ArticleFrontiers in plant science2016
De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species.
Article in Frontiers in plant science, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 36 citations in OpenAlex.
- Characterization and development of transcriptome-derived novel EST-SSR markers to assess genetic diversity in3 Biotech · 2023Article
- Elucidating the Mesocarp Drupe Transcriptome of Açai (International journal of molecular sciences · 2023Article
- Transcriptome Analysis Reveals Genes Associated with Flooding Tolerance in Mulberry Plants.Life (Basel, Switzerland) · 2023Article
- Genic microsatellite marker characterization and development in little millet (Panicum sumatrense) using transcriptome sequencing.Scientific reports · 2021Article
- Genetic Divergence and Relationship AmongFrontiers in genetics · 2020Article
- An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis).PloS one · 2020Article
- Reference gene selection for real-time quantitative PCR normalization in Hemarthria compressa and Hemarthria altissima leaf tissue.Molecular biology reports · 2019Article
- The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants.Scientific reports · 2018Article
- SSR marker development and intraspecific genetic divergence exploration of Chrysanthemum indicum based on transcriptome analysis.BMC genomics · 2018Article
- Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.Molecules (Basel, Switzerland) · 2018Review
- Identification of Putative Precursor Genes for the Biosynthesis of Cannabinoid-Like Compound inFrontiers in plant science · 2018Article
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- De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development.Scientific reports · 2017Article
- Development of Novel Polymorphic EST-SSR Markers in Bailinggu (Pleurotus tuoliensis) for Crossbreeding.Genes · 2017Article
- Enriching Genomic Resources and Transcriptional Profile Analysis ofInternational journal of genomics · 2017Article
- Transcriptomic Identification of Drought-Related Genes and SSR Markers in Sudan Grass Based on RNA-Seq.Frontiers in plant science · 2017Article
- RNA-Seq Analysis Provides the First Insights into the Phylogenetic Relationship and Interspecific Variation betweenFrontiers in plant science · 2017Article
- Article
- Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial GrassFrontiers in plant science · 2017Article
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Authors and funding
12 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa "Yaan" and H. altissima "1110." Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for "Yaan" and "1110," respectively. In addition, a total of 86,731 "Yaan" and 48,645 "1110" unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11-87.04%) of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.
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