Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions

Abstract

The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological functions. Here we use new evolutionary models to infer gene family histories across complete yeast genomes; these models allow us to estimate the relative genome-wide rates of gene birth, death, innovation and extinction (loss of an entire family) for the first time. We show that the rates of gene family evolution vary both between gene families and between species. We are also able to identify those families that have experienced rapid lineage specific expansion/contraction and show that these families are enriched for specific functions. Moreover, we find that families with specific functions are repeatedly expanded in multiple species, suggesting the presence of common adaptations and that these family expansions/contractions are not random. Additionally, we identify potential specialisations, unique to specific species, in the functions of lineage specific expanded families. These results suggest that an important mechanism in the evolution of genome content is the presence of lineage-specific gene family changes.

Rapid functional and evolutionary changes follow gene duplication in yeast

“…After a whole genome duplication (WGD) event in yeast approximately 88% of duplicated genes were lost over a period of 100 million years [ 9 ], and yeast species display a large turnover of duplicate genes [ 10 ]. There may be selection pressure to remove a duplicate if it results in an imbalance of protein subunits in a protein complex [ 11 ], and duplicate retention may be influenced by selection from the environment for specific functions [ 12 ].…”

DupliPHY-Web: a web server for DupliPHY and DupliPHY-ML

“…The BDIE model is more biologically relevant than our previous models ( Ames et al , 2012 ) and aims to describe more processes in the evolution of gene families ( Ames et al , 2014 ). We benchmarked both the BDI and BDIE models on simulated data and found both models can accurately infer ancestral gene family sizes ( Supplementary File 1 ).…”

“…Previously, we have released the software DupliPHY ( Ames et al , 2012 ) that provides weighted parsimony and maximum likelihood methods to accurately infer the evolutionary histories of gene families. The software has been used to identify lineage-specific expansions of gene families in yeast ( Ames et al , 2014 ). DupliPHY works on gene copy number counts to infer gene family evolution and is different from tree reconciliation methods that infer duplication and loss events based on gene and species trees ( Larget et al , 2010 ).…”

Expansion and Conservation of Biosynthetic Gene Clusters in Pathogenic Pyrenophora spp.

“…Furthermore, during meiosis, chromosome breakage fusion cycles begin with the loss of telomeres which causes the instability of the distal regions, and potential fusion of sister chromatids [56]. The site of breakage during separation in erroneously fused sister chromatids can lead to sequence duplication, deletion and rearrangement [56][57][58]. Therefore, breakage fusion events may have also contributed to NPRS duplication in Ptt.…”