Abstract
BackgroundThe hop bush, Dodonaea viscosa, is a trans-oceanic species distributed oversix continents. It evolved in Australia where it is found over a wide range of habitat types and is an ecologically important species. Limited genomic resources are currently available for this species, thus our understanding of its evolutionary history and ecological adaptation is restricted. Here, we present a comprehensive transcriptome dataset for future genomic studies into this species.MethodsWe performed Illumina sequencing of cDNA prepared from leaf tissue collected from seven populations of D. viscosa ssp. angustissima and spatulata distributed along an environmental gradient in South Australia. Sequenced reads were assembled to provide a transcriptome resource. Contiguous sequences (contigs) were annotated using BLAST searches against the NCBI non-redundant database and gene ontology definitions were assigned. Single nucleotide polymorphisms were detected for the establishment of a genetic marker set. A comparison between the two subspecies was also carried out.ResultsIllumina sequencing returned 268,672,818 sequence reads, which were de novoassembled into 105,125 contigs. Contigs with significant BLAST alignments (E value < 1e-5)numbered at 44,191, with 38,311 of these having their most significant hits to sequences from land plant species. Gene Ontology terms were assigned to 28,440 contigs and KEGG analysis identified 146 pathways that the gene products from 5,070 contigs are potentially involved in. The subspecies comparison identified 8,494 fixed SNP differences across 3,979 contiguous sequences, indicating a level of genetic differentiation between them. Across all samples, 248,235 SNPs were detected.ConclusionsWe have established a significant genomic data resource for D. viscosa,providing a comprehensive transcriptomic reference. Genetic differences among morphologically distinct subspecies were found. A wide range of putative gene regions were identified along with a large set of variable SNP markers, providing a basis for studies into the evolution and ecological adaptation of D. viscosa.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1987-1) contains supplementary material, which is available to authorized users.
Highlights
The hop bush, Dodonaea viscosa, is a trans-oceanic species distributed oversix continents
The species evolved on mainland Australia [1] and its wind-dispersed seeds are thought to be capable of traversing long distances over oceans due to their high physical dormancy [2]
Of the 227,376,588 cleaned reads, only 72.3 % were incorporated into contigs in the de novo assembly
Summary
The hop bush, Dodonaea viscosa, is a trans-oceanic species distributed oversix continents. It evolved in Australia where it is found over a wide range of habitat types and is an ecologically important species. (hop bush) is a dioecious woody shrub with a worldwide distribution across six continents, spanning from 33°N (in California) to 44°S (in New Zealand’s South Island). The species evolved on mainland Australia [1] and its wind-dispersed seeds are thought to be capable of traversing long distances over oceans due to their high physical dormancy [2]. Hop bush is very widely distributed across a broad range of ecosystems and exhibits high levels of phenotypic variation. Viscosa, burmanniana, and angustifolia, have extra-Australian distributions, whereas ssp. angustissima, cuneata, mucronata, and spatulata are all found only within Australia
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