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Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome.

Kelley JL, Passow CN, Plath M, Arias Rodriguez L, Yee MC, Tobler M - BMC Genomics (2012)

Bottom Line: We describe general and oxidative stress response genes as well as genes involved in pathways induced by hypoxia or involved in sulfide metabolism.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics, Stanford University, Stanford, CA 94305, USA. joanna.l.kelley@gmail.com

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.

Description: 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.

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Blast2GO assignment for 17,286 P. mexicana and 9,721 P. reticulata sequences. Significant differences in the frequency of different categories are highlighted with an asterisk. The numbers next to each colored slice of the pie chart represent the number of genes in the respective category.
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Figure 2: Blast2GO assignment for 17,286 P. mexicana and 9,721 P. reticulata sequences. Significant differences in the frequency of different categories are highlighted with an asterisk. The numbers next to each colored slice of the pie chart represent the number of genes in the respective category.

Mentions: The 29,792 sequences with a match in the SwissProt or NR databases were further annotated with Gene Ontology (GO) terms based on the Uniprot database, which yielded results for 22,184 (74.5%) of sequences. Of these, 13,002 sequences were annotated with a biological process GO term, 13,623 with a molecular function, and 14,430 with a cellular component. The relative frequency of level 2 GO terms is visualized in Figure 2. We also compared the representation of records in each generic slim between P. mexicana and P. reticulata. While representation was qualitatively very similar between the two species, 20 out of 30 level 5 GO categories exhibited significant differences across species even when accounting for the effects for multiple testing (Chi2 ≥ 13.545, P ≤ 0.0002, α’ = 0.001).


Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome.

Kelley JL, Passow CN, Plath M, Arias Rodriguez L, Yee MC, Tobler M - BMC Genomics (2012)

Blast2GO assignment for 17,286 P. mexicana and 9,721 P. reticulata sequences. Significant differences in the frequency of different categories are highlighted with an asterisk. The numbers next to each colored slice of the pie chart represent the number of genes in the respective category.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3585874&req=5

Figure 2: Blast2GO assignment for 17,286 P. mexicana and 9,721 P. reticulata sequences. Significant differences in the frequency of different categories are highlighted with an asterisk. The numbers next to each colored slice of the pie chart represent the number of genes in the respective category.
Mentions: The 29,792 sequences with a match in the SwissProt or NR databases were further annotated with Gene Ontology (GO) terms based on the Uniprot database, which yielded results for 22,184 (74.5%) of sequences. Of these, 13,002 sequences were annotated with a biological process GO term, 13,623 with a molecular function, and 14,430 with a cellular component. The relative frequency of level 2 GO terms is visualized in Figure 2. We also compared the representation of records in each generic slim between P. mexicana and P. reticulata. While representation was qualitatively very similar between the two species, 20 out of 30 level 5 GO categories exhibited significant differences across species even when accounting for the effects for multiple testing (Chi2 ≥ 13.545, P ≤ 0.0002, α’ = 0.001).

Bottom Line: We describe general and oxidative stress response genes as well as genes involved in pathways induced by hypoxia or involved in sulfide metabolism.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics, Stanford University, Stanford, CA 94305, USA. joanna.l.kelley@gmail.com

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.

Description: 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.

Show MeSH
Related in: MedlinePlus