scholarly journals Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers

2015 ◽  
Author(s):  
Alison Dawn Scott ◽  
Noah Stenz ◽  
David Baum
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Land Plant ◽  
Sequoia Sempervirens ◽  
Duplicate Genes ◽  
Whole Genome ◽  
Coast Redwood ◽  
Gene Copies ◽  
Close Relatives ◽  
Genome Donors

Whereas polyploidy is common and an important evolutionary factor in most land plant lineages it is a real rarity in gymnosperms. Coast redwood (Sequoia sempervirens) is the only hexaploid conifer and one of just two naturally polyploid conifer species. Numerous hypotheses about the mechanism of polyploidy in Sequoia and parental genome donors have been proffered over the years, primarily based on morphological and cytological data, but it remains unclear how Sequoia became polyploid and why this lineage overcame an apparent gymnosperm barrier to whole-genome duplication (WGD). We sequenced transcriptomes and used phylogenetic inference, Bayesian concordance analysis, and paralog age distributions to resolve relationships among gene copies in hexaploid coast redwood and its close relatives. Our data show that hexaploidy in the coast redwood lineage is best explained by autopolyploidy or, if there was allopolyploidy, this was restricted to within the Californian redwood clade. We found that duplicate genes have more similar sequences than would be expected given evidence from fossil guard cell size which suggest that polyploidy dates to the Eocene. Conflict between molecular and fossil estimates of WGD can be explained if diploidization occurred very slowly following whole genome duplication. We extrapolate from this to suggest that the rarity of polyploidy in conifers may be due to slow rates of diploidization in this clade.

scholarly journals Whole genome duplication in coast redwood ( Sequoia sempervirens ) and its implications for explaining the rarity of polyploidy in conifers

2016 ◽  
Vol 211 (1) ◽  
pp. 186-193 ◽  
Author(s):  
Alison Dawn Scott ◽  
Noah W. M. Stenz ◽  
Pär K. Ingvarsson ◽  
David A. Baum
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Sequoia Sempervirens ◽  
Whole Genome ◽  
Coast Redwood

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 Differential retention and divergent resolution of duplicate genes following whole-genome duplication

2014 ◽  
Vol 24 (10) ◽  
pp. 1665-1675 ◽  
Author(s):  
Casey L. McGrath ◽  
Jean-Francois Gout ◽  
Parul Johri ◽  
Thomas G. Doak ◽  
Michael Lynch
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Duplicate Genes ◽  
Whole Genome ◽  
Differential Retention

scholarly journals Genome and Karyotype Reorganization after Whole Genome Duplication in Free-Living Flatworms of the Genus Macrostomum

2020 ◽  
Vol 21 (2) ◽  
pp. 680 ◽  
Author(s):  
Kira S. Zadesenets ◽  
Ilyas Y. Jetybayev ◽  
Lukas Schärer ◽  
Nikolay B. Rubtsov
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Dna Probes ◽  
Chromosome Organization ◽  
Whole Genome ◽  
Telomeric Dna ◽  
Comparative Cytogenetics ◽  
Karyotype Instability ◽  
Close Relatives

The genus Macrostomum represents a diverse group of rhabditophoran flatworms with >200 species occurring around the world. Earlier we uncovered karyotype instability linked to hidden polyploidy in both M. lignano (2n = 8) and its sibling species M. janickei (2n = 10), prompting interest in the karyotype organization of close relatives. In this study, we investigated chromosome organization in two recently described and closely related Macrostomum species, M. mirumnovem and M. cliftonensis, and explored karyotype instability in laboratory lines and cultures of M. lignano (DV1/10, 2n = 10) and M. janickei in more detail. We revealed that three of the four studied species are characterized by karyotype instability, while M. cliftonensis showed a stable 2n = 6 karyotype. Next, we performed comparative cytogenetics of these species using fluorescent in situ hybridization (FISH) with a set of DNA probes (including microdissected DNA probes generated from M. lignano chromosomes, rDNA, and telomeric DNA). To explore the chromosome organization of the unusual 2n = 9 karyotype discovered in M. mirumnovem, we then generated chromosome-specific DNA probes for all chromosomes of this species. Similar to M. lignano and M. janickei, our findings suggest that M. mirumnovem arose via whole genome duplication (WGD) followed by considerable chromosome reshuffling. We discuss possible evolutionary scenarios for the emergence and reorganization of the karyotypes of these Macrostomum species and consider their suitability as promising animal models for studying the mechanisms and regularities of karyotype and genome evolution after a recent WGD.

