an Indian black gram provides the foundational genomic resources for the improvement of important agronomic traits and ultimately will help in accelerating black gram breeding programs. |
| first_indexed | 2024-12-10T03:37:16Z |
| format | Article |
| id | doaj.art-3782797333db401787cabc08ca3ed9e0 |
| institution | Directory Open Access Journal |
| issn | 1940-3372 |
| language | English |
| last_indexed | 2024-12-10T03:37:16Z |
| publishDate | 2022-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj.art-3782797333db401787cabc08ca3ed9e02022-12-22T02:03:41ZengWileyThe Plant Genome1940-33722022-09-01153n/an/a10.1002/tpg2.20234Long‐read‐based draft genome sequence of Indian black gram IPU‐94‐1 ‘Uttara’: Insights into disease resistance and seed storage protein genesHeena Ambreen0Praveen Kumar Oraon1Daniel Regie Wahlang2Rama Rao Satyawada3Surekha Katiyar‐Agarwal4Manu Agarwal5Arun Jagannath6Amar Kumar7Roli Budhwar8Rohit Nandan Shukla9Shailendra Goel10Dep. of Botany Univ. of Delhi Delhi 110007 IndiaDep. of Botany Univ. of Delhi Delhi 110007 IndiaDep. of Biotechnology & Bioinformatics North‐Eastern Hill Univ. Shillong 793022 IndiaDep. of Biotechnology & Bioinformatics North‐Eastern Hill Univ. Shillong 793022 IndiaDep. of Plant Molecular Biology Univ. of Delhi South Campus, Benito Juarez Road New Delhi 110021 IndiaDep. of Botany Univ. of Delhi Delhi 110007 IndiaDep. of Botany Univ. of Delhi Delhi 110007 IndiaDep. of Botany Univ. of Delhi Delhi 110007 IndiaBionivid Technology Pvt. Limited Bengaluru 560043 IndiaBionivid Technology Pvt. Limited Bengaluru 560043 IndiaDep. of Botany Univ. of Delhi Delhi 110007 IndiaAbstract Black gram [Vigna mungo (L.) Hepper var. mungo] is a warm‐season legume highly prized for its protein content along with significant folate and iron proportions. To expedite the genetic enhancement of black gram, a high‐quality draft genome from the center of origin of the crop is indispensable. Here, we established a draft genome sequence of an Indian black gram cultivar, ‘Uttara’ (IPU 94‐1), known for its high resistance to mungbean yellow mosaic virus. Pacific Biosciences of California, Inc. (PacBio) single‐molecule real‐time (SMRT) and Illumina sequencing assembled a draft reference‐guided assembly with a cumulative size of ∼454.4 Mb, of which, 444.4 Mb was anchored on 11 pseudomolecules corresponding to 11 chromosomes. Uttara assembly denotes features of a high‐quality draft genome illustrated through high N50 value (42.88 Mb), gene completeness (benchmarking universal single‐copy ortholog [BUSCO] score 94.17%) and low levels of ambiguous nucleotides (N) percent (0.0005%). Gene discovery using transcript evidence predicted 28,881 protein‐coding genes, from which, ∼95% were functionally annotated. A global survey of genes associated with disease resistance revealed 119 nucleotide binding site–leucine rich repeat (NBS‐LRR) proteins, while 23 genes encoding seed storage proteins (SSPs) were discovered in black gram. A large set of microsatellite loci were discovered for marker development in the crop. Our draft genome of an Indian black gram provides the foundational genomic resources for the improvement of important agronomic traits and ultimately will help in accelerating black gram breeding programs.https://doi.org/10.1002/tpg2.20234 |
| spellingShingle | Heena Ambreen Praveen Kumar Oraon Daniel Regie Wahlang Rama Rao Satyawada Surekha Katiyar‐Agarwal Manu Agarwal Arun Jagannath Amar Kumar Roli Budhwar Rohit Nandan Shukla Shailendra Goel Long‐read‐based draft genome sequence of Indian black gram IPU‐94‐1 ‘Uttara’: Insights into disease resistance and seed storage protein genes The Plant Genome |
| title | Long‐read‐based draft genome sequence of Indian black gram IPU‐94‐1 ‘Uttara’: Insights into disease resistance and seed storage protein genes |
| title_full | Long‐read‐based draft genome sequence of Indian black gram IPU‐94‐1 ‘Uttara’: Insights into disease resistance and seed storage protein genes |
| title_fullStr | Long‐read‐based draft genome sequence of Indian black gram IPU‐94‐1 ‘Uttara’: Insights into disease resistance and seed storage protein genes |
| title_full_unstemmed | Long‐read‐based draft genome sequence of Indian black gram IPU‐94‐1 ‘Uttara’: Insights into disease resistance and seed storage protein genes |
| title_short | Long‐read‐based draft genome sequence of Indian black gram IPU‐94‐1 ‘Uttara’: Insights into disease resistance and seed storage protein genes |
| title_sort | long read based draft genome sequence of indian black gram ipu 94 1 uttara insights into disease resistance and seed storage protein genes |
| url | https://doi.org/10.1002/tpg2.20234 |
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