Dataset Information

Development of 16 single-copy nuclear gene markers for Oreocharis auricula, a perennial herb in China.

ABSTRACT: Premise:We developed single-copy nuclear DNA markers for a perennial herb, Oreocharis auricula (Gesneriaceae), to help infer the evolutionary history of the genus Oreocharis in subtropical China. Methods and Results:We screened 834 putative single-copy nuclear genes from transcriptomes of 11 species of Primulina using the Illumina HiSeq 2000 platform. Based on the screening results, we developed 16 primer sets for accessions of O. auricula representing three wild populations. The number of alleles per locus ranged from three to 34. The levels of expected and observed heterozygosity varied from 0.000 to 0.372 and 0.000 to 0.650, respectively. The markers were successfully cross-amplified in the related species O. magnidens, O. speciosa, O. maximowiczii, and O. henryana. Conclusions:The newly developed markers will facilitate further studies on genetic diversity and phylogeographic structure throughout the distributional range of O. auricula. Additionally, these markers may be useful for other related species in Gesneriaceae.

SUBMITTER: Sun Z

PROVIDER: S-EPMC6858290 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Development of 16 single-copy nuclear gene markers for <i>Oreocharis auricula</i>, a perennial herb in China.

Sun Zhixia Z Feng Chao C Yang Lihua L Kong Hanghui H

Applications in plant sciences 20191114 11

<h4>Premise</h4>We developed single-copy nuclear DNA markers for a perennial herb, <i>Oreocharis auricula</i> (Gesneriaceae), to help infer the evolutionary history of the genus <i>Oreocharis</i> in subtropical China.<h4>Methods and results</h4>We screened 834 putative single-copy nuclear genes from transcriptomes of 11 species of <i>Primulina</i> using the Illumina HiSeq 2000 platform. Based on the screening results, we developed 16 primer sets for accessions of <i>O. auricula</i> representing ...[more]

PMID: 31832286

Similar Datasets

Project description:BackgroundMolecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales.Principal findingsWe present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs-curated broadly across ferns-that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group.ConclusionsThe 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation.

Project description:Understanding adaptive genetic variation of plant populations and their vulnerabilities to climate change are critical to preserve biodiversity and subsequent management interventions. To this end, landscape genomics may represent a cost-efficient approach for investigating molecular signatures underlying local adaptation. Tetrastigma hemsleyanum is, in its native habitat, a widespread perennial herb of warm-temperate evergreen forest in subtropical China. Its ecological and medicinal values constitute a significant revenue for local human populations and ecosystem. Using 30,252 single nucleotide polymorphisms (SNPs) derived from reduced-representation genome sequencing in 156 samples from 24 sites, we conducted a landscape genomics study of the T. hemsleyanum to elucidate its genomic variation across multiple climate gradients and genomic vulnerability to future climate change. Multivariate methods identified that climatic variation explained more genomic variation than that of geographical distance, which implied that local adaptation to heterogeneous environment might represent an important source of genomic variation. Among these climate variables, winter precipitation was the strongest predictor of the contemporary genetic structure. F ST outlier tests and environment association analysis totally identified 275 candidate adaptive SNPs along the genetic and environmental gradients. SNP annotations of these putatively adaptive loci uncovered gene functions associated with modulating flowering time and regulating plant response to abiotic stresses, which have implications for breeding and other special agricultural aims on the basis of these selection signatures. Critically, modelling revealed that the high genomic vulnerability of our focal species via a mismatch between current and future genotype-environment relationships located in central-northern region of the T. hemsleyanum's range, where populations require proactive management efforts such as assistant adaptation to cope with ongoing climate change. Taken together, our results provide robust evidence of local climate adaption for T. hemsleyanum and further deepen our understanding of adaptation basis of herbs in subtropical China.

Dataset Information

Development of 16 single-copy nuclear gene markers for Oreocharis auricula, a perennial herb in China.

Publications

Development of 16 single-copy nuclear gene markers for <i>Oreocharis auricula</i>, a perennial herb in China.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets