Genome-wide analysis of purple acid phosphatase structure and expression in ten vegetable species

BMC Genomics
Lulu Xie, Qingmao Shang

Abstract

Acquisition of external phosphorus (P) and optimisation of internal P are essential for plant growth and development, and insufficient availability of P in soils is a major challenge in agriculture. Members of the purple acid phosphatase (PAP) family of enzymes are candidates for increasing P use efficiency. Herein, we identified PAP homologs in the genomes of 10 vegetable species, along with Arabidopsis thaliana and Amborella trichopoda as references, to provide fundamental knowledge for this family. Phylogenetic analysis of protein sequences revealed nine distinct clades, indicating that functional differentiation of extant PAPs was established prior to the emergence of early angiosperms, and conserved among homologs in each clade. Analysis of transcript abundance in different tissues (root, stem, leaf, flower, and fruit) and following phosphates (Pi) starvation treatments from published RNA-seq transcriptome datasets facilitated comprehensive evaluation of expression patterns, and some groups of tissue-specific and Pi starvation-induced PAPs were characterised. Conserved motifs identified from upstream sequences of homologs that are highly expressed in particular tissues or following starvation treatment suggests that diverg...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Oct 24, 1997·Science·R L TatusovD J Lipman
Jul 30, 1999·Structure·L W GuddatJ L Martin
Oct 8, 1999·Archives of Biochemistry and Biophysics·G SchenkJ de Jersey
May 29, 2002·Molecular Biology and Evolution·Ziheng Yang, Rasmus Nielsen
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Sep 4, 2003·Genome Research·Li LiDavid S Roos
Mar 9, 2005·Current Opinion in Plant Biology·Keith L Adams, Jonathan F Wendel
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Jan 23, 2008·The New Phytologist·Wing-Yen Francisca LiHon-Ming Lam
Oct 15, 2008·Systematic Biology·Alexandros StamatakisJacques Rougemont
Jan 27, 2009·Journal of Experimental Botany·Wei-Yi LinTzyy-Jen Chiou
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
May 22, 2009·Nucleic Acids Research·Timothy L BaileyWilliam S Noble
Jul 26, 2011·Database : the Journal of Biological Databases and Curation·Rhoda J KinsellaPaul Flicek
Jun 14, 2012·The New Phytologist·Erik J VeneklaasJohn A Raven
Dec 12, 2012·Nature Biotechnology·Cole TrapnellLior Pachter
Jul 31, 2013·BMC Plant Biology·Sridhar RavichandranBalakrishnan Prithiviraj
Jan 15, 2014·Journal of Integrative Plant Biology·Zhaoliang ZhangWilliam J Lucas
Jan 31, 2014·Proceedings of the National Academy of Sciences of the United States of America·José M Franco-ZorrillaRoberto Solano
Mar 4, 2014·Annual Review of Plant Biology·Damar Lizbeth López-ArredondoLuis Herrera-Estrella
Aug 8, 2015·Planta·Nrisingha DeyIndu B Maiti
Jan 1, 2014·Horticulture Research·Sara LonghiDaniel J Sargent
May 21, 2016·Cell·Ronan C O'MalleyJoseph R Ecker
Oct 14, 2017·Molecular Biology and Evolution·Jinpeng WangXiyin Wang

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Citations

Apr 24, 2019·International Journal of Molecular Sciences·Chaoyan YinWenfeng Li
Sep 3, 2019·Frontiers in Plant Science·Katrin Wacker-FesterMareike Kavka

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Datasets Mentioned

BETA
AF236109

Methods Mentioned

BETA
RNA-seq

Software Mentioned

MEGA
Tomtom
RAxML
iTol
PAML
NGS QC toolkit
MAFFT
Codeml
orthoMCL
hmmsearch

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