Distinct, Ecotype-Specic Genome and Proteome Signatures in the Marine Cyanobacteria Prochlorococcus

Abstract

TitleChloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. R E S E A R C H A R T I C L E Open AccessChloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes AbstractBackground: Tortula ruralis, a widely distributed species in the moss family Pottiaceae, is increasingly used as a model organism for the study of desiccation tolerance and mechanisms of cellular repair. In this paper, we present the chloroplast genome sequence of T. ruralis, only the second published chloroplast genome for a moss, and the first for a vegetatively desiccation-tolerant plant.Results: The Tortula chloroplast genome is~123,500 bp, and differs in a number of ways from that of Physcomitrella patens, the first published moss chloroplast genome. For example, Tortula lacks the~71 kb inversion found in the large single copy region of the Physcomitrella genome and other members of the Funariales. Also, the Tortula chloroplast genome lacks petN, a gene found in all known land plant plastid genomes. In addition, an unusual case of nucleotide polymorphism was discovered. Conclusions: Although the chloroplast genome of Tortula ruralis differs from that of the only other sequenced moss, Physcomitrella patens, we have yet to determine the biological significance of the differences. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for mosses) of the generation of DNA markers for fine-level phylogenetic studies, or to investigate individual variation within populations.

Chloroplast genome variation and phylogenetic relationships of Atractylodes species

“…In this study, we did not annotate the ycf15 and ycf68 genes because we identified them as pseudogenes containing several internal stop codons [18]. In certain cases, ycf2, rpl23 and accD are absent from the chloroplast genomes [19][20][21]; however, but these genes are indeed present in Atractylodes. The chloroplast genome is conserved similar to the majority of plants; no rearrangement events were detected in all species.…”

The complete chloroplast genome of Fissidens nobilis Griff. (Fissidentaceae, Bryophyta)

“…It is longer than that of one of the neighbor species, Syntrichia ruralis by 2,332 bp (Oliver et al. 2010 ). It contains 127 genes (82 protein-coding genes, 8 rRNAs, and 37 tRNAs), in which nine genes (four rRNAs and five tRNAs) are duplicated in IR regions.…”

Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species

“…Therefore and In addition to phylogenetic analysis based on plastidic genomes, it is imperative to understand the chloroplast genome in order to logically design our next generation transplastomics. Accordingly, chloroplast genomes of many species have been sequenced (7)(8)(9)(10)(11)(12)(13)(14).…”