Abstract
BackgroundThe Hawaiian honeycreepers are an avian adaptive radiation containing many endangered and extinct species. They display a dramatic range of phenotypic variation and are a model system for studies of evolution, conservation, disease dynamics and population genetics. Development of a genome-scale resources for this group would augment the quality of research focusing on Hawaiian honeycreepers and facilitate comparative avian genomic research.ResultsWe assembled the genome sequence of a Hawaii amakihi (Hemignathus virens),and identified ~3.9 million single nucleotide polymorphisms (SNPs) in the genome. Using the amakihi genome as a reference, we also identified ~156,000 SNPs in RAD tag (restriction site associated DNA) sequencing of five honeycreeper species (palila [Loxioides bailleui], Nihoa finch [Telespiza ultima], iiwi [Vestiaria coccinea], apapane [Himatione sanguinea], and amakihi). SNPs are distributed throughout the amakihi genome, and the individual sequenced shows several large regions of low heterozygosity on chromosomes 1, 5, 6, 8 and 11. SNPs from RAD tag sequencing were also found throughout the genome but were found to be more densely located on microchromosomes, apparently a result of differential distribution of the particular site recognized by restriction enzyme BseXI.ConclusionsThe amakihi genome sequence will be useful for comparative avian genomics research and provides a significant resource for studies in such areas as disease ecology, evolution, and conservation genetics. The genome sequences will enable mapping of transcriptome data for honeycreepers and comparison of gene sequences between avian taxa. Researchers will be able to use the large number of SNP markers to genotype honeycreepers in regions of interest or across the whole genome. There are enough markers to enable use of methods such as genome-wide association studies (GWAS) that will allow researchers to make connections between phenotypic diversity of honeycreepers and specific genetic variants. Genome-wide markers will also help resolve phylogenetic and population genetic questions in honeycreepers.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1098) contains supplementary material, which is available to authorized users.
Highlights
The Hawaiian honeycreepers are an avian adaptive radiation containing many endangered and extinct species
Our results provide a set of genomic resources for Hawaiian honeycreepers that will facilitate research on disease interactions, metapopulation dynamics, adaptive radiations, and genome evolution
The results yield a large number of genome wide markers, both from heterozygous sites in the sequenced individual and discovered using RAD tags with other honeycreeper species
Summary
The Hawaiian honeycreepers are an avian adaptive radiation containing many endangered and extinct species They display a dramatic range of phenotypic variation and are a model system for studies of evolution, conservation, disease dynamics and population genetics. Genome-scale resources for non-traditional model organisms have become a reality over a short period of time, due in a large part to the commercialization of sequencing-by-synthesis ( called next-generation sequencing) technology [7]. Initial examinations of these genomes have revealed that there is a high degree of synteny among avian species, confirming hypotheses from cytogenetic studies [8]. Recent work shows that small inversions may be common when comparing distantly-related avian taxa [10]
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