Chloroplast phylogenomic analyses resolve deep-level relationships of an intractable bamboo tribe Arundinarieae (poaceae)

Systematic Biology
Peng-Fei MaDe-Zhu Li

Abstract

The temperate woody bamboos constitute a distinct tribe Arundinarieae (Poaceae: Bambusoideae) with high species diversity. Estimating phylogenetic relationships among the 11 major lineages of Arundinarieae has been particularly difficult, owing to a possible rapid radiation and the extremely low rate of sequence divergence. Here, we explore the use of chloroplast genome sequencing for phylogenetic inference. We sampled 25 species (22 temperate bamboos and 3 outgroups) for the complete genome representing eight major lineages of Arundinarieae in an attempt to resolve backbone relationships. Phylogenetic analyses of coding versus noncoding sequences, and of different regions of the genome (large single copy and small single copy, and inverted repeat regions) yielded no well-supported contradicting topologies but potential incongruence was found between the coding and noncoding sequences. The use of various data partitioning schemes in analysis of the complete sequences resulted in nearly identical topologies and node support values, although the partitioning schemes were decisively different from each other as to the fit to the data. Our full genomic data set substantially increased resolution along the backbone and provided stro...Continue Reading

References

Jan 1, 1985·Annual Review of Genetics·J D Palmer
Jun 1, 1997·Computer Applications in the Biosciences : CABIOS·A Rambaut, N C Grassly
Jan 27, 1999·Bioinformatics·D Posada, K A Crandall
Aug 30, 2001·Proceedings of the National Academy of Sciences of the United States of America·M S Rosenberg, S Kumar
Dec 26, 2001·Bioinformatics·H Shimodaira, M Hasegawa
Jun 25, 2002·Systematic Biology·Hidetoshi Shimodaira
Sep 14, 2002·Systematic Biology·Derrick J Zwickl, David M Hillis
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Sep 19, 2003·Trends in Plant Science·Neil Jones, Andreas Houben
Feb 18, 2004·Systematic Biology·Johan A A NylanderJosé Luis Nieves-Aldrey
Jun 8, 2004·Bioinformatics·Stacia K WymanJeffrey L Boore
Jan 22, 2005·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Apr 30, 2005·Nature Reviews. Genetics·Frédéric DelsucHervé Philippe
Oct 14, 2005·Molecular Biology and Evolution·Daniel H Huson, David Bryant
Oct 26, 2005·Systematic Biology·John J WiensTod W Reeder
Feb 24, 2006·Trends in Genetics : TIG·Olivier JeffroyHervé Philippe
Jul 25, 2006·Systematic Biology·Shannon M HedtkeDavid M Hillis
Nov 16, 2006·PLoS Biology·Antonis Rokas, Sean B Carroll
Feb 16, 2007·Trends in Ecology & Evolution·James B Whitfield, Peter J Lockhart
May 10, 2007·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Jul 31, 2007·Systematic Biology·Jeremy M Brown, Alan R Lemmon
Dec 1, 2007·Proceedings of the National Academy of Sciences of the United States of America·Robert K JansenJeffrey L Boore
Dec 1, 2007·Proceedings of the National Academy of Sciences of the United States of America·Michael J MooreDouglas E Soltis
Dec 28, 2007·Current Biology : CB·Pascal-Antoine ChristinNicolas Salamin
Feb 16, 2008·Systematic Biology·Shuguang JianDouglas E Soltis
Mar 25, 2008·Molecular Phylogenetics and Evolution·Yanis Bouchenak-KhelladiTrevor R Hodkinson
Jun 28, 2008·Science·Shannon J HackettTamaki Yuri
Aug 13, 2008·Molecular Biology and Evolution·Pascal-Antoine ChristinGuillaume Besnard
Oct 11, 2008·Nature Biotechnology·Jay Shendure, Hanlee Ji
Jan 29, 2010·Proceedings. Biological Sciences·Luis M ValentePablo Vargas
Feb 24, 2010·Proceedings of the National Academy of Sciences of the United States of America·Michael J MooreDouglas E Soltis
Dec 28, 2010·Systematic Biology·J Gordon BurleighTodd J Vision

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Citations

Dec 30, 2015·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Yan-Ci YangGuifang Zhao
Jun 25, 2016·Genome Biology·Henry DaniellWan-Jung Chang
Jul 26, 2016·Frontiers in Plant Science·Yanci YangGuifang Zhao
Jul 6, 2016·Scientific Reports·Xin YaoRichard T Corlett
Oct 30, 2016·Frontiers in Plant Science·Tao ZhouGuifang Zhao
Apr 20, 2017·Frontiers in Plant Science·Pan LiCheng-Xin Fu
Oct 16, 2015·Evolutionary Bioinformatics Online·Da-Cheng Hao, Pei-Gen Xiao
Jul 6, 2017·Frontiers in Plant Science·Yuan HuangJiahui Chen
Jul 4, 2019·BMC Plant Biology·Xu ZhangHang Sun
Jan 14, 2017·Frontiers in Plant Science·Sean V BurkeMelvin R Duvall
Feb 18, 2017·BMC Genomics·Xinyi GuoMarcus A Koch
Mar 21, 2018·Journal of Molecular Evolution·Erika ViljoenDavid J G Rees
Feb 27, 2018·Frontiers in Plant Science·Yin-Huan WangTing-Shuang Yi
Nov 28, 2018·Scientific Reports·Carolina Osuna-MascaróFrancisco Perfectti
Dec 13, 2018·Annals of Botany·Jacqueline HeckenhauerRosabelle Samuel

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