Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

BMC Plant Biology
Feng SongXue-Jun Ge

Abstract

Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminate Calligonum species. In this study, the complete plastid genomes (plastome) for 32 accessions of 21 Calligonum species is sequenced to not only generate the first complete plastome sequence for the genus Calligonum but to also 1) Assess the ability of the complete plastome sequence to discern species within the group, and 2) screen the plastome sequence for a cost-effective DNA barcode that can be used in future studies to resolve taxonomic relationships within the group. The whole plastomes of Calligonum species possess a typical quadripartite structure. The size of the Calligonum plastome is approximately 161 kilobase pairs (kbp), and encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Based on ML phylogenetic tree analyses, the complete plastome has higher species identification (78%) than combinations of standard DNA barcodes (rbcL + matK + nrITS, 56%). Five newly screened gene regions (ndhF, trnS-G, trnC-petN, ndhF-rpl32, rpl32-trnL) had high species resolution...Continue Reading

References

Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Jun 8, 2004·Bioinformatics·Stacia K WymanJeffrey L Boore
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Aug 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·UNKNOWN CBOL Plant Working Group
Sep 29, 2009·Trends in Plant Science·Jin ChenHuabin Hu
Nov 22, 2011·Proceedings of the National Academy of Sciences of the United States of America·UNKNOWN China Plant BOL GroupGuang-Wen Duan
Nov 24, 2011·Proceedings of the National Academy of Sciences of the United States of America·Peter M Hollingsworth
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Aug 1, 2012·Nature Methods·Diego DarribaDavid Posada
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Mar 29, 2014·Biological Reviews of the Cambridge Philosophical Society·Xiwen LiShilin Chen
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Jan 29, 2016·Molecular Ecology·Eric CoissacPierre Taberlet
May 14, 2016·Molecular Ecology·Lucie Zinger, Hervé Philippe
Aug 3, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Peter M HollingsworthAlex D Twyford
Jan 24, 2017·The Plant Journal : for Cell and Molecular Biology·Julian Tonti-FilippiniIan Small
May 10, 2017·Nucleic Acids Research·Michael TillichStephan Greiner
Oct 14, 2017·Molecular Biology and Evolution·Julio RozasAlejandro Sánchez-Gracia
Feb 2, 2018·Scientific Reports·Katarzyna KrawczykJakub Sawicki
Apr 5, 2018·BMC Evolutionary Biology·V ManzanillaH J de Boer
May 4, 2018·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
Jun 14, 2019·Genome Génome / Conseil National De Recherches Canada
Aug 17, 2018·Mitochondrial DNA. Part B, Resources·Lingjian GuiYingying Liu

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Methods Mentioned

BETA
PCR

Software Mentioned

CodeML
SAMtools
MAFFT
Mauve
Organellar Genome Draw
Trimmomatic
MrBayes
FigTree
DOGMA
jModeltest

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