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Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

Overview of attention for article published in BMC Genomics, January 2016
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Title
Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes
Published in
BMC Genomics, January 2016
DOI 10.1186/s12864-015-2343-1
Pubmed ID
Authors

Jun Zou, Dandan Hu, Peifa Liu, Harsh Raman, Zhongsong Liu, Xianjun Liu, Isobel A. P. Parkin, Boulos Chalhoub, Jinling Meng

Abstract

There are three basic Brassica genomes (A, B, and C) and three parallel sets of subgenomes distinguished in the diploid Brassica (i.e.: B. rapa, A(r)A(r); B. nigra, B(ni)B(ni); B. oleracea, C(o)C(o)) and the derived allotetraploid species (i.e.: B. juncea, A(j)A(j)B(j)B(j); B. napus, A(n)A(n)C(n)C(n); B. carinata, B(c)B(c)C(c)C(c)). To understand subgenome differentiation in B. juncea in comparison to other A genome-carrying Brassica species (B. rapa and B. napus), we constructed a dense genetic linkage map of B. juncea, and conducted population genetic analysis on diverse lines of the three A-genome carrying Brassica species using a genotyping-by-sequencing approach (DArT-seq). A dense genetic linkage map of B. juncea was constructed using an F2 population derived from Sichuan Yellow/Purple Mustard. The map included 3329 DArT-seq markers on 18 linkage groups and covered 1579 cM with an average density of two markers per cM. Based on this map and the alignment of the marker sequences with the physical genome of Arabidopsis thaliana, we observed strong co-linearity of the ancestral blocks among the different A subgenomes but also considerable block variation. Comparative analyses at the level of genome sequences of B. rapa and B. napus, and marker sequence anchored on the genetic map of B. juncea, revealed a total of 30 potential inversion events across large segments and 20 potential translocation events among the three A subgenomes. Population genetic analysis on 26 accessions of the three A genome-carrying Brassica species showed that the highest genetic distance were estimated when comparing A(j)-A(n) than between A(n)-A(r) and A(j)-A(r) subgenome pairs. The development of the dense genetic linkage map of B. juncea with informative DArT-seq marker sequences and availability of the reference sequences of the A(r), and A(n)C(n) genomes allowed us to compare the A subgenome structure of B. juncea (A(j)) . Our results suggest that strong co-linearity exists among the three A Brassica genomes (A(r), A(n) and A(j)) but with apparent subgenomic variation. Population genetic analysis on three A-genome carrying Brassica species support the idea that B. juncea has distinct genomic diversity, and/or evolved from a different A genome progenitor of B. napus.

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Mendeley readers

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The data shown below were compiled from readership statistics for 43 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 2%
Pakistan 1 2%
Unknown 41 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 10 23%
Researcher 8 19%
Student > Master 7 16%
Other 3 7%
Student > Bachelor 2 5%
Other 6 14%
Unknown 7 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 29 67%
Biochemistry, Genetics and Molecular Biology 6 14%
Unknown 8 19%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 06 January 2016.
All research outputs
#20,300,248
of 22,837,982 outputs
Outputs from BMC Genomics
#9,282
of 10,655 outputs
Outputs of similar age
#330,305
of 393,343 outputs
Outputs of similar age from BMC Genomics
#248
of 264 outputs
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