Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum
Abstract Background Genome sequencing technologies have been improved at an exponential pace but precise chromosome-scale genome assembly still remains a great challenge. The draft genome of cultivated G. arboreum was sequenced and assembled with shotgun sequencing approach, however, it contains sev...
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doaj-d98012519f584c34b0695b7cff53f65b2020-11-25T03:12:40ZengBMCBMC Genomics1471-21642020-07-0121111410.1186/s12864-020-06814-5Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreumJavaria Ashraf0Dongyun Zuo1Hailiang Cheng2Waqas Malik3Qiaolian Wang4Youping Zhang5Muhammad Ali Abid6Qiuhong Yang7Xiaoxu Feng8John Z. Yu9Guoli Song10Institute of Cotton Research, Chinese Academy of Agricultural SciencesInstitute of Cotton Research, Chinese Academy of Agricultural SciencesInstitute of Cotton Research, Chinese Academy of Agricultural SciencesGenomics Lab, Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya UniversityInstitute of Cotton Research, Chinese Academy of Agricultural SciencesInstitute of Cotton Research, Chinese Academy of Agricultural SciencesGenomics Lab, Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya UniversityCollege of Life Sciences, Tarim UniversityInstitute of Cotton Research, Chinese Academy of Agricultural SciencesCrop Germplasm Research Unit, Southern Plains Agricultural Research Center, US Department of Agriculture–Agricultural Research Service (USDA-ARS)Institute of Cotton Research, Chinese Academy of Agricultural SciencesAbstract Background Genome sequencing technologies have been improved at an exponential pace but precise chromosome-scale genome assembly still remains a great challenge. The draft genome of cultivated G. arboreum was sequenced and assembled with shotgun sequencing approach, however, it contains several misassemblies. To address this issue, we generated an improved reassembly of G. arboreum chromosome 12 using genetic mapping and reference-assisted approaches and evaluated this reconstruction by comparing with homologous chromosomes of G. raimondii and G. hirsutum. Results In this study, we generated a high quality assembly of the 94.64 Mb length of G. arboreum chromosome 12 (A_A12) which comprised of 144 scaffolds and contained 3361 protein coding genes. Evaluation of results using syntenic and collinear analysis of reconstructed G. arboreum chromosome A_A12 with its homologous chromosomes of G. raimondii (D_D08) and G. hirsutum (AD_A12 and AD_D12) confirmed the significant improved quality of current reassembly as compared to previous one. We found major misassemblies in previously assembled chromosome 12 (A_Ca9) of G. arboreum particularly in anchoring and orienting of scaffolds into a pseudo-chromosome. Further, homologous chromosomes 12 of G. raimondii (D_D08) and G. arboreum (A_A12) contained almost equal number of transcription factor (TF) related genes, and showed good collinear relationship with each other. As well, a higher rate of gene loss was found in corresponding homologous chromosomes of tetraploid (AD_A12 and AD_D12) than diploid (A_A12 and D_D08) cotton, signifying that gene loss is likely a continuing process in chromosomal evolution of tetraploid cotton. Conclusion This study offers a more accurate strategy to correct misassemblies in sequenced draft genomes of cotton which will provide further insights towards its genome organization.http://link.springer.com/article/10.1186/s12864-020-06814-5Genetic mapReference-assisted assemblySyntenic relationshipGene lossTranscription factor |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Javaria Ashraf Dongyun Zuo Hailiang Cheng Waqas Malik Qiaolian Wang Youping Zhang Muhammad Ali Abid Qiuhong Yang Xiaoxu Feng John Z. Yu Guoli Song |
spellingShingle |
Javaria Ashraf Dongyun Zuo Hailiang Cheng Waqas Malik Qiaolian Wang Youping Zhang Muhammad Ali Abid Qiuhong Yang Xiaoxu Feng John Z. Yu Guoli Song Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum BMC Genomics Genetic map Reference-assisted assembly Syntenic relationship Gene loss Transcription factor |
author_facet |
Javaria Ashraf Dongyun Zuo Hailiang Cheng Waqas Malik Qiaolian Wang Youping Zhang Muhammad Ali Abid Qiuhong Yang Xiaoxu Feng John Z. Yu Guoli Song |
author_sort |
Javaria Ashraf |
title |
Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum |
title_short |
Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum |
title_full |
Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum |
title_fullStr |
Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum |
title_full_unstemmed |
Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum |
title_sort |
improved reconstruction and comparative analysis of chromosome 12 to rectify mis-assemblies in gossypium arboreum |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2020-07-01 |
description |
Abstract Background Genome sequencing technologies have been improved at an exponential pace but precise chromosome-scale genome assembly still remains a great challenge. The draft genome of cultivated G. arboreum was sequenced and assembled with shotgun sequencing approach, however, it contains several misassemblies. To address this issue, we generated an improved reassembly of G. arboreum chromosome 12 using genetic mapping and reference-assisted approaches and evaluated this reconstruction by comparing with homologous chromosomes of G. raimondii and G. hirsutum. Results In this study, we generated a high quality assembly of the 94.64 Mb length of G. arboreum chromosome 12 (A_A12) which comprised of 144 scaffolds and contained 3361 protein coding genes. Evaluation of results using syntenic and collinear analysis of reconstructed G. arboreum chromosome A_A12 with its homologous chromosomes of G. raimondii (D_D08) and G. hirsutum (AD_A12 and AD_D12) confirmed the significant improved quality of current reassembly as compared to previous one. We found major misassemblies in previously assembled chromosome 12 (A_Ca9) of G. arboreum particularly in anchoring and orienting of scaffolds into a pseudo-chromosome. Further, homologous chromosomes 12 of G. raimondii (D_D08) and G. arboreum (A_A12) contained almost equal number of transcription factor (TF) related genes, and showed good collinear relationship with each other. As well, a higher rate of gene loss was found in corresponding homologous chromosomes of tetraploid (AD_A12 and AD_D12) than diploid (A_A12 and D_D08) cotton, signifying that gene loss is likely a continuing process in chromosomal evolution of tetraploid cotton. Conclusion This study offers a more accurate strategy to correct misassemblies in sequenced draft genomes of cotton which will provide further insights towards its genome organization. |
topic |
Genetic map Reference-assisted assembly Syntenic relationship Gene loss Transcription factor |
url |
http://link.springer.com/article/10.1186/s12864-020-06814-5 |
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