title: Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome.
abstract: BACKGROUND
  Elucidating the genomic basis of adaptation and speciation is a major challenge in natural systems with large quantities of environmental and phenotypic data, mostly because of the scarcity of genomic resources for non-model organisms. The Atlantic molly (Poecilia mexicana, Poeciliidae) is a small livebearing fish that has been extensively studied for evolutionary ecology research, particularly because this species has repeatedly colonized extreme environments in the form of caves and toxic hydrogen sulfide containing springs. In such extreme environments, populations show strong patterns of adaptive trait divergence and the emergence of reproductive isolation. Here, we used RNA-sequencing to assemble and annotate the first transcriptome of P. mexicana to facilitate ecological genomics studies in the future and aid the identification of genes underlying adaptation and speciation in the system.
  
  
  METHODS
  We provide the first annotated reference transcriptome of P. mexicana. Our transcriptome shows high congruence with other published fish transcriptomes, including that of the guppy, medaka, zebrafish, and stickleback. Transcriptome annotation uncovered the presence of candidate genes relevant in the study of adaptation to extreme environments. We describe general and oxidative stress response genes as well as genes involved in pathways induced by hypoxia or involved in sulfide metabolism. To facilitate future comparative analyses, we also conducted quantitative comparisons between P. mexicana from different river drainages. 106,524 single nucleotide polymorphisms were detected in our dataset, including potential markers that are putatively fixed across drainages. Furthermore, specimens from different drainages exhibited some consistent differences in gene regulation.
  
  
  CONCLUSIONS
  Our study provides a valuable genomic resource to study the molecular underpinnings of adaptation to extreme environments in replicated sulfide spring and cave environments. In addition, this study adds to the increasing number of genomic resources in the family Poeciliidae, which are widely used in comparative analyses of behavior, ecology, evolution, and medical genetics.
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA 94305, USA. joanna.l.kelley@gmail.com
authors.forename: Joanna L
authors.initials: JL
authors.lastname: Kelley
authors.forename: Courtney N
authors.initials: CN
authors.lastname: Passow
authors.forename: Martin
authors.initials: M
authors.lastname: Plath
authors.forename: Lenin
authors.initials: L
authors.lastname: Arias Rodriguez
authors.forename: Muh-Ching
authors.initials: MC
authors.lastname: Yee
authors.forename: Michael
authors.initials: M
authors.lastname: Tobler
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D015687:Cell Hypoxia / Q000235:genetics; D005786:Gene Expression Regulation; D049810:Genetic Speciation; D016678:Genome; D023281:Genomics; D008969:Molecular Sequence Data; D018384:Oxidative Stress / Q000235:genetics; D011036:Poecilia / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017423:Sequence Analysis, RNA; D013440:Sulfides / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
chemical_list: D013440:Sulfides