Document Type
Article
Publication Date
2019
Publication Title
Frontiers in Ecology and Evolution
Abstract
The freshwater livebearing fish genus Poeciliopsis (Poeciliidae) constitutes a valuable research system for questions within the field of evolutionary ecology, including life history evolution (e.g., multiple origins of placentas), intergenomic conflict, evolution of sex (with the existence of several asexual hybrid biotypes), and biogeography (reviewed in Mateos et al., 2019). Despite its importance, a robust phylogenetic framework, and genomic resources are lacking for this taxon. Herein, we report the first whole genome draft sequence of a member of this genus: Poeciliopsis occidentalis Baird and Girard (1853), the Gila topminnow. Poeciliopsis occidentalis, along with its sister lineage P. sonoriensis Girard (1859) (the Yaqui topminnow), are currently considered separate species (Miller et al., 2005). They are distributed in Mexico and the United States, where they are listed (as subspecies of P. occidentalis sensu lato; Sonoran topminnow, “guatopote de Sonora” in Spanish) as threatened and endangered, respectively. P. occidentalis s.l. has several interesting biological features, whose study would benefit from annotated genomes. First, it has an intermediate level of placentation (matrotrophy index) within a clade (i.e., Leptorhaphis group) that contains members with higher (i.e., P. prolifica) and lower (i.e., P. infans) matrotrophy indices (Reznick et al., 2002). Secondly, it is the sexual host of the oldest known asexual hybrid biotype of the genus Poeciliopsis (i.e., the hybridogen Poeciliopsis monacha-occidentalis; Quattro et al., 1992). Moreover, P. occidentalis s.l. has an unresolved phylogenetic position, possibly due to incomplete lineage sorting, and/or reticulation (Mateos et al., 2019). In addition, the taxonomy and status of evolutionary significant units (ESUs) within P. occidentalis s.l. are controversial, as additional ESUs have been proposed (Vrijenhoek et al., 1985; Hedrick and Hurt, 2012). The genome sequence of P. occidentalis will thus be a valuable resource for macroevolutionary and molecular evolution studies of the genus, as well as for phylogeographic and conservation genetics research. In the work presented herein, we used the “linked-reads” Chromium System (10x Genomics, Pleasanton, CA, USA) to sequence, assemble, and annotate a draft genome of P. occidentalis. The resulting assembly had a contig and scaffold N50 of 0.103 and 1.540 Mbp, respectively.
Recommended Citation
Mateos, Mariana; Kang, Du; Klopp, Christophe; Parrinello, Hugues; García-Olazábal, Mateo; Schumer, Molly; Jue, Nathaniel K.; Guiguen, Yann; and Schartl, Manfred, "Draft Genome Assembly and Annotation of the Gila Topminnow Poeciliopsis occidentalis" (2019). School of Natural Sciences Faculty Publications and Presentations. 74.
https://digitalcommons.csumb.edu/sns_fac/74
Comments
Published in Frontiers in Ecology and Evolution by Frontiers Media. Available via doi: 10.3389/fevo.2019.00404.
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