scholarly journals Selective constraints on coding sequences of nervous system genes are a major determinant of duplicate gene retention in vertebrates

2016 ◽  
Author(s):  
Julien Roux ◽  
Jialin Liu ◽  
Marc Robinson-Rechavi
Keyword(s):  
Nervous System ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Duplicate Genes ◽  
Whole Genome ◽  
Coding Sequences ◽  
Whole Genome Duplications ◽  
Genome Duplications

AbstractThe evolutionary history of vertebrates is marked by three ancient whole-genome duplications: two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched the genome for specific genes, such as slow evolving genes, but this selective retention process is not well understood. To understand what drives the long-term preservation of duplicate genes, we characterized duplicated genes in terms of their expression patterns. We used a new method of expression enrichment analysis, TopAnat, applied to in situ hybridization data from thousands of genes from zebrafish and mouse. We showed that the presence of expression in the nervous system is a good predictor of a higher rate of retention of duplicate genes after whole-genome duplication. Further analyses suggest that purifying selection against the toxic effects of misfolded or misinteracting proteins, which is particularly strong in non-renewing neural tissues, likely constrains the evolution of coding sequences of nervous system genes, leading indirectly to the preservation of duplicate genes after whole-genome duplication. Whole-genome duplications thus greatly contributed to the expansion of the toolkit of genes available for the evolution of profound novelties of the nervous system at the base of the vertebrate radiation.

scholarly journals Origin of horsetails and the role of whole-genome duplication in plant macroevolution

2019 ◽  
Vol 286 (1914) ◽  
pp. 20191662 ◽  
Author(s):  
James W. Clark ◽  
Mark N. Puttick ◽  
Philip C. J. Donoghue
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Morphological Evolution ◽  
Land Plant ◽  
Plant Evolution ◽  
Whole Genome ◽  
Geological Time ◽  
Term Survival

Whole-genome duplication (WGD) has occurred commonly in land plant evolution and it is often invoked as a causal agent in diversification, phenotypic and developmental innovation, as well as conferring extinction resistance. The ancient and iconic lineage of Equisetum is no exception, where WGD has been inferred to have occurred prior to the Cretaceous–Palaeogene (K–Pg) boundary, coincident with WGD events in angiosperms. In the absence of high species diversity, WGD in Equisetum is interpreted to have facilitated the long-term survival of the lineage. However, this characterization remains uncertain as these analyses of the Equisetum WGD event have not accounted for fossil diversity. Here, we analyse additional available transcriptomes and summarize the fossil record. Our results confirm support for at least one WGD event shared among the majority of extant Equisetum species. Furthermore, we use improved dating methods to constrain the age of gene duplication in geological time and identify two successive Equisetum WGD events. The two WGD events occurred during the Carboniferous and Triassic, respectively, rather than in association with the K–Pg boundary. WGD events are believed to drive high rates of trait evolution and innovations, but analysed trends of morphological evolution across the historical diversity of Equisetum provide little evidence for further macroevolutionary consequences following WGD. WGD events cannot have conferred extinction resistance to the Equisetum lineage through the K–Pg boundary since the ploidy events occurred hundreds of millions of years before this mass extinction and we find evidence of extinction among fossil polyploid Equisetum lineages. Our findings precipitate the need for a review of the proposed roles of WGDs in biological innovation and extinction survival in angiosperm and non-angiosperm lineages alike.

Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1249-1257
Author(s):  
Ilya Ruvinsky ◽  
Lee M Silver ◽  
Jeremy J Gibson-Brown
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Families ◽  
Vertebrate Evolution ◽  
Whole Genome ◽  
Vertebrate Genome ◽  
T Box ◽  
Genetic Complexity ◽  
History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

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