scholarly journals Early genome duplications in conifers and other seed plants

2015 ◽  
Vol 1 (10) ◽  
pp. e1501084 ◽  
Author(s):  
Zheng Li ◽  
Anthony E. Baniaga ◽  
Emily B. Sessa ◽  
Moira Scascitelli ◽  
Sean W. Graham ◽  
...  
Keyword(s):  
Genome Duplication ◽  
Repetitive Element ◽  
Flowering Plants ◽  
Genomic Research ◽  
Seed Plants ◽  
Genome Duplications ◽  
Conifer Genome ◽  
Element Activity ◽  
Phylogenomic Analyses ◽  
Gene Age

Polyploidy is a common mode of speciation and evolution in angiosperms (flowering plants). In contrast, there is little evidence to date that whole genome duplication (WGD) has played a significant role in the evolution of their putative extant sister lineage, the gymnosperms. Recent analyses of the spruce genome, the first published conifer genome, failed to detect evidence of WGDs in gene age distributions and attributed many aspects of conifer biology to a lack of WGDs. We present evidence for three ancient genome duplications during the evolution of gymnosperms, based on phylogenomic analyses of transcriptomes from 24 gymnosperms and 3 outgroups. We use a new algorithm to place these WGD events in phylogenetic context: two in the ancestry of major conifer clades (Pinaceae and cupressophyte conifers) and one inWelwitschia(Gnetales). We also confirm that a WGD hypothesized to be restricted to seed plants is indeed not shared with ferns and relatives (monilophytes), a result that was unclear in earlier studies. Contrary to previous genomic research that reported an absence of polyploidy in the ancestry of contemporary gymnosperms, our analyses indicate that polyploidy has contributed to the evolution of conifers and other gymnosperms. As in the flowering plants, the evolution of the large genome sizes of gymnosperms involved both polyploidy and repetitive element activity.

scholarly journals Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae

2016 ◽  
Author(s):  
Michael S. Barker ◽  
Zheng Li ◽  
Thomas I. Kidder ◽  
Chris R. Reardon ◽  
Zhao Lai ◽  
...  
Keyword(s):  
Gene Family ◽  
Linkage Map ◽  
Evolutionary History ◽  
Genome Duplication ◽  
Nuclear Gene ◽  
Flowering Plants ◽  
The Family ◽  
History Of ◽  
Phylogenomic Analyses

AbstractPremise of the studyLike many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature.MethodsWe sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy.Key resultsWe found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia.ConclusionsOur analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from a high density Lactuca linkage map, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.

Checklist of ferns and seed plants of the Golden Gate Highlands National Park, South Africa

Bothalia ◽  
2010 ◽  
Vol 40 (2) ◽  
pp. 205-218 ◽  
Author(s):  
M. E. Daemane ◽  
B-E. Van Wyk ◽  
A. Moteetee
Keyword(s):  
South Africa ◽  
National Park ◽  
Flowering Plants ◽  
Seed Plants ◽  
Golden Gate ◽  
Infraspecific Taxa

A list of flowering plants and ferns has been compiled for the Golden Gate Highlands National Park, which occupies an area of 11 346 hectares but excludes the adjacent QwaQwa National Park. The checklist comprises 846 taxa (823 species and 23 infraspecific taxa) representing 359 genera in 101 families. Eleven of the species are recorded in the Red Data List (Raimondo et al. 2010) and 64 species are naturalized exotics.

scholarly journals Simultaneous parsimony jackknife analysis of 2538rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants

1998 ◽  
Vol 213 (3-4) ◽  
pp. 259-287 ◽  
Author(s):  
Mari K�llersj� ◽  
James S. Farris ◽  
Mark W. Chase ◽  
Birgitta Bremer ◽  
Michael F. Fay ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Flowering Plants ◽  
Land Plants ◽  
Seed Plants ◽  
Green Plants ◽  
Jackknife Analysis

scholarly journals Ancient Genome Duplications Did Not Structure the Human Hox-Bearing Chromosomes

2001 ◽  
Vol 11 (5) ◽  
pp. 771-780 ◽  
Author(s):  
Austin L. Hughes ◽  
Jack da Silva ◽  
Robert Friedman
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Duplication ◽  
Genome Duplication ◽  
Gene Families ◽  
Gene Duplications ◽  
Human Chromosomes ◽  
Time Period ◽  
Genome Duplications

