scholarly journals Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Sean P. Gordon ◽  
Bruno Contreras-Moreira ◽  
Joshua J. Levy ◽  
Armin Djamei ◽  
Angelika Czedik-Eysenberg ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Genomic Analysis ◽  
Polyploid Genome

scholarly journals Asymmetric Divergence in Transmitted SNPs of DNA Replication/Transcription and Their Impact on Gene Expression in Polyploid Brassica napus

2021 ◽  
Vol 12 ◽  
Author(s):  
Minqiang Tang ◽  
Juanling Li ◽  
Xu Hu ◽  
Lu Sun ◽  
MMU Helal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Replication ◽  
Brassica Napus ◽  
Genome Evolution ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expression Levels ◽  
Dna And Rna ◽  
Polyploid Genome ◽  
Gene Expression Levels

The marked increase in plant genomic data has provided valuable resources for investigating the dynamic evolution of duplicate genes in polyploidy. Brassica napus is an ideal model species for investigating polyploid genome evolution. The present study comprehensively analyzed DNA and RNA variation of two representative B. napus inbredlines, Zhongshuang11 and Zhongyou821, and we investigated gene expression levels of An and Cn subgenomes in multiple tissues of the two lines. The distribution of transmitted single nucleotide polymorphisms (SNPs) was significantly different in two subgenomes of B. napus. Gene expression levels were significantly negatively correlated with number of variations in replication and transcription of the corresponding genes, but were positively correlated with the ratios of transmitted SNPs from DNA to RNA. We found a higher density of SNP variation in An than that in Cn during DNA replication and more SNPs were transmitted to RNA during transcription, which may contribute to An expression dominance. These activities resulted in asymmetrical gene expression in polyploid B. napus. The SNPs transmitted from DNA to RNA could be an important complement feature in comparative genomics, and they may play important roles in asymmetrical genome evolution in polyploidy.

scholarly journals The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Peng Xu ◽  
Jian Xu ◽  
Guangjian Liu ◽  
Lin Chen ◽  
Zhixiong Zhou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Evolution ◽  
Common Carp ◽  
Cyprinus Carpio ◽  
Diploid Progenitor ◽  
Promoter Regions ◽  
Expression Bias ◽  
The Common ◽  
Polyploid Genome ◽  
Reference Genomes

Abstract Common carp (Cyprinus carpio) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid genome evolution in vertebrates. Here, we generate three chromosome-level reference genomes of C. carpio and compare to related diploid Cyprinid genomes. We identify a Barbinae lineage as potential diploid progenitor of C. carpio and then divide the allotetraploid genome into two subgenomes marked by a distinct genome similarity to the diploid progenitor. We estimate that the two diploid progenitors diverged around 23 Mya and merged around 12.4 Mya based on the divergence rates of homoeologous genes and transposable elements in two subgenomes. No extensive gene losses are observed in either subgenome. Instead, we find gene expression bias across surveyed tissues such that subgenome B is more dominant in homoeologous expression. CG methylation in promoter regions may play an important role in altering gene expression in allotetraploid C. carpio.

scholarly journals Limited DNA repair gene repertoire in Ascomycete yeast revealed by comparative genomics

2019 ◽  
Author(s):  
Shira Milo ◽  
Reut Harari Misgav ◽  
Einat Hazkani-Covo ◽  
Shay Covo
Keyword(s):  
Dna Repair ◽  
Genome Evolution ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Gene Repertoire ◽  
Dna Repair Genes ◽  
Repair Gene ◽  
Brettanomyces Bruxellensis ◽  
Dna Repair Gene ◽  
Repair Genes

Abstract Ascomycota is the largest phylogenetic group of fungi that includes species important to human health and wellbeing. DNA repair is important for fungal survival and genome evolution. Here, we describe a detailed comparative genomic analysis of DNA repair genes in Ascomycota. We determined the DNA repair gene repertoire in Taphrinomycotina, Saccharomycotina, Leotiomycetes, Sordariomycetes, Dothideomycetes, and Eurotiomycetes. The subphyla of yeasts, Saccharomycotina and Taphrinomycotina, have a smaller DNA repair gene repertoire comparing to Pezizomycotina. Some genes were absent from most, if not all, yeast species. To study the conservation of these genes in Pezizomycotina, we used the GLOOME algorithm that provides the expectations of gain or loss of genes given the tree topology. Genes that were absent from most of the species of Taphrinomycotina or Saccharomycotina showed lower conservation in Pezizomycotina. This suggests that the absence of some DNA repair in yeasts is not random; genes with a tendency to be lost in other classes are missing. We ranked the conservation of DNA repair genes in Ascomycota. We found that Rad51 and its paralogs were less conserved than other recombinational proteins, suggesting that there is a redundancy between Rad51 and its paralogs, at least in some species. Finally, based on the repertoire of UV repair genes, we found conditions that differentially kill the wine pathogen Brettanomyces bruxellensis and not Saccharomyces cerevisiae. In summary, our analysis provides testable hypotheses to the role of DNA repair proteins in the genome evolution of Ascomycota.

