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Title: Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes

Journal Article · · BMC Genomics
 [1];  [2];  [2];  [3];  [4];  [5];  [5];  [6];  [6];  [7]
  1. US Dept. of Agriculture (USDA), Columbia, MO (United States). Agricultural Research Service (ARS). Mid-West Area; Univ. of Missouri, Columbia, MO (United States). Plant Genetics Research Unit; DOE/OSTI
  2. Univ. of California, Berkeley, CA (United States). Dept of Integrative Biology
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences
  4. Genome Project Solutions, Inc, Hercules, CA (United States)
  5. Univ. of Washington, Seattle, WA (United States). Dept. of Biology
  6. Utah State Univ., Logan, UT (United States). Dept. of Biology
  7. The New York Botanical Garden, Bronx, NY (United States). The Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies
+ Show Author Affiliations

Background: 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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1626405
Journal Information:
BMC Genomics, Journal Name: BMC Genomics Journal Issue: 1 Vol. 11; ISSN 1471-2164
Publisher:
SpringerCopyright Statement
Country of Publication:
United States
Language:
English

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Additional file 1 of Chloroplast genomes of Caragana tibetica and Caragana turkestanica: structures and comparative analysis dataset January 2024
The evolution of the plastid chromosome in land plants: gene content, gene order, gene function journal March 2011
PBR1 selectively controls biogenesis of photosynthetic complexes by modulating translation of the large chloroplast gene Ycf1 in Arabidopsis journal May 2016
Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis journal August 2017
The extraordinary variation of the organellar genomes of the Aneura pinguis revealed advanced cryptic speciation of the early land plants journal August 2017
ycf1, the most promising plastid DNA barcode of land plants journal February 2015
The complete chloroplast genome of Fissidens nobilis Griff. (Fissidentaceae, Bryophyta) journal July 2019
Phylogeny of haplolepideous mosses — challenges and perspectives journal September 2012
Gene loss and genome rearrangement in the plastids of five Hemiparasites in the family Orobanchaceae journal February 2018
Reference-Free Comparative Genomics of 174 Chloroplasts journal November 2012
Comparative analysis of complete plastid genomes from wild soybean (Glycine soja) and nine other Glycine species journal August 2017
First chloroplast genomics study of Phoenix dactylifera (var. Naghal and Khanezi): A comparative analysis journal July 2018
The chloroplast genome of the desiccation-tolerant moss Pseudocrossidium replicatum (Taylor) R.H. Zander journal June 2019
Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum journal August 2018
The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske journal March 2018
A comparison of 16 DNA regions for use as phylogenetic markers in the pleurocarpous moss genus Plagiothecium (Hypnales) journal April 2014

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