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Neotropical cichlids (Cichlinae: Heroini)

ABSTRACT: Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: when data agree to disagree

PROVIDER: PRJNA690533 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR13644500_1.fastq.gz	Fastqsanger.gz
	SRR13644500_2.fastq.gz	Fastqsanger.gz
	SRR13644501_1.fastq.gz	Fastqsanger.gz
	SRR13644501_2.fastq.gz	Fastqsanger.gz
	SRR13644502_1.fastq.gz	Fastqsanger.gz

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Project description:Diversity and evolution of Middle American cichlids

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Molecular characterization of MHC class IIB genes of sympatric Neotropical cichlids.

Project description:BACKGROUND:The Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. Due to this complexity, however, MHC remains to be characterized in many species including any Neotropical cichlid fish. Neotropical crater lake cichlids are ideal models to study evolutionary processes as they display one of the most convincing examples of sympatric and repeated parallel radiation events within and among isolated crater lakes. RESULTS:Here, we characterized the genes of MHC class IIB chain of the Midas cichlid species complex (Amphilophus cf. citrinellus) including fish from five lakes in Nicaragua. We designed 19 new specific primers anchored in a stepwise fashion in order to detect all alleles present. We obtained 866 genomic DNA (gDNA) sequences from thirteen individuals and 756 additional sequences from complementary DNA (cDNA) of seven of those individuals. We identified 69 distinct alleles with up to 25 alleles per individual. We also found considerable intron length variation and mismatches of alleles detected in cDNA and gDNA suggesting that some loci have undergone pseudogenization. Lastly, we created a model of protein structure homology for each allele and identified their key structural components. CONCLUSIONS:Overall, the Midas cichlid has one of the most diverse repertoires of MHC class IIB genes known, which could serve as a powerful tool to elucidate the process of divergent radiations, colonization and speciation in sympatry.

| S-EPMC5310070 | biostudies-literature

Syngnathiform Fishes

Project description:Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements

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Pike cichlids Crenicichla

Project description:Phylogenomics of the pike cichlids (Cichlidae: Crenicichla): the rapid evolution and trophic diversification of an incipient species flock

| PRJNA396208 | ENA

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