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Plant J. 2018 Feb;93(3):515-533. doi: 10.1111/tpj.13801.

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.

Author information

1
Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany.
2
Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany.
3
Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany.
4
INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France.
5
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, D-06466, Stadt Seeland, Germany.
6
HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
7
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829, Cologne, Germany.
8
VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium.
9
Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium.
10
Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain.
11
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
12
Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
13
Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS, UMR 7256 (IMM FR 3479), Marseille, France.
14
DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.
15
Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
16
Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
17
Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
18
Boyce Thompson Institute, Ithaca, NY, 14853, USA.
19
Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
20
University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA.
21
New York Botanical Garden, Bronx, NY, 10458, USA.
22
Vertis Biotechnologie AG, Lise-Meitner-Str. 30, 85354, Freising, Germany.
23
Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany.
24
Department of Biology, Université Laval, Québec, G1V 0A6, Canada.
25
Department of Plant Biology, University of Geneva, Sciences III, Geneva 4, CH-1211, Switzerland.
26
Department of Plant Biology & Pathology Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
27
Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
28
Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
29
BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
30
Shenzhen Huahan Gene Life Technology Co. Ltd, Shenzhen, China.
31
Department of Biology, Washington University, St. Louis, MO, USA.
32
WZW, Technical University Munich, Munich, Germany.
33
BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany.
34
URGI, INRA, Université Paris-Saclay, 78026, Versailles, France.

Abstract

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.

KEYWORDS:

Physcomitrella patens ; chromosome; duplication; evolution; genome; methylation; moss; plant; synteny

PMID:
29237241
DOI:
10.1111/tpj.13801
[Indexed for MEDLINE]

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