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Plant Biotechnol J:异源四倍体芥菜基因组

已有 561 次阅读 2020-10-22 08:25 |个人分类:每日摘要|系统分类:论文交流

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

第一作者Kumar Paritosh

第一单位印度德里大学

通讯作者Deepak Pental


 Abstract 


背景回顾Brassica juncea (AABB), commonly referred to as mustard, is a natural allopolyploid of two diploid species – B. rapa (AA) and B. nigra (BB).


主要研究: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.


结果1-进一步组装:Contigs were corrected for the misassemblies and scaffolded with BioNano optical mapping.


结果2-黑芥基因组: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.


结果3-染色体组装: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.


结果4-基因组特征: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.


结论: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.


 摘  要 


芥菜(Brassica juncea,AABB)是一个由两个二倍体自然组成的异源多倍体,两个二倍体植物分别是白菜Brassica rapa(AA)和黑芥Brassica nigra(BB)。本文中,作者基于约100x的Pacbio测序数据,组装了一个产油型芥菜品种Varuna的基因组,contig N50的大小超过5Mb。作者进一步通过BioNano光学图谱对contigs进行了纠错,并进一步组装成scaffolds。此外,作者还基于Illumina测序和Oxford Nanopore测序数据,组装了黑芥Brassica nigra(BB)的基因组,并用其结果来验证Varuna基因组中B套基因组的组装结果。作者开发了两套含有大量GBS标记的芥菜连锁图谱,并将组装获得的scaffolds和contigs挂载到了18个连锁群上。所获得的Varuna染色体层面的组装结果要优于先前蔬菜型芥菜品种Tumida的组装。作者进一步对Varuna基因组的转座子、着丝粒重复序列、基因含量以及基因块关联进行了分析。与A套基因组相比,B套基因组包含更多的LTR/Gypsy逆转座子、不同的着丝粒重复序列以及大量的黑芥特有的基因簇,这也导致了A、B两套基因组之间基因共线性区域的断裂。芥菜品种Varuna基因组的报道将对在南亚以及其他地区广泛种植的产油型芥菜的育种工作有所助益。


 通讯作者 


**Deepak Pental**


个人简介:

1971年,印度潘贾布大学,学士;

1973年,印度潘贾布大学,硕士;

1978年,美国罗格斯大学,博士;

1978-1984年,诺丁汉大学,博后。


研究方向:芥菜和棉花的育种


doi: 10.1111/pbi.13492


Journal: Plant Biotechnology Journal

Published date: Oct 19, 2020



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