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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 #369214

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

Location: Crop Germplasm Research

Title: The genome sequence of Gossypioides kirkii illustrates a descending dysploidy in plants

item Udall, Joshua - Josh
item LONG, EVAN - Cornell University
item RAMARAJ, THIRUVARANGAN - National Center For Genome Resources
item CONOVER, JUSTIN - Iowa State University
item YUAN, DAOJUN - Iowa State University
item GROVER, CORRINNE - Iowa State University
item GONG, LEI - Northeast Normal University
item ARICK, MARK - Mississippi State University
item MASONBRINK, RICK - Iowa State University
item PETERSON, DANIEL - Mississippi State University
item WENDEL, JONATHAN - Iowa State University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/5/2019
Publication Date: 11/27/2019
Citation: Udall, J.A., Long, E., Ramaraj, T., Conover, J.L., Yuan, D., Grover, C.E., Gong, L., Arick, M.A., Masonbrink, R.E., Peterson, D.G., Wendel, J.F. 2019. The genome sequence of Gossypioides kirkii illustrates a descending dysploidy in plants. Frontiers in Plant Science. 10:1541.

Interpretive Summary: A common pattern of chromosomal evolution in eukaryotes is the loss or gain of a chromosome, but the responsible processes remain unclear. To clarify the mechanism of chromosome loss, we sequenced the genome of Gossypioides kirkii, which has one less chromosome per haploid complement (n=12) than its close relatives in the cotton tribe (n=13). We demonstrate using comparative genomics that chromosome loss in G. kirkii could have been the result of the breakage-fusion-bridge process (BFB) first described by Barbara McClintock over 80 years ago to explain chromosomal anomalies in maize. Here we use the stable genomic phylogeny of Gossypium to demonstrate the origins of a single chromosome loss affecting three current chromosomes.

Technical Abstract: One of the extraordinary aspects of plant genome evolution is variation in chromosome number, particularly that among closely related species. This is exemplified by the cotton genus (Gossypium) and its relatives, where most species and genera have a base chromosome number of 13. The two exceptions are sister genera that have n=12 (the Hawaiian Kokia and the East African and Madagascan Gossypioides). We generated a high-quality genome sequence of Gossypioides kirkii (n=12) using PacBio, Bionano, and Hi-C technologies, and compared this assembly to genome sequences of Kokia (n=12) and Gossypium diploids (n=13). Previous analysis demonstrated that the directionality of their reduced chromosome number was through large structural, chromosomal rearrangements. A series of structural rearrangements were identified comparing the de novo G. kirkii genome sequence to genome sequences of Gossypium, including chromosomal fusions and inversions. Genome comparison between G. kirkii and Gossypium suggests that multiple steps are required to generate the extant structural differences, among which could be a series of breakage-fusion-bridge cycles after chromosome or chromatid end-to-end fusion.