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Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies inGossypium arboreum

文献类型： 外文期刊

作者： Ashraf, Javaria 1 ; Zuo, Dongyun 2 ; Cheng, Hailiang 2 ; Malik, Waqas 3 ; Wang, Qiaolian 2 ; Zhang, Youping 2 ; Abid, Muhammad Ali 3 ; Yang, Qiuhong 4 ; Feng, Xiaoxu 2 ; Yu, John Z. 5 ; Song, Guoli 2 ;

作者机构： 1.Chinese Acad Agr Sci, Inst Cotton Res, Anyang 455000, Peoples R China

2.Zhengzhou Univ, State Key Lab Cotton Biol, Zhengzhou Res Base, Zhengzhou 450001, Peoples R China

3.Bahauddin Zakariya Univ, Fac Agr Sci & Technol, Dept Plant Breeding & Genet, Genom Lab, Multan 60000, Punjab, Pakistan

4.Tarim Univ, Coll Life Sci, Alar 843300, Peoples R China

5.USDA ARS, Crop Germplasm Res Unit, Southern Plains Agr Res Ctr, College Stn, TX 77845 USA

关键词： Genetic map; Reference-assisted assembly; Syntenic relationship; Gene loss; Transcription factor

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2020 年 21 卷 1 期

页码：

收录情况： SCI

摘要： 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 cultivatedG. arboreumwas sequenced and assembled with shotgun sequencing approach, however, it contains several misassemblies. To address this issue, we generated an improved reassembly ofG. arboreumchromosome 12 using genetic mapping and reference-assisted approaches and evaluated this reconstruction by comparing with homologous chromosomes ofG. raimondiiandG. hirsutum. Results In this study, we generated a high quality assembly of the 94.64 Mb length ofG. arboreumchromosome 12 (A_A12) which comprised of 144 scaffolds and contained 3361 protein coding genes. Evaluation of results using syntenic and collinear analysis of reconstructedG. arboreumchromosome A_A12 with its homologous chromosomes ofG. raimondii(D_D08) andG. 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) ofG. arboreumparticularly in anchoring and orienting of scaffolds into a pseudo-chromosome. Further, homologous chromosomes 12 ofG. raimondii(D_D08) andG. 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.

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