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.
Highlights
Chloroplasts are plant-specific organelles that conduct photosynthesis, providing essential energy for the synthesis of starch, fatty acids, pigments, and amino acids [1,2]
Chloroplast genomes exist as circular DNA, with the size ranging from 120 kb to 150 kb, and generally have a highly conserved quadripartite organization composed of two copies of inverted repeats (IRs), which separate the large single copy (LSC) and small single copy (SSC) regions [3,4]
Chloroplast genomes usually contain 110–130 unique genes encoding 4 rRNAs, 30–31 tRNAs, and 80–90 proteins; these encode ribosomal proteins and RNA polymerase subunits involved in protein synthesis, thylakoid proteins, and the Rubisco large subunit for photosynthesis, as well as protein subunits for an NADH dehydrogenase complex, which mediates redox reactions [2,5]
Summary
Chloroplasts are plant-specific organelles that conduct photosynthesis, providing essential energy for the synthesis of starch, fatty acids, pigments, and amino acids [1,2]. Chloroplast genomes usually contain 110–130 unique genes encoding 4 rRNAs, 30–31 tRNAs, and 80–90 proteins; these encode ribosomal proteins and RNA polymerase subunits involved in protein synthesis, thylakoid proteins, and the Rubisco large subunit for photosynthesis, as well as protein subunits for an NADH dehydrogenase complex, which mediates redox reactions [2,5]. Plastid genome resources with .420 records have been established These provide a vast amount of high-resolution information that can be exploited in phylogenetic and ecological studies, making it possible to track the evolutionary history of a species after obtaining the full sequence of its chloroplast genome. Antarctic 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. We report the complete chloroplast genome, transcriptome profiles of the coding/noncoding genes, and the posttranscriptional processing by RNA editing in the chloroplast system
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