scholarly journals Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

2014 ◽  
Author(s):  
Gavin Douglas ◽  
Gesseca Gos ◽  
Kim Steige ◽  
Adriana Salcedo ◽  
Karl Holm ◽  
...  
Keyword(s):  
Positive Selection ◽  
Whole Genome Duplication ◽  
Gene Loss ◽  
Genome Duplication ◽  
Strong Support ◽  
Plant Evolution ◽  
Flowering Plant ◽  
Whole Genome ◽  
Widespread Species ◽  
Genome Wide

Whole genome duplication events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm. Whole genome data provide strong support for recent hybrid origins of the tetraploid species within the last 100-300,000 years from two diploid progenitors in the Capsella genus. Major-effect inactivating mutations are frequent, but many were inherited from the parental species and show no evidence of being fixed by positive selection. Despite a lack of large-scale gene loss, we observe a decrease in the efficacy of natural selection genome-wide, due to the combined effects of demography, selfing and genome redundancy from whole genome duplication. Our results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that non-functionalization can receive a 'head start' through a legacy of deleterious variants and differential expression originating in parental diploid populations.

scholarly journals Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

2015 ◽  
Vol 112 (9) ◽  
pp. 2806-2811 ◽  
Author(s):  
Gavin M. Douglas ◽  
Gesseca Gos ◽  
Kim A. Steige ◽  
Adriana Salcedo ◽  
Karl Holm ◽  
...  
Keyword(s):  
Positive Selection ◽  
Large Scale ◽  
Gene Loss ◽  
Strong Support ◽  
Purifying Selection ◽  
Plant Evolution ◽  
Flowering Plant ◽  
Whole Genome ◽  
Widespread Species ◽  
Genome Wide

Whole-genome duplication (WGD) events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection, and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole-genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm. Whole-genome data provide strong support for recent hybrid origins of the tetraploid species within the past 100,000–300,000 y from two diploid progenitors in the Capsella genus. Major-effect inactivating mutations are frequent, but many were inherited from the parental species and show no evidence of being fixed by positive selection. Despite a lack of large-scale gene loss, we observe a decrease in the efficacy of natural selection genome-wide due to the combined effects of demography, selfing, and genome redundancy from WGD. Our results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that nonfunctionalization can receive a “head start” through a legacy of deleterious variants and differential expression originating in parental diploid populations.

scholarly journals Excision Dominates Pseudogenization During Fractionation After Whole Genome Duplication and in Gene Loss After Speciation in Plants

2020 ◽  
Vol 11 ◽  
Author(s):  
Zhe Yu ◽  
Chunfang Zheng ◽  
Victor A. Albert ◽  
David Sankoff
Keyword(s):  
Whole Genome Duplication ◽  
Gene Loss ◽  
Genome Duplication ◽  
Duplicate Genes ◽  
Whole Genome ◽  
Coding Sequence ◽  
Genome Doubling ◽  
Whole Genome Doubling ◽  
Synteny Blocks ◽  
Genomic Divergence

We take advantage of synteny blocks, the analytical construct enabled at the evolutionary moment of speciation or polyploidization, to follow the independent loss of duplicate genes in two sister species or the loss through fractionation of syntenic paralogs in a doubled genome. By examining how much sequence remains after a contiguous series of genes is deleted, we find that this residue remains at a constant low level independent of how many genes are lost—there are few if any relics of the missing sequence. Pseudogenes are rare or extremely transient in this context. The potential exceptions lie exclusively with a few examples of speciation, where the synteny blocks in some larger genomes tolerate degenerate sequence during genomic divergence of two species, but not after whole genome doubling in the same species where fractionation pressure eliminates virtually all non-coding sequence.

scholarly journals Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Kai-Hua Jia ◽  
Hui Liu ◽  
Ren-Gang Zhang ◽  
Jie Xu ◽  
Shan-Shan Zhou ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Whole Genome Duplication ◽  
Sequence Variation ◽  
Genome Duplication ◽  
Ornamental Plants ◽  
Plant Evolution ◽  
Genomic Rearrangements ◽  
Genome Wide Analysis ◽  
Salvia Splendens ◽  
Genome Wide

AbstractPolyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.

scholarly journals Comparative Inference of Duplicated Genes Produced by Polyploidization in Soybean Genome

2013 ◽  
Vol 2013 ◽  
pp. 1-4
Author(s):  
Yanmei Yang ◽  
Jinpeng Wang ◽  
Jianyong Di
Keyword(s):  
Statistical Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Duplication Event ◽  
Plant Evolution ◽  
Soybean Genome ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Genome Duplication Event ◽  
Scientific Value

Soybean (Glycine max) is one of the most important crop plants for providing protein and oil. It is important to investigate soybean genome for its economic and scientific value. Polyploidy is a widespread and recursive phenomenon during plant evolution, and it could generate massive duplicated genes which is an important resource for genetic innovation. Improved sequence alignment criteria and statistical analysis are used to identify and characterize duplicated genes produced by polyploidization in soybean. Based on the collinearity method, duplicated genes by whole genome duplication account for 70.3% in soybean. From the statistical analysis of the molecular distances between duplicated genes, our study indicates that the whole genome duplication event occurred more than once in the genome evolution of soybean, which is often distributed near the ends of chromosomes.

scholarly journals An ancient whole-genome duplication event and its contribution to flavor compounds in the tea plant (Camellia sinensis)

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Ya Wang ◽  
Fei Chen ◽  
Yuanchun Ma ◽  
Taikui Zhang ◽  
Pengchuan Sun ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Tea Plant ◽  
Plant Evolution ◽  
Plant Genome ◽  
Whole Genome ◽  
Biosynthesis Pathway ◽  
Duplicated Genes ◽  
Tandem Gene Duplication ◽  
Tea Plants

AbstractTea, coffee, and cocoa are the three most popular nonalcoholic beverages in the world and have extremely high economic and cultural value. The genomes of four tea plant varieties have recently been sequenced, but there is some debate regarding the characterization of a whole-genome duplication (WGD) event in tea plants. Whether the WGD in the tea plant is shared with other plants in order Ericales and how it contributed to tea plant evolution remained unanswered. Here we re-analyzed the tea plant genome and provided evidence that tea experienced only WGD event after the core-eudicot whole-genome triplication (WGT) event. This WGD was shared by the Polemonioids-Primuloids-Core Ericales (PPC) sections, encompassing at least 17 families in the order Ericales. In addition, our study identified eight pairs of duplicated genes in the catechins biosynthesis pathway, four pairs of duplicated genes in the theanine biosynthesis pathway, and one pair of genes in the caffeine biosynthesis pathway, which were expanded and retained following this WGD. Nearly all these gene pairs were expressed in tea plants, implying the contribution of the WGD. This study shows that in addition to the role of the recent tandem gene duplication in the accumulation of tea flavor-related genes, the WGD may have been another main factor driving the evolution of tea flavor.

scholarly journals ExOrthist: a tool to infer exon orthologies at any evolutionary distance

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yamile Márquez ◽  
Federica Mantica ◽  
Luca Cozzuto ◽  
Demian Burguera ◽  
Antonio Hermoso-Pulido ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Sequence Conservation ◽  
Evolutionary Distance ◽  
Whole Genome ◽  
Bioinformatic Tools ◽  
Genome Wide ◽  
Exon Sequence ◽  
Splicing Patterns

AbstractSeveral bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in different evolutionary scenarios: whole genome duplication in frogs and convergence of Nova-regulated splicing networks (https://github.com/biocorecrg/ExOrthist).

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