Dataset Information

Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa.

ABSTRACT: BACKGROUND: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. 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. METHODS:We 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. RESULTS:Illumina 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. CONCLUSIONS:We 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.

SUBMITTER: Christmas MJ

PROVIDER: S-EPMC4609105 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

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Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa.

Christmas Matthew J MJ Biffin Ed E Lowe Andrew J AJ

BMC genomics 20151016

<h4>Background</h4>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. 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.<h4>Methods ...[more]

PMID: 26474753

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Project description:Intraspecific plant functional trait variation provides mechanistic insight into persistence and can infer population adaptive capacity. However, most studies explore intraspecific trait variation in systems where geographic and environmental distances co-vary. Such a design reduces the certainty of trait-environment associations, and it is imperative for studies that make trait-environment associations be conducted in systems where environmental distance varies independently of geographic distance. Here we explored trait variation in such a system, and aimed to: (i) quantify trait variation of parent and offspring generations, and associate this variation to parental environments; (ii) determine the traits which best explain population differences; (iii) compare parent and offspring trait-trait relationships. We characterized 15 plant functional traits in eight populations of a shrub with a maximum separation ca. 100 km. Populations differed markedly in aridity and elevation, and environmental distance varied independently of geographic distance. We measured traits in parent populations collected in the field, as well as their offspring reared in greenhouse conditions. Parent traits regularly associated with their environment. These associations were largely lost in the offspring generation, indicating considerable phenotypic plasticity. An ordination of parent traits showed clear structure with strong influence of leaf area, specific leaf area, stomatal traits, isotope δ13C and δ15N ratios, and Narea, whereas the offspring ordination was less structured. Parent trait-trait correlations were in line with expectations from the leaf economic spectrum. We show considerable trait plasticity in the woody shrub over microgeographic scales (<100 km), indicating it has the adaptive potential within a generation to functionally acclimate to a range of abiotic conditions. Since our study shrub is commonly used for restoration in southern Australia and local populations do not show strong genetic differentiation in functional traits, the potential risks of transferring seed across the broad environmental conditions are not likely to be a significant issue.

Project description:Dodonaea viscosa Jacq (Sapindaceae) is a medicinal plant with a worldwide distribution. The species has undergone enormous taxonomic changes which caused confusion amongst plant users. In Kenya, for example, two varieties are known to exist based on morphology, i.e., D. viscosa var. viscosa along the coast, and D. viscosa var. angustifolia in the Kenyan inland. These two taxa are recognized as distinct species in some reports. This prompted us to apply metabolomics to understand the relationship among naturally occurring populations of D. viscosa in Kenya, and to identify compounds that can assist in taxonomic delineation of the different varieties of D. viscosa from different parts of Kenya. The phytochemical variability of Kenyan D. viscosa var. angustifolia populations collected from four different geographical regions (Nanyuki, Machakos, Nairobi, and Narok) and one coastal D. viscosa var. viscosa (the Gazi) were analyzed by LC-MS using a metabolomics-driven approach. Four known compounds, two diterpenoids (dodonic acid (1), hautriwaic acid lactone (3), and two flavonoids (5,7,4',5'-tetrahydroxy-3,6,2'-trimethoxyflavone (2) and catechin (4)) were isolated and purified from the Gazi coastal collection. The presence of these compounds and their relative abundance in other populations was determined by LC-MS analyses. Multivariate statistical analyses of LC-MS data was used for the visualization of the patterns of variation and identification of additional compounds. Eleven discriminant compounds responsible for separating chemometric clusters were tentatively identified. In an antimicrobial assay, hautriwaic acid lactone (3) and catechin (4) were the most active compounds followed by the extract from the coastal (Gazi) population. The clustering pattern of the five populations of D. viscosa suggested that the metabolite profiles were influenced by geo-environmental conditions and did not support the current classification of D. viscosa based on morphology. This study disputes the current classification of D. viscosa in Kenya and recommends revision using tools such as molecular phylogenetics.

Dataset Information

Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa.

Publications

Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa.

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