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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #353075

Research Project: Advanced Genomic and Bioinformatic Tools for Accelerated Cotton Genetic Improvement

Location: Crop Germplasm Research

Title: Improved reconstruction and comparative analysis of chromosome 12 to rectify mis-assemblies in Gossypium arboreum

Author
item ASHRAF, JAVARIA - Chinese Academy Of Agricultural Sciences
item ZUO, DONGYUN - Chinese Academy Of Agricultural Sciences
item CHENG, HAILIANG - Chinese Academy Of Agricultural Sciences
item MALIK, WAQAS - Bahauddin Zakariya University
item WANG, QIAOLIAN - Chinese Academy Of Agricultural Sciences
item ZHANG, YOUPING - Chinese Academy Of Agricultural Sciences
item ABID, MUHAMMAD ALI - Bahauddin Zakariya University
item YANG, QIUHONG - Chinese Academy Of Agricultural Sciences
item FENG, XIAOXU - Chinese Academy Of Agricultural Sciences
item Yu, John
item SONG, GUOLI - Chinese Academy Of Agricultural Sciences

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/9/2020
Publication Date: 7/8/2020
Citation: Ashraf, J., Zuo, D., Cheng, H., Malik, W., Wang, Q., Zhang, Y., Abid, M., Yang, Q., Feng, X., Yu, J., Song, G. 2020. Improved reconstruction and comparative analysis of chromosome 12 to rectify mis-assemblies in Gossypium arboreum. Biomed Central (BMC) Genomics. 21: Article 470. https://doi.org/10.1186/s12864-020-06814-5.
DOI: https://doi.org/10.1186/s12864-020-06814-5

Interpretive Summary: Although next-generation sequencing (NGS) technologies significantly improved the efficiency of genome sequencing, great challenges remain in accurate assembling of such complex plant genomes as cotton. Recent comparative analysis revealed various mis-assemblies in the previously sequenced genome of G. arboreum, a cultivated diploid cotton. These mis-assemblies have complicated the application of genomic information in cotton improvement. To solve this problem, we developed a high-quality assembly of G. arboreum chromosome 12 by genetic mapping and reference-assisted assembly approaches. The newly completed re-assembly corresponds precisely to homologous chromosomes of G. raimondii and G. hirsutum genomes, further confirming its significantly improved quality for cotton improvement. Results from this study validated the current assembling strategy that identifies and corrects mis-assemblies in draft genome sequences, and provides additional insights into cotton genome structures and genetic applications.

Technical Abstract: Genome sequencing technologies have been improved rapidly but precise chromosome-scale assembling of genomes continues to be of a great challenge. Comparative analysis reported that previously sequenced genome of G. arboreum contained various mis-assemblies. To address this problem, we generated significantly accurate high-quality assembly of G. arboreum chromosome 12 by genetic mapping and reference-assisted assembly approaches. We discovered major mis-assemblies in previously assembled chromosome 12 of G. arboreum, particularly in anchoring and orienting of scaffolds into a pseudo-molecule. Evaluation of the results that correspond to homologous chromosomes of G. raimondii and G. hirsutum further confirmed the significantly improved quality of current re-assembly. This study offers a more accurate strategy towards the correction of mis-assemblies in cotton draft genome sequences to provide further insights into the genome organization in cotton.