The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants

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2019-11-01
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Udall, Joshua
Long, Evan
Ramaraj, Thiruvarangan
Conover, Justin
Yuan, Daojun
Grover, Corrinne
Gong, Lei
Arick, Mark
Masonbrink, Rick
Peterson, Daniel
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Wendel, Jonathan
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Ecology, Evolution and Organismal Biology

The Department of Ecology, Evolution, and Organismal Biology seeks to teach the studies of ecology (organisms and their environment), evolutionary theory (the origin and interrelationships of organisms), and organismal biology (the structure, function, and biodiversity of organisms). In doing this, it offers several majors which are codirected with other departments, including biology, genetics, and environmental sciences.

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The Department of Ecology, Evolution, and Organismal Biology was founded in 2003 as a merger of the Department of Botany, the Department of Microbiology, and the Department of Zoology and Genetics.

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2003–present

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Genome Informatics Facility
The Genome Informatics Facility serves as a centralized resource of expertise on the application of emerging sequencing technologies and open source software as applied to biological systems. Its mission is to integrate this knowledge into pipelines that are easy to understand and use by faculty, staff and students to enable the transformation of ‘big data’ into data that dramatically accelerates our understanding of biology and evolutionary processes.
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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 rearrangements. A series of structural rearrangements were identified comparing the de novo G. kirkii genome sequence to genome sequences of Gossypium, including chromosome fusions and inversions. Genome comparison between G. kirkii and Gossypium suggests that multiple steps are required to generate the extant structural differences.

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This article is published as Udall JA, Long E, Ramaraj T, Conover JL, Yuan D, Grover CE, Gong L, Arick MA II, Masonbrink RE, Peterson DG and Wendel JF (2019) The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants. Front. Plant Sci. 10:1541. doi: 10.3389/fpls.2019.01541.

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