Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding

PloS One
Birgit KerstenM Fladung

Abstract

Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in a...Continue Reading

References

Dec 5, 1995·Proceedings of the National Academy of Sciences of the United States of America·C W Birky
Mar 21, 2001·Apoptosis : an International Journal on Programmed Cell Death·H U SimonF Levi-Schaffer
Mar 1, 1967·Journal of Theoretical Biology·L Sagan
Jun 6, 2002·The Plant Journal : for Cell and Molecular Biology·Nan YaoShigeyuki Mayama
Nov 6, 2002·The Plant Cell·Stan D WullschlegerGail Taylor
Jan 22, 2004·Nature Reviews. Genetics·Jeremy N TimmisWilliam Martin
May 4, 2004·Plant Physiology·Jiabin TangLihuang Zhu
Jun 8, 2004·Bioinformatics·Stacia K WymanJeffrey L Boore
Dec 1, 2007·Proceedings of the National Academy of Sciences of the United States of America·Robert K JansenJeffrey L Boore
Feb 12, 2008·Current Opinion in Plant Biology·David B Neale, Pär K Ingvarsson
Feb 1, 1993·Genome Génome / Conseil National De Recherches Canada·J W BarrettC Strobeck
Aug 21, 2008·Journal of Integrative Plant Biology·Jie YuChang-Lu Wang
Nov 19, 2008·Annual Review of Plant Biology·Tatjana KleineDario Leister
Aug 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·UNKNOWN CBOL Plant Working Group
Nov 17, 2009·Trends in Plant Science·Ralph Bock
Feb 4, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Patrick J Keeling
May 4, 2010·Clinical Obstetrics and Gynecology·Keith A Hansen, Kathleen M Eyster
Jul 14, 2010·Nature Biotechnology·Christian WalterWout Boerjan
Jul 17, 2010·Journal of the American College of Cardiology·Alison E Baird
Mar 23, 2011·Plant Molecular Biology·Susann WickeDietmar Quandt
Mar 30, 2011·The Plant Journal : for Cell and Molecular Biology·Beverley R Green
Jul 14, 2011·PloS One·Maximo RivarolaPablo D Rabinowicz
Oct 16, 2012·Planta·Rhea Stoppel, Jörg Meurer
Jan 31, 2013·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Stephan Greiner, Ralph Bock
May 10, 2013·Mitochondrial DNA·Honghai ZhangGuangshuai Liu
Aug 27, 2013·PloS One·Jianju FengKangshan Mao
Feb 22, 2014·Molecular Biology and Evolution·Andan ZhuJeffrey P Mower
Mar 29, 2014·Biological Reviews of the Cambridge Philosophical Society·Xiwen LiShilin Chen
Apr 15, 2015·Genome Biology and Evolution·David Roy Smith

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Citations

Mar 2, 2018·International Journal of Molecular Sciences·Malte MaderBirgit Kersten
Mar 7, 2020·Molecular Ecology Resources·Luisa BresadolaDaniel Wegmann
Oct 4, 2019·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Deyou QiuGuiling Sun
Jan 19, 2021·Mitochondrial DNA. Part B, Resources·Li ZhangYuan Huang
Feb 16, 2017·Mitochondrial DNA. Part B, Resources·Mi Na ChoiEung-Jun Park
Mar 1, 2019·G3 : Genes - Genomes - Genetics·Wolfram Georg BrennerBirgit Kersten
May 11, 2021·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Bruno Cesar RossiniCelso Luis Marino

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Datasets Mentioned

BETA
EF489041
KM091932
AP008956
HQ874649
KP861984
KT337313
KT429213

Methods Mentioned

BETA
transgenic
Assay
Chip
PCR
genotyping

Software Mentioned

BlastN
MITOFY webserver
DOGMA
ORF finder
stats
SeqMan Pro
miSeq
IonTorrent
UPGMA
MITOFY

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