Abstract
BackgroundKiwi represent the most basal extant avian lineage (paleognaths) and exhibit biological attributes that are unusual or extreme among living birds, such as large egg size, strong olfaction, nocturnality, flightlessness and long lifespan. Despite intense interest in their evolution and their threatened status, genomic resources for kiwi were virtually non-existent until the recent publication of a single genome. Here we present the most comprehensive kiwi transcriptomes to date, obtained via Illumina sequencing of whole blood and de novo assembly of mRNA sequences of eight individuals from each of the two rarest kiwi species, little spotted kiwi (LSK; Apteryx owenii) and rowi (A. rowi).ResultsSequences obtained were orthologous with a wide diversity of functional genes despite the sequencing of a single tissue type. Individual and composite assemblies contain more than 7900 unique protein coding transcripts in each of LSK and rowi that show strong homology with chicken (Gallus gallus), including those associated with growth, development, disease resistance, reproduction and behavior. The assemblies also contain 66,909 SNPs that distinguish between LSK and rowi, 12,384 SNPs among LSK (associated with 3088 genes), and 29,313 SNPs among rowi (associated with 4953 genes). We found 3084 transcripts differentially expressed between LSK and rowi and 150 transcripts differentially expressed between the sexes. Of the latter, 83 could be mapped to chicken chromosomes with 95% syntenic with chromosome Z.ConclusionsOur study has simultaneously sequenced multiple species, sexes, and individual kiwi at thousands of genes, and thus represents a significant leap forward in genomic resources available for kiwi. The expression pattern we observed among chromosome Z related genes in kiwi is similar to that observed in ostriches and emu, suggesting a common and ancestral pattern of sex chromosome homomorphy, recombination, and gene dosage among living paleognaths. The transcriptome assemblies described here will provide a rich resource for polymorphic marker development and studies of adaptation of these highly unusual and endangered birds.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2714-2) contains supplementary material, which is available to authorized users.
Highlights
Kiwi represent the most basal extant avian lineage and exhibit biological attributes that are unusual or extreme among living birds, such as large egg size, strong olfaction, nocturnality, flightlessness and long lifespan
While a more comprehensive transcriptome could have been obtained from sequencing messenger RNA (mRNA) from various tissues, our non-lethal sampling means that we can continue to monitor our study birds to explore additional genotype-phenotype relationships in the future
20,152 little spotted kiwi (LSK) and 23,830 rowi transcripts had a predicted full or partial Open Reading Frame (ORF) greater than 100 amino acids, which we focused our analyses on subsequently
Summary
Kiwi represent the most basal extant avian lineage (paleognaths) and exhibit biological attributes that are unusual or extreme among living birds, such as large egg size, strong olfaction, nocturnality, flightlessness and long lifespan. Many at-risk populations will have experienced genetic bottleneck effects, small population size, and inbreeding, which can result in low levels of genetic diversity and strong gametic disequilibrium and make discovery of large numbers of independent polymorphic markers challenging. These difficulties initially slowed the development and use of genomic tools for endangered species, and the full application and power of conservation genomics to improve species management is only becoming evident [4,5,6,7,8,9]. Conservation management, occurs at the population level, with a focus on understanding and maintaining genetic diversity within and between species
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