ArticlePloS one2014
Combined analysis of the chloroplast genome and transcriptome of the Antarctic vascular plant Deschampsia antarctica Desv.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- A first comparison of miRNA profiles of Antarctic Deschampsia antarctica ecotypes with Triticum aestivum upon single or combined salt and drought stresses.Functional & integrative genomics · 2026Article
- Comprehensive analysis of chloroplast genome evolution in Poaceae: codon usage patterns, selection pressures, and phylogenomic relationships.BMC genomics · 2026Article
- Comparative chloroplast genomes of Dactylicapnos species: insights into phylogenetic relationships.BMC plant biology · 2024Article
- Comparative and phylogenetic analyses based on the complete chloroplast genome ofFrontiers in plant science · 2024Article
- Characterization and Comparative Analysis of Chloroplast Genomes in FiveInternational journal of molecular sciences · 2022Article
- A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms.International journal of molecular sciences · 2022Article
- Newly reported chloroplast genome of Sinosenecio albonervius Y. Liu & Q. E. Yang and comparative analyses with other Sinosenecio species.BMC genomics · 2022Article
- Article
- Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change onPlants (Basel, Switzerland) · 2022Article
- Comparative and Phylogenetic Analysis Based on the Chloroplast Genome ofFrontiers in plant science · 2022Article
- Noncoding RNA: An Insight into Chloroplast and Mitochondrial Gene Expressions.Life (Basel, Switzerland) · 2021Review
- Complete Chloroplast Genomes ofFrontiers in plant science · 2021Article
- Evolutionary Origins of Drought Tolerance in Spermatophytes.Frontiers in plant science · 2021Article
- A New Chloroplast DNA Extraction Protocol Significantly Improves the Chloroplast Genome Sequence Quality of Foxtail Millet (Setaria italica (L.) P. Beauv.).Scientific reports · 2019Article
- The implication of plastid transcriptome analysis in petaloid monocotyledons: A case study of Lilium lancifolium (Liliaceae, Liliales).Scientific reports · 2019Article
- The Plastid Genome of Deschampsia cespitosa (Poaceae).Molecules (Basel, Switzerland) · 2019Article
- Article
- Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case.BMC genomics · 2018Article
- Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0.BMC bioinformatics · 2018Article
- The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske.International journal of molecular sciences · 2018Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAntarctic hairgrass (Deschampsia antarctica Desv.) is the only natural grass species in the maritime Antarctic. It has been researched as an important ecological marker and as an extremophile plant for studies on stress tolerance. Despite its importance, little genomic information is available for D. antarctica. Here, we report the complete chloroplast genome, transcriptome profiles of the coding/noncoding genes, and the posttranscriptional processing by RNA editing in the chloroplast system.
resultsThe complete chloroplast genome of D. antarctica is 135,362 bp in length with a typical quadripartite structure, including the large (LSC: 79,881 bp) and small (SSC: 12,519 bp) single-copy regions, separated by a pair of identical inverted repeats (IR: 21,481 bp). It contains 114 unique genes, including 81 unique protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Sequence divergence analysis with other plastomes from the BEP clade of the grass family suggests a sister relationship between D. antarctica, Festuca arundinacea and Lolium perenne of the Poeae tribe, based on the whole plastome. In addition, we conducted high-resolution mapping of the chloroplast-derived transcripts. Thus, we created an expression profile for 81 protein-coding genes and identified ndhC, psbJ, rps19, psaJ, and psbA as the most highly expressed chloroplast genes. Small RNA-seq analysis identified 27 small noncoding RNAs of chloroplast origin that were preferentially located near the 5'- or 3'-ends of genes. We also found >30 RNA-editing sites in the D. antarctica chloroplast genome, with a dominance of C-to-U conversions.
conclusionsWe assembled and characterized the complete chloroplast genome sequence of D. antarctica and investigated the features of the plastid transcriptome. These data may contribute to a better understanding of the evolution of D. antarctica within the Poaceae family for use in molecular phylogenetic studies and may also help researchers understand the characteristics of the chloroplast transcriptome.
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