A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies.

Nucleic Acids Research
Junha ShinSushmita Roy

Abstract

Comparative functional genomics offers a powerful approach to study species evolution. To date, the majority of these studies have focused on the transcriptome in mammalian and yeast phylogenies. Here, we present a novel multi-species proteomic dataset and a computational pipeline to systematically compare the protein levels across multiple plant species. Globally we find that protein levels diverge according to phylogenetic distance but is more constrained than the mRNA level. Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved. To interpret the evolutionary patterns of conservation and divergence, we develop a novel network-based integrative analysis pipeline that combines publicly available transcriptomic datasets to define co-expression modules. Our analysis pipeline can be used to relate the changes in protein levels to different species-specific phenotypic traits. We present a case study with the rhizobia-legume symbiosis process that supports the role of autophagy in this symbiotic association.

Associated Datasets

References

Apr 12, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Sven BergmannNaama Barkai
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Mar 25, 2006·PLoS Biology·Gavin C Conant, Kenneth H Wolfe
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Oct 12, 2007·Nature·Chris Todd Hittinger, Sean B Carroll
Nov 3, 2009·Current Opinion in Genetics & Development·Dana J WohlbachAviv Regev
Nov 11, 2010·Nucleic Acids Research·Rasko LeinonenUNKNOWN International Nucleotide Sequence Database Collaboration
Jul 26, 2011·Database : the Journal of Biological Databases and Curation·Rhoda J KinsellaPaul Flicek
Oct 21, 2011·Nature·David BrawandHenrik Kaessmann
Mar 14, 2012·Nature Reviews. Genetics·Christine Vogel, Edward M Marcotte
Mar 24, 2012·Annual Review of Biochemistry·Ariel BensimonRuedi Aebersold
Apr 12, 2012·Plant, Cell & Environment·Sara MovahediKlaas Vandepoele
Jun 12, 2012·Cell·Shu XiaoSheng Zhong
Jun 19, 2012·Nature Reviews. Genetics·Irene Gallego RomeroYoav Gilad
Sep 6, 2012·Systematic Biology·Yi-Chieh WuManolis Kellis
Feb 27, 2013·Chemical Reviews·Yaoyang ZhangJohn R Yates
Mar 7, 2013·Trends in Plant Science·Pierre-Marc DelauxJean-Michel Ané
Jun 26, 2013·ELife·Dawn A ThompsonAviv Regev
Oct 22, 2013·Molecular & Cellular Proteomics : MCP·Alexander S HebertJoshua J Coon
Jun 7, 2014·Genome Research·Wenfeng Qian, Jianzhi Zhang
Nov 8, 2014·Nucleic Acids Research·Rachael P HuntleyClaire O'Donovan
Dec 4, 2014·Cell Reports·Romain ChristianoTobias C Walther
Feb 18, 2015·Frontiers in Plant Science·Ravi GuptaSun T Kim
Oct 27, 2015·The Plant Cell·Swarup Roy Choudhury, Sona Pandey
Nov 19, 2015·Nucleic Acids Research·Paul Julian KerseyDaniel M Staines
Jun 12, 2016·Plant Physiology·Nicholas PanchyShin-Han Shiu
Jul 9, 2016·Genome Biology·Alessandra BreschiRoderic Guigó
Jul 17, 2016·Current Opinion in Plant Biology·Lei Li, Jen Sheen
Dec 3, 2016·Nucleic Acids Research·UNKNOWN The Gene Ontology Consortium
Dec 3, 2016·Nucleic Acids Research·Minoru KanehisaKanae Morishima

❮ Previous
Next ❯

Citations

Mar 27, 2021·Expert Review of Proteomics·J V Jorrin Novo
Nov 18, 2021·Functional & Integrative Genomics·Fabricio Almeida-Silva, Thiago M Venancio

❮ Previous
Next ❯

Datasets Mentioned

BETA
PXD013606

Methods Mentioned

BETA
acetylation
RNA-seq
transgenic
Hi-C

Software Mentioned

Ensembl Plants
TreeFix
HiC
MaxQuant
Muscari Clustering AlgoRIthm
Sequence Read Archive ( SRA
KEGG
MUSCARI
Muscari (
PAML

Related Concepts

Related Feeds

Autophagy & Model Organisms

Autophagy is a cellular process that allows degradation by the lysosome of cytoplasmic components such as proteins or organelles. Here is the latest research on autophagy & model organisms