Family-Specific Gains and Losses of Protein Domains in the Legume and Grass Plant Families

Evolutionary Bioinformatics Online
Akshay YadavSteven B Cannon

Abstract

Protein domains can be regarded as sections of protein sequences capable of folding independently and performing specific functions. In addition to amino-acid level changes, protein sequences can also evolve through domain shuffling events such as domain insertion, deletion, or duplication. The evolution of protein domains can be studied by tracking domain changes in a selected set of species with known phylogenetic relationships. Here, we conduct such an analysis by defining domains as "features" or "descriptors," and considering the species (target + outgroup) as instances or data-points in a data matrix. We then look for features (domains) that are significantly different between the target species and the outgroup species. We study the domain changes in 2 large, distinct groups of plant species: legumes (Fabaceae) and grasses (Poaceae), with respect to selected outgroup species. We evaluate 4 types of domain feature matrices: domain content, domain duplication, domain abundance, and domain versatility. The 4 types of domain feature matrices attempt to capture different aspects of domain changes through which the protein sequences may evolve-that is, via gain or loss of domains, increase or decrease in the copy number of dom...Continue Reading

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Methods Mentioned

BETA
ubiquitination
deubiquitination
phosphotransferase
diphosphotransferase

Software Mentioned

HMMER
hmmscan

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