The fact that there are four homeobox (Hox) clusters in most vertebrates but only one in invertebrates is often cited as evidence for the hypothesis that two rounds of genome duplication by polyploidization occurred early in vertebrate history. In addition, it has been observed in humans and other mammals that numerous gene families include paralogs on two or more of the fourHox-bearing chromosomes (the chromosomes bearing theHox clusters; i.e., human chromosomes 2, 7, 12, and 17), and the existence of these paralogs has been taken as evidence that these genes were duplicated along with the Hox clusters by polyploidization. We tested this hypothesis by phylogenetic analysis of 42 gene families including members on two or more of the humanHox-bearing chromosomes. In 32 of these families there was evidence against the hypothesis that gene duplication occurred simultaneously with duplication of the Hox clusters. Phylogenies of 14 families supported the occurrence of one or more gene duplications before the origin of vertebrates, and of 15 gene duplication times estimated for gene families evolving in a clock-like manner, only six were dated to the same time period early in vertebrate history during which the Hox clusters duplicated. Furthermore, of gene families duplicated around the same time as the Hoxclusters, the majority showed topologies inconsistent with their having duplicated simultaneously with the Hox clusters. The results thus indicate that ancient events of genome duplication, if they occurred at all, did not play an important role in structuring the mammalian Hox-bearing chromosomes.

scholarly journals OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates

2019 ◽  
Author(s):  
Param Priya Singh ◽  
Hervé Isambert
Keyword(s):  
Teleost Fish ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Genetic Diseases ◽  
Genomic Analysis ◽  
Biased Sampling ◽  
Whole Genome ◽  
Genome Duplications ◽  
Evolutionary Genomic ◽  
The Impact

Abstract All vertebrates including human have evolved from an ancestor that underwent two rounds of whole genome duplication (2R-WGD). In addition, teleost fish underwent an additional third round of genome duplication (3R-WGD). The genes retained from these genome duplications, so-called ohnologs, have been instrumental in the evolution of vertebrate complexity, development and susceptibility to genetic diseases. However, the identification of vertebrate ohnologs has been challenging, due to lineage specific genome rearrangements since 2R- and 3R-WGD. We previously identified vertebrate ohnologs using a novel synteny comparison across multiple genomes. Here, we refine and apply this approach on 27 vertebrate genomes to identify ohnologs from both 2R- and 3R-WGD, while taking into account the phylogenetically biased sampling of available species. We assemble vertebrate ohnolog pairs and families in an expanded OHNOLOGS v2 database. We find that teleost fish have retained more 2R-WGD ohnologs than mammals and sauropsids, and that these 2R-ohnologs have retained significantly more ohnologs from the subsequent 3R-WGD than genes without 2R-ohnologs. Interestingly, species with fewer extant genes, such as sauropsids, have retained similar or higher proportions of ohnologs. OHNOLOGS v2 should allow deeper evolutionary genomic analysis of the impact of WGD on vertebrates and can be freely accessed at http://ohnologs.curie.fr.

scholarly journals The Sea Lamprey Meiotic Map Resolves Ancient Vertebrate Genome Duplications

2014 ◽  
Author(s):  
Jeramiah Smith
Keyword(s):  
Genome Duplication ◽  
Strong Support ◽  
Sea Lamprey ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Segmental Duplications ◽  
Vertebrate Genome ◽  
Vertebrate Lineage ◽  
Comparative Maps ◽  
Genome Duplications

Gene and genome duplications serve as an important reservoir of material for the evolution of new biological functions. It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey, a representative of an ancient lineage that diverged from all other vertebrates approximately 550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1N ~ 99), spanning a total of 5,570.25 cM. Comparative mapping data yield strong support for one ancient whole genome duplication but do not strongly support a hypothetical second event. Rather, these comparative maps reveal several evolutionary independent segmental duplications occurring over the last 600+ million years of chordate evolution. This refined history of vertebrate genome duplication should permit more precise investigations into the evolution of vertebrate gene functions.

scholarly journals Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants

2016 ◽  
Vol 113 (43) ◽  
pp. 12328-12333 ◽  
Author(s):  
Qidong Jia ◽  
Guanglin Li ◽  
Tobias G. Köllner ◽  
Jianyu Fu ◽  
Xinlu Chen ◽  
...  
Keyword(s):  
Flowering Plants ◽  
Terpene Synthase ◽  
Seed Plants ◽  
Terpene Synthases ◽  
The Third ◽  
Wide Range ◽  
Prenyl Diphosphate ◽  
Bacteria And Fungi ◽  
Selaginella Moellendorffii ◽  
Catalytic Functions