scholarly journals High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution

2017 ◽  
Vol 91 (2) ◽  
pp. 278-291 ◽  
Author(s):  
Artem S. Kasianov ◽  
Anna V. Klepikova ◽  
Ivan V. Kulakovskiy ◽  
Evgeny S. Gerasimov ◽  
Anna V. Fedotova ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Genome Assembly ◽  
Regulatory Elements ◽  
High Quality ◽  
Early Stages ◽  
Polyploid Genome ◽  
High Quality Genome

Chromosome structural changes in diploid and tetraploid A genomes of Gossypium

Genome ◽  
2006 ◽  
Vol 49 (4) ◽  
pp. 336-345 ◽  
Author(s):  
Aparna Desai ◽  
Peng W Chee ◽  
Junkang Rong ◽  
O Lloyd May ◽  
Andrew H Paterson
Keyword(s):  
Genome Evolution ◽  
Linkage Mapping ◽  
Structural Variation ◽  
Structural Changes ◽  
Diploid Species ◽  
Gossypium Arboreum ◽  
Linkage Groups ◽  
Recombination Rates ◽  
A Genome ◽  
Polyploid Genome

The genus Gossypium, which comprises a divergent group of diploid species and several recently formed allotetraploids, offers an excellent opportunity to study polyploid genome evolution. In this study, chromosome structural variation among the A, At, and D genomes of Gossypium was evaluated by comparative genetic linkage mapping. We constructed a fully resolved RFLP linkage map for the diploid A genome consisting of 275 loci using an F2 interspecific Gossypium arboreum × Gossypium herbaceum family. The 13 chromosomes of the A genome are represented by 12 large linkage groups in our map, reflecting an expected interchromosomal translocation between G. arboreum and G. herbaceum. The A-genome chromosomes are largely collinear with the D genomes, save for a few small inversions. Although the 2 diploid mapping parents represent the closest living relatives of the allotetraploid At-genome progenitor, 2 translocations and 7 inversions were observed between the A and At genomes. The recombination rates are similar between the 2 diploid genomes; however, the At genome shows a 93% increase in recombination relative to its diploid progenitors. Elevated recombination in the Dt genome was reported previously. These data on the At genome thus indicate that elevated recombination was a general property of allotetraploidy in cotton.Key words: comparative mapping, polyploidy, genome evolution, inversions, translocations, RFLP.

scholarly journals Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention

2017 ◽  
Author(s):  
Terezie Mandáková ◽  
Zheng Li ◽  
Michael S. Barker ◽  
Martin A. Lysak
Keyword(s):  
Genome Evolution ◽  
Chromosome Numbers ◽  
Phylogenetic Analyses ◽  
Whole Genome ◽  
Gene Retention ◽  
Plant Groups ◽  
Genome Duplications ◽  
Number Variation ◽  
Polyploid Genome ◽  
Whole Transcriptome Analysis

SummaryHybridization and polyploidy followed by genome-wide diploidization significantly impacted the diversification of land plants. The ancient At-α whole-genome duplication (WGD) preceded the diversification of crucifers (Brassicaceae). Some genera and tribes also experienced younger, mesopolyploid WGDs concealed by subsequent genome diploidization. Here we tested if multiple base chromosome numbers originated due to genome diploidization after independent mesopolyploid WGDs and how diploidization impacted post-polyploid gene retention. Sixteen species representing ten Brassicaceae tribes were analyzed by comparative chromosome painting and/or whole-transcriptome analysis of gene age distributions and phylogenetic analyses of gene duplications. Overall, we found evidence for at least 13 independent mesopolyploidies followed by different degrees of diploidization across the Brassicaceae. New mesotetraploid events were uncovered for tribes Anastaticeae, Iberideae and Schizopetaleae, and mesohexaploid WGDs for Cochlearieae and Physarieae. In contrast, we found convergent patterns of gene retention and loss among these independent WGDs. Our combined analyses of Brassicaceae genomic data indicate that the extant chromosome number variation in many plant groups, and especially polybasic but monophyletic taxa, can result from clade-specific genome duplications followed by diploidization. Our observation of parallel gene retention and loss across multiple independent WGDs provides one of the first multi-species tests that post-polyploid genome evolution is predictable.Significance statementOur data show that multiple base chromosome numbers in some Brassicaceae clades originated due to genome diploidization following multiple independent whole-genome duplications (WGD). The parallel gene retention/loss across independent WGDs and diploidizations provides one of the first tests that post-polyploid genome evolution is predictable.

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