Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition lines
The economically valuable oil crop Brassica napus (AACC, 2n=38), which arose from interspecific hybridization between the diploid ancestors Brassica rapa (AA, 2n=20) and Brassica oleracea (CC, 2n=18), has a complex genome. More than 10% of the assembled sequences, most of which belong to the C subge...
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doaj-64de64e1cedc41a2b836b18b36ea975e2021-06-08T04:41:13ZengElsevierJournal of Integrative Agriculture2095-31192019-07-0118715411546Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition linesDong-ao HUO0Bin ZHU1Gui-fu TIAN2Xu-ye DU3Juan GUO4Meng-xian CAI5School of Life Sciences, Buckwheat Research Center, Guizhou Normal University, Guiyang 550025, P.R.ChinaSchool of Life Sciences, Buckwheat Research Center, Guizhou Normal University, Guiyang 550025, P.R.ChinaSchool of Life Sciences, Buckwheat Research Center, Guizhou Normal University, Guiyang 550025, P.R.ChinaSchool of Life Sciences, Buckwheat Research Center, Guizhou Normal University, Guiyang 550025, P.R.ChinaSchool of Life Sciences, Buckwheat Research Center, Guizhou Normal University, Guiyang 550025, P.R.ChinaCorrespondence CAI Meng-xian, Tel: +86-851-83227351; School of Life Sciences, Buckwheat Research Center, Guizhou Normal University, Guiyang 550025, P.R.ChinaThe economically valuable oil crop Brassica napus (AACC, 2n=38), which arose from interspecific hybridization between the diploid ancestors Brassica rapa (AA, 2n=20) and Brassica oleracea (CC, 2n=18), has a complex genome. More than 10% of the assembled sequences, most of which belong to the C subgenome, have not been anchored to the corresponding chromosome. Previously, a complete set of monosomic alien addition lines (MAALs, C1–C9) with each of the nine C-subgenome chromosomes added to the extracted A subgenome was obtained from the allotetraploid B. napus donor Oro, after the ancestral B. rapa (RBR Oro) genome was restored. These MAALs effectively reduced the complexity of the B. napus genome. Here, we determined the expression values of genes on unanchored scaffolds in the MAALs and RBR Oro. Then, multiple comparisons of these gene expression values were used to determine the affiliations of the non-anchored scaffolds on which the genes were located. In total, 54.68% (44.11 Mb) of the 80.67 Mb of non-anchored scaffolds belonging to the C subgenome were assigned to corresponding C chromosomes. This work highlights the potential value of these MAALs in improving the genome quality of B. napus.http://www.sciencedirect.com/science/article/pii/S2095311919626353Brassica napusgenome sequenceRNA-seqmonosomic alien addition linesscaffolds |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Dong-ao HUO Bin ZHU Gui-fu TIAN Xu-ye DU Juan GUO Meng-xian CAI |
spellingShingle |
Dong-ao HUO Bin ZHU Gui-fu TIAN Xu-ye DU Juan GUO Meng-xian CAI Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition lines Journal of Integrative Agriculture Brassica napus genome sequence RNA-seq monosomic alien addition lines scaffolds |
author_facet |
Dong-ao HUO Bin ZHU Gui-fu TIAN Xu-ye DU Juan GUO Meng-xian CAI |
author_sort |
Dong-ao HUO |
title |
Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition lines |
title_short |
Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition lines |
title_full |
Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition lines |
title_fullStr |
Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition lines |
title_full_unstemmed |
Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition lines |
title_sort |
assignment of unanchored scaffolds in genome of brassica napus by rna-seq analysis in a complete set of brassica rapa-brassica oleracea monosomic addition lines |
publisher |
Elsevier |
series |
Journal of Integrative Agriculture |
issn |
2095-3119 |
publishDate |
2019-07-01 |
description |
The economically valuable oil crop Brassica napus (AACC, 2n=38), which arose from interspecific hybridization between the diploid ancestors Brassica rapa (AA, 2n=20) and Brassica oleracea (CC, 2n=18), has a complex genome. More than 10% of the assembled sequences, most of which belong to the C subgenome, have not been anchored to the corresponding chromosome. Previously, a complete set of monosomic alien addition lines (MAALs, C1–C9) with each of the nine C-subgenome chromosomes added to the extracted A subgenome was obtained from the allotetraploid B. napus donor Oro, after the ancestral B. rapa (RBR Oro) genome was restored. These MAALs effectively reduced the complexity of the B. napus genome. Here, we determined the expression values of genes on unanchored scaffolds in the MAALs and RBR Oro. Then, multiple comparisons of these gene expression values were used to determine the affiliations of the non-anchored scaffolds on which the genes were located. In total, 54.68% (44.11 Mb) of the 80.67 Mb of non-anchored scaffolds belonging to the C subgenome were assigned to corresponding C chromosomes. This work highlights the potential value of these MAALs in improving the genome quality of B. napus. |
topic |
Brassica napus genome sequence RNA-seq monosomic alien addition lines scaffolds |
url |
http://www.sciencedirect.com/science/article/pii/S2095311919626353 |
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