The Plastid Genome of Deschampsia cespitosa (Poaceae).

Jorge O Chiapella,Josef Greimler,Michael H J Barfuss,Zhi-Qing Xue

doi:10.3390/molecules24020216

Abstract

Plastid genome analysis of non-model organisms provides valuable information for basic research e.g., molecular evolutionary genomics, phylogeny and phylogeography. Deschampsia cespitosa is the most widespread species of the genus and it is a common grass that is found across Eurasia and North America. Scattered populations in regions of appropriate ecological conditions are also found in Australia, New Zealand and southern South America, where it is sympatric with D. antarctica. We analyzed the plastid genome of a sample of Deschampsia cespitosa of the Austrian Alps using high-throughput sequencing. The plastid (cp) genome shows the typical quadripartite structure with a length of 135,340 bp, comprising a large single-copy (LSC) region of 79,992 bp, a small single-copy (SSC) region of 12,572 bp and two inverted repeats (IR) regions of 21,388 bp each. It contains 115 genes, including 85 protein-coding genes, four ribosomal RNA genes and 30 transfer RNA genes. The GC content (%), number of repeats and microsatellites, RNA editing sites and codon usage were highly similar to those of D. antarctica. The results of this present study highlight the extremely conserved nature of the cp genome in this group, since the comparison involved individuals separated by about 13,000 km, from the Alps to Antarctica.

Highlights

The rapid decrease in costs of next-generation sequencing methods has resulted in an increase in the availability of completed plastid genomes [1], enabling comparisons at the genomic level even between closely related species [2,3]
The BEP clade comprises the majority of the grasses of cold-temperate regions; plastid genome size ranges from 134,5 (Triticum aestivum)
Available evidence points to D. cespitosa as its closest relative, and, we focus here on the common species D. cespitosa, a tussock-forming, wind-pollinated, self-incompatible species with wide morphological variation throughout its large, nearly cosmopolitan distribution

Summary

Introduction

The rapid decrease in costs of next-generation sequencing methods has resulted in an increase in the availability of completed plastid (cp) genomes [1], enabling comparisons at the genomic level even between closely related species [2,3]. The amount of cp genomes increased from 800 in 2016 [4] to about 2400 in 2018 [5], which allowing for close examination of features [6] and whole plastid-based phylogenetic relationships [2,7]. Plastid genomes of angiosperms range in size from 120 to 170 kb [8]. The cp genomes are highly conserved in a quadripartite organization, namely, a main large single-copy (LSC), a small single-copy (SSC) region and two inverted repeats (IRs) [9]; functional categories include (i) protein-coding genes,. In the grass family (Poaceae), the cp genome size roughly varies from 134 kb in Oryza sativa [11] to 140 kb in Sorghum bicolor [12]. The BEP clade comprises the majority of the grasses of cold-temperate regions; plastid genome size ranges from 134,5 (Triticum aestivum)

Objectives

Methods

Results

Conclusion