Genome-wide identification and expression analysis of PUB genes in cotton

BMC Genomics
Xuke LuWuwei Ye

Abstract

The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stresses, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and a necessity when studying the mechanisms of stress- tolerance in cotton. In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely localized in cells, but primarily in the nucleus. The PUBs in cotton were classified into six subfamilies (A-F) on the basis of phylogenetic analysis, which was testified by the analysis of conserved motifs and exon-intron structures. Chromosomal localization analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment analysis, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs in A2 and D5 were found; however no tandem duplications in A2 o...Continue Reading

References

Sep 22, 2000·Trends in Cell Biology·P K JacksonJ D Reimann
Aug 10, 2001·Trends in Plant Science·C AzevedoK Shirasu
Feb 28, 2002·Molecular Biology and Evolution·Zhenglong GuWen-Hsiung Li
Feb 28, 2002·Genome Biology·Fyodor A KondrashovEugene V Koonin
Jul 13, 2002·Trends in Biochemical Sciences·Douglas M CyrCam Patterson
Sep 5, 2002·Genes & Development·J Wade HarperMark J Solomon
Apr 8, 2003·Molecular Biology and Evolution·David S SenchinaJonathan F Wendel
Jun 14, 2003·Science·Cyrus ChothiaSarah A Teichmann
Sep 21, 2004·Annual Review of Plant Biology·Jan Smalle, Richard D Vierstra
Dec 8, 2004·The Plant Cell·Jennifer MoonMark Estelle
Mar 24, 2005·Journal of Molecular Evolution·Leif SchauserJens Stougaard
Jun 6, 2006·Proteins·Chin-Sheng YuJenn-Kang Hwang
Jun 20, 2008·Molecular Genetics and Genomics : MGG·Sihai YangJian-Qun Chen
Nov 19, 2008·Nature Reviews. Genetics·Gavin C Conant, Kenneth H Wolfe
Apr 9, 2009·Nature Reviews. Molecular Cell Biology·Brenda A Schulman, J Wade Harper
May 9, 2009·Nature Reviews. Molecular Cell Biology·Richard D Vierstra
Jun 27, 2009·The New Phytologist·Lex E Flagel, Jonathan F Wendel
Oct 24, 2009·Nature Reviews. Molecular Cell Biology·Yihong Ye, Michael Rape
Jan 13, 2011·The Plant Journal : for Cell and Molecular Biology·Jong-Jin ParkGynheung An
Jan 6, 2012·Nucleic Acids Research·Yupeng WangAndrew H Paterson
Jul 26, 2012·Plant Signaling & Behavior·Wei LiGuo-Liang Wang
Aug 28, 2012·Nature Genetics·Kunbo WangShuxun Yu
May 31, 2013·Journal of Integrative Plant Biology·Yu-Xian Zhu, Fu-Guang Li
May 20, 2014·Nature Genetics·Fuguang LiShuxun Yu
May 7, 2015·Nucleic Acids Research·Robert D FinnSean R Eddy
Dec 18, 2015·Nucleic Acids Research·Robert D FinnAlex Bateman
Mar 3, 2019·Plant Science : an International Journal of Experimental Plant Biology·Xuke LuWuwei Ye

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Methods Mentioned

BETA
ubiquitination
PCR
electrophoresis

Software Mentioned

HMMER3
MCScanX
BLASTP
BLASTN
ClustalX1
SMART
MapInspect
MEGA6
GSDS2
Circos

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