TY - JOUR
T1 - A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes
AU - Paritosh, Kumar
AU - Yadava, Satish Kumar
AU - Singh, Priyansha
AU - Bhayana, Latika
AU - Mukhopadhyay, Arundhati
AU - Gupta, Vibha
AU - Bisht, Naveen Chandra
AU - Zhang, Jianwei
AU - Kudrna, David A.
AU - Copetti, Dario
AU - Wing, Rod A.
AU - Reddy Lachagari, Vijaya Bhasker
AU - Pradhan, Akshay Kumar
AU - Pental, Deepak
N1 - Funding Information:
The work was supported by the Department of Biotechnology (DBT), Government of India through a 'Centre of Excellence on Genome Mapping and Molecular Breeding of Brassicas (Grant No. BT/01/COE/08/06‐II)' and 'DBT‐UDSC Partnership Centre on Genetic Manipulation of Brassicas (Grant No. BT/01/NDDB/UDSC/2016)'. DP was supported by a J C Bose Fellowship from the Department of Science and Technology (DST) and by the Council of Scientific and Industrial Research (CSIR) as a Distinguished Scientist. Travel of KP to Arizona Genome Centre was supported by the National Dairy Development Board. We thank Alex Hastie, Bionano Genomics, for carrying out the optical mapping experiments at their centre.
Publisher Copyright:
© 2020 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
PY - 2021/3
Y1 - 2021/3
N2 - Brassica juncea (AABB), commonly referred to as mustard, is a natural allopolyploid of two diploid species—B. rapa (AA) and B. nigra (BB). We report a highly contiguous genome assembly of an oleiferous type of B. juncea variety Varuna, an archetypical Indian gene pool line of mustard, with ~100× PacBio single-molecule real-time (SMRT) long reads providing contigs with an N50 value of >5 Mb. Contigs were corrected for the misassemblies and scaffolded with BioNano optical mapping. We also assembled a draft genome of B. nigra (BB) variety Sangam using Illumina short-read sequencing and Oxford Nanopore long reads and used it to validate the assembly of the B genome of B. juncea. Two different linkage maps of B. juncea, containing a large number of genotyping-by-sequencing markers, were developed and used to anchor scaffolds/contigs to the 18 linkage groups of the species. The resulting chromosome-scale assembly of B. juncea Varuna is a significant improvement over the previous draft assembly of B. juncea Tumida, a vegetable type of mustard. The assembled genome was characterized for transposons, centromeric repeats, gene content and gene block associations. In comparison to the A genome, the B genome contains a significantly higher content of LTR/Gypsy retrotransposons, distinct centromeric repeats and a large number of B. nigra specific gene clusters that break the gene collinearity between the A and the B genomes. The B. juncea Varuna assembly will be of major value to the breeding work on oleiferous types of mustard that are grown extensively in south Asia and elsewhere.
AB - Brassica juncea (AABB), commonly referred to as mustard, is a natural allopolyploid of two diploid species—B. rapa (AA) and B. nigra (BB). We report a highly contiguous genome assembly of an oleiferous type of B. juncea variety Varuna, an archetypical Indian gene pool line of mustard, with ~100× PacBio single-molecule real-time (SMRT) long reads providing contigs with an N50 value of >5 Mb. Contigs were corrected for the misassemblies and scaffolded with BioNano optical mapping. We also assembled a draft genome of B. nigra (BB) variety Sangam using Illumina short-read sequencing and Oxford Nanopore long reads and used it to validate the assembly of the B genome of B. juncea. Two different linkage maps of B. juncea, containing a large number of genotyping-by-sequencing markers, were developed and used to anchor scaffolds/contigs to the 18 linkage groups of the species. The resulting chromosome-scale assembly of B. juncea Varuna is a significant improvement over the previous draft assembly of B. juncea Tumida, a vegetable type of mustard. The assembled genome was characterized for transposons, centromeric repeats, gene content and gene block associations. In comparison to the A genome, the B genome contains a significantly higher content of LTR/Gypsy retrotransposons, distinct centromeric repeats and a large number of B. nigra specific gene clusters that break the gene collinearity between the A and the B genomes. The B. juncea Varuna assembly will be of major value to the breeding work on oleiferous types of mustard that are grown extensively in south Asia and elsewhere.
KW - Brassica juncea
KW - Brassica nigra
KW - breeding
KW - evolution
KW - gene blocks
KW - genome assembly
KW - long-read sequencing
KW - oilseed mustard
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U2 - 10.1111/pbi.13492
DO - 10.1111/pbi.13492
M3 - Article
C2 - 33073461
AN - SCOPUS:85096612322
SN - 1467-7644
VL - 19
SP - 602
EP - 614
JO - Plant Biotechnology Journal
JF - Plant Biotechnology Journal
IS - 3
ER -