A Single, Shared Triploidy in Three Species of Parasitic Nematodes

Abstract

The root-knot nematodes of the genus Meloidogyne are important and damaging parasites capable of infecting most flowering plants. Within this genus, several species of the Meloidogyne incognita group show evidence of paleopolyploidy in their genomes. We used our software tool POInT, the Polyploidy Orthology Inference Tool, to phylogenetically model the gene losses that followed that polyploidy. These models, and simulations based on them, show that three of these species (M. incognita, M. arenaria and M. javanica) descend from a single common hybridization event that yielded triplicated genomes with three distinguishable subgenomes. While one of the three subgenomes shows elevated gene loss rates relative to the other two, this subgenome does not show elevated sequence divergence. In all three species, ancestral loci where two of the three gene copies have been lost are less likely to have orthologs in Caenorhabditis elegans that are lethal when knocked down than are ancestral loci with surviving duplicate copies.

The lasting after-effects of an ancient polyploidy on the genomes of teleosts

“…We have developed a pipeline [58,62] for inferring blocks of double-conserved synteny (DCS) from a group of genomes sharing a WGD and an unduplicated reference genome (here spotted gar). This tool uses sequence similarity to identify homologous genes and then infers the products of a WGD by seeking to maximize the number of homologs that are members of such DCS blocks (Methods).…”

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

“…With the benefit of a new genome sequence from Crambe hispanica, presented here, we analyzed the Brassica WGT with our tool for modeling post-polyploidy genome evolution: POInT (the Polyploidy Orthology Inference Tool) (Conant and Wolfe 2008a). POInT, which we recently extended to allow the analysis of WGTs (Schoonmaker et al 2020), probabilistically infers the orthologous regions surviving from ancient duplications/triplications; it can be used to test for biases in fractionation without ad hoc assumptions. Moreover, POInT's models operate on complete genomes along a phylogeny (Dunn et al 2018;Smith et al 2020), helping to mask rearrangements in single genomes and giving larger synteny blocks (Emery et al 2018).…”

“…We sought to first confirm the two-step hexaploidy model and its relationship to the observed three subgenomes in the extant genomes. POInT, which we recently extended to allow the analysis of WGTs (Schoonmaker et al 2020), is ideally suited to this task, because it can model homoeolog losses phylogenetically and test for biases in fractionation without ad hoc assumptions. We find strong support for the two-step WGT formation model and for the first time give evidence for a significant gap in time between the two events.…”

“…When a new polyploid genome is created by the merging of similar but not identical progenitor species, it is referred to as an allopolyploid. Among allopolyploidies, the preferential retention of gene copies (homoeologs) from one of the parental subgenomes, known as biased fractionation, has been observed in yeast, maize, cotton, monkeyflower, Arabidopsis, Brassica, and nematodes (Thomas et al 2006;Conant and Wolfe 2008a;Cheng et al 2012;Parkin et al 2014;Renny-Byfield et al 2015;Edger et al 2017;Emery et al 2018;Schoonmaker et al 2020). Allopolyploids also show a tendency for genes from one of the subgenomes to be more highly expressed, and silencing or loss of genes from the remaining subgenomes is correspondingly more likely (Thomas et al 2006;Schnable et al 2011;Yoo et al 2014).…”

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

“…When a new polyploid genome is created by the merging of similar but not identical progenitor species, it is referred to as an allopolyploid. Among allopolyploidies, the preferential retention of gene copies (homoeologs) from one of the parental subgenomes, known as biased fractionation, has been observed in yeast, maize, cotton, monkeyflower, Arabidopsis, Brassica, and nematodes (Thomas et al 2006;Conant and Wolfe 2008a;Cheng et al 2012;Parkin et al 2014;Renny-Byfield et al 2015;Edger et al 2017;Emery et al 2018;Schoonmaker et al 2020). Allopolyploids also show a tendency for genes from one of the subgenomes to be more highly expressed, and silencing or loss of genes from the remaining subgenomes is correspondingly more likely (Thomas et al 2006;Schnable et al 2011;Yoo et al 2014).…”