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A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

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Title A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes
 
Creator Paritosh, Kumar
Yadava, Satish Kumar
Singh, Priyansha
Bhayana, Latika
Mukhopadhyay, Arundhati
Gupta, Vibha
Bisht, Naveen C.
Zhang, Jianwei
Kudrna, David A
Copetti, Dario
Wing, Rod A
Reddy, Vijay Bhaskar
Pradhan, Akshay Kumar
Pental, Deepak
 
Subject Brassica juncea
oilseed mustard
B. nigra
long‐read sequencing
genome assembly
gene blocks
evolution
breeding
 
Description Accepted date: 19 October 2020
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 ~100x PacBio single‐molecule real‐time (SMRT) long‐reads providing contigs with an N50 value of >5Mb. 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.
The work was supported by the Department of Biotechnology (DBT), Government of India
through a Centre of Excellence (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
center.
 
Date 2020-10-21T09:35:32Z
2020-10-21T09:35:32Z
2020
 
Type Article
 
Identifier Plant Biotechnology Journal, (In Press)
1467-7652
https://doi.org/10.1111/pbi.13492
https://onlinelibrary.wiley.com/doi/10.1111/pbi.13492
http://223.31.159.10:8080/jspui/handle/123456789/1116
 
Language en_US
 
Format application/pdf
 
Publisher John Wiley & Sons