Author:
Chávez Montes Ricardo A.,Ulloa Mauricio,Biniashvili Tammy,Zackay Arik,Kfir Nir,Lopez-Arredondo Damar,Herrera-Estrella Luis
Abstract
Abstract
Background
Gossypium barbadense L. Pima cotton is known for its resistance to Fusarium wilt and for producing fibers of superior quality highly prized in the textile market. We report a high-quality genome assembly and annotation of Pima-S6 cotton and its comparison at the chromosome and protein level to other ten Gossypium published genome assemblies.
Results
Synteny and orthogroup analyses revealed important differences on chromosome structure and annotated proteins content between our Pima-S6 and other publicly available G. barbadense assemblies, and across Gossypium assemblies in general. Detailed synteny analyses revealed chromosomal rearrangements between Pima-S6 and other Pima genomes on several chromosomes, with three major inversions in chromosomes A09, A13 and D05, raising questions about the true chromosome structure of Gossypium barbadense genomes.
Conclusion
Analyses of the re-assembled and re-annotated genome of the close relative G. barbadense Pima 3–79 using our Pima-S6 assembly suggest that contig placement of some recent G. barbadense assemblies might have been unduly influenced by the use of the G. hirsutum TM-1 genome as the anchoring reference. The Pima-S6 reference genome provides a valuable genomic resource and offers new insights on genomic structure, and can serve as G. barbadense genome reference for future assemblies and further support FOV4-related studies and breeding efforts.
Funder
National Institute of Food and Agriculture
Cotton Incorporated
GURI
USDA-ARS-NACA
Publisher
Springer Science and Business Media LLC
Reference68 articles.
1. United States department of agriculture, foreign agricultural service. (https://apps.fas.usda.gov/psdonline/app/index.html#/app/downloads, accessed on December 2021).
2. Percival AE, Wendel JF, Stewart JM. Taxonomy and germplasm resources. In: Smith CW, Cothren JT, editors. Cotton; origin, history, Technology, and production. New York: John Wiley & Sons, Inc; 1999. pp. 33–63.
3. Wendel JF, Cronn RC. Polyploidy and the evolutionary history of cotton. In: Advances in agronomy. Academic press; 2003. pp. 139–86.
4. Ulloa M, Abdurakhmonov IY, Perez -MC, Percy R, Stewart JMcD. Genetic diversity and population structure of cotton (Gossypium spp.) of the New World assessed by SSR markers. Botany. 2013;91:251–9.
5. Chen ZJ, Sreedasyam A, Ando A, Song Q, De Santiago LM, Hulse-Kemp AM, et al. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nat Genet. 2020;52:525–33.
Cited by
5 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献