The vast abundance of terpene natural products in nature is due to enzymes known as terpene synthases (TPSs) that convert acyclic prenyl diphosphate precursors into a multitude of cyclic and acyclic carbon skeletons. Yet the evolution of TPSs is not well understood at higher levels of classification. Microbial TPSs from bacteria and fungi are only distantly related to typical plant TPSs, whereas genes similar to microbial TPS genes have been recently identified in the lycophyte Selaginella moellendorffii. The goal of this study was to investigate the distribution, evolution, and biochemical functions of microbial terpene synthase-like (MTPSL) genes in other plants. By analyzing the transcriptomes of 1,103 plant species ranging from green algae to flowering plants, putative MTPSL genes were identified predominantly from nonseed plants, including liverworts, mosses, hornworts, lycophytes, and monilophytes. Directed searching for MTPSL genes in the sequenced genomes of a wide range of seed plants confirmed their general absence in this group. Among themselves, MTPSL proteins from nonseed plants form four major groups, with two of these more closely related to bacterial TPSs and the other two to fungal TPSs. Two of the four groups contain a canonical aspartate-rich “DDxxD” motif. The third group has a “DDxxxD” motif, and the fourth group has only the first two “DD” conserved in this motif. Upon heterologous expression, representative members from each of the four groups displayed diverse catalytic functions as monoterpene and sesquiterpene synthases, suggesting these are important for terpene formation in nonseed plants.

scholarly journals Multiple large-scale gene and genome duplications during the evolution of hexapods

2018 ◽  
Vol 115 (18) ◽  
pp. 4713-4718 ◽  
Author(s):  
Zheng Li ◽  
George P. Tiley ◽  
Sally R. Galuska ◽  
Chris R. Reardon ◽  
Thomas I. Kidder ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Large Scale ◽  
Plant Evolution ◽  
Minor Role ◽  
Animal Evolution ◽  
Gene Retention ◽  
Insect Phylogeny ◽  
Genome Duplications ◽  
History Of ◽  
Gene Age

Polyploidy or whole genome duplication (WGD) is a major contributor to genome evolution and diversity. Although polyploidy is recognized as an important component of plant evolution, it is generally considered to play a relatively minor role in animal evolution. Ancient polyploidy is found in the ancestry of some animals, especially fishes, but there is little evidence for ancient WGDs in other metazoan lineages. Here we use recently published transcriptomes and genomes from more than 150 species across the insect phylogeny to investigate whether ancient WGDs occurred during the evolution of Hexapoda, the most diverse clade of animals. Using gene age distributions and phylogenomics, we found evidence for 18 ancient WGDs and six other large-scale bursts of gene duplication during insect evolution. These bursts of gene duplication occurred in the history of lineages such as the Lepidoptera, Trichoptera, and Odonata. To further corroborate the nature of these duplications, we evaluated the pattern of gene retention from putative WGDs observed in the gene age distributions. We found a relatively strong signal of convergent gene retention across many of the putative insect WGDs. Considering the phylogenetic breadth and depth of the insect phylogeny, this observation is consistent with polyploidy as we expect dosage balance to drive the parallel retention of genes. Together with recent research on plant evolution, our hexapod results suggest that genome duplications contributed to the evolution of two of the most diverse lineages of eukaryotes on Earth.

scholarly journals Polyploidy and the Evolution of Complex Traits

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Lukasz Huminiecki ◽  
Gavin C. Conant
Keyword(s):  
Complex Traits ◽  
Genome Duplication ◽  
Single Gene ◽  
Whole Genome ◽  
Gene Duplications ◽  
Evolutionary Potential ◽  
Evolutionary Transitions ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Modern Evolutionary Theory

We explore how whole-genome duplications (WGDs) may have given rise to complex innovations in cellular networks, innovations that could not have evolved through sequential single-gene duplications. We focus on two classical WGD events, one in bakers’ yeast and the other at the base of vertebrates (i.e., two rounds of whole-genome duplication: 2R-WGD). Two complex adaptations are discussed in detail: aerobic ethanol fermentation in yeast and the rewiring of the vertebrate developmental regulatory network through the 2R-WGD. These two examples, derived from diverged branches on the eukaryotic tree, boldly underline the evolutionary potential of WGD in facilitating major evolutionary transitions. We close by arguing that the evolutionary importance of WGD may require updating certain aspects of modern evolutionary theory, perhaps helping to synthesize a new evolutionary systems biology.

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