scholarly journals A comparative phylogenetic approach for dating whole genome duplication events

2004 ◽  
Vol 20 (2) ◽  
pp. 180-185 ◽  
Author(s):  
B. A. Chapman ◽  
J. E. Bowers ◽  
S. R. Schulze ◽  
A. H. Paterson
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Duplication Events

scholarly journals Artificial whole genome duplication in paleopolyploid sturgeons yields highest documented chromosome number in vertebrates

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ievgen Lebeda ◽  
Petr Ráb ◽  
Zuzana Majtánová ◽  
Martin Flajšhans
Keyword(s):  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Mitotic Division ◽  
Chromosome Count ◽  
Whole Genome ◽  
Acipenser Baerii ◽  
Ploidy Levels ◽  
Duplication Events ◽  
C Value

AbstractCritically endangered sturgeons, having undergone three whole genome duplication events, represent an exceptional example of ploidy plasticity in vertebrates. Three extant ploidy groups, combined with autopolyploidization, interspecific hybridization and the fertility of hybrids are important issues in sturgeon conservation and aquaculture. Here we demonstrate that the sturgeon genome can undergo numerous alterations of ploidy without severe physiological consequences, producing progeny with a range of ploidy levels and extremely high chromosome numbers. Artificial suppression of the first mitotic division alone, or in combination with suppression of the second meiotic division of functionally tetraploid zygotes (4n, C-value = 4.15) of Siberian sturgeon Acipenser baerii and Russian sturgeon A. gueldenstaedtii resulted in progeny of various ploidy levels—diploid/hexaploid (2n/6n) mosaics, hexaploid, octoploid juveniles (8n), and dodecaploid (12n) larvae. Counts between 477 to 520 chromosomes in octoploid juveniles of both sturgeons confirmed the modal chromosome numbers of parental species had been doubled. This exceeds the highest previously documented chromosome count among vertebrates 2n ~ 446 in the cyprinid fish Ptychobarbus dipogon.

scholarly journals Phylogeny and multiple independent whole‐genome duplication events in the Brassicales

2020 ◽  
Vol 107 (8) ◽  
pp. 1148-1164
Author(s):  
Makenzie E. Mabry ◽  
Julia M. Brose ◽  
Paul D. Blischak ◽  
Brittany Sutherland ◽  
Wade T. Dismukes ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Duplication Events

scholarly journals Two ancient genome duplication events shape diversity in Hibiscus L. (Malvaceae)

2020 ◽  
Author(s):  
Jonna Sofia Eriksson ◽  
Christine D. Bacon ◽  
Dominic J. Bennett ◽  
Bernard E. Pfeil ◽  
Bengt Oxelman ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Genome Size ◽  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Single Copy ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Genome Doubling ◽  
Duplication Events

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e., genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole genome duplication events, we tested a series of scenarios describing different polyploidization events.Results: Using target sequence capture, we generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. Species of Hibiscus shared one genome duplication with H. syriacus and one whole genome duplication occurred along the branch leading to H. syriacus.Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

scholarly journals Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)

2021 ◽  
Author(s):  
Jonna Sofia Eriksson ◽  
Christine D. Bacon ◽  
Dominic J. Bennett ◽  
Bernard E. Pfeil ◽  
Bengt Oxelman ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Single Copy ◽  
Target Sequence ◽  
Whole Genome ◽  
Genome Doubling ◽  
Sequence Capture ◽  
Duplication Events

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

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