scholarly journals One thousand plant transcriptomes and the phylogenomics of green plants

Nature ◽  
2019 ◽  
Vol 574 (7780) ◽  
pp. 679-685 ◽  
Author(s):  
Keyword(s):  
Genome Evolution ◽  
Nuclear Gene ◽  
Gene Families ◽  
Plant Genome ◽  
Gene Trees ◽  
Green Plants ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Multiple Species ◽  
The One

Abstract Green plants (Viridiplantae) include around 450,000–500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

scholarly journals Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions

GigaScience ◽  
2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Zheng Li ◽  
Michael S Barker
Keyword(s):  
Gene Family ◽  
False Positive Rate ◽  
Nuclear Gene ◽  
Plant Evolution ◽  
Plant Genome ◽  
Total Evidence ◽  
Whole Genome ◽  
Green Plants ◽  
Whole Genome Duplications ◽  
Genome Duplications

Abstract Background Polyploidy, or whole-genome duplications (WGDs), repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced >1,000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. As an accompaniment to the capstone publication, this article provides expanded methodological details, results validation, and descriptions of newly released datasets that will aid researchers who wish to use the extended data generated by the 1KP project. Results In the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place 244 putative ancient WGDs across the Viridiplantae. Here, we provide an expanded explanation of our approach by describing our methodology and walk-through examples. We also evaluated the consistency of our WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole-genome synteny analyses and our total evidence approach may minimize the false-positive rate throughout the dataset. Conclusions We release 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots from the 1KP capstone paper. These resources will be useful for many future analyses on gene and genome evolution in green plants.

scholarly journals Inferring putative ancient whole genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions

2019 ◽  
Author(s):  
Zheng Li ◽  
Michael S Barker
Keyword(s):  
Gene Family ◽  
Nuclear Gene ◽  
Plant Evolution ◽  
Plant Genome ◽  
Total Evidence ◽  
Whole Genome ◽  
Data Set ◽  
Green Plants ◽  
Whole Genome Duplications ◽  
Genome Duplications

AbstractPolyploidy or whole genome duplications (WGDs) repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced over 1000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. In the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place ancient WGDs. Overall, 244 putative ancient WGDs were inferred across the Viridiplantae. Here, we describe these analyses and evaluate the consistency of the WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole genome synteny analyses and our total evidence approach may minimize the false positive rate throughout the data set. Given these resources will be useful for many future analyses on gene and genome evolution in green plants, we release 383,679 nuclear gene family phylogenies and 2,306 gene age distribution (Ks) plots from the 1KP capstone paper.

scholarly journals Synteny-Guided Resolution of Gene Trees Clarifies the Functional Impact of Whole-Genome Duplications

2020 ◽  
Vol 37 (11) ◽  
pp. 3324-3337
Author(s):  
Elise Parey ◽  
Alexandra Louis ◽  
Cédric Cabau ◽  
Yann Guiguen ◽  
Hugues Roest Crollius ◽  
...  
Keyword(s):  
Gene Families ◽  
Sequence Evolution ◽  
Whole Genome ◽  
Gene Trees ◽  
Ensembl Database ◽  
Whole Genome Duplications ◽  
Gene Copies ◽  
Genome Duplications ◽  
Phenotypic Robustness ◽  
New Gene

Abstract Whole-genome duplications (WGDs) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-descended species, which hinders the exploration of functional consequences of WGDs. Here, we present Synteny-guided CORrection of Paralogies and Orthologies (SCORPiOs), a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-My-old WGD at the origin of teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,394) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art methods. Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade.

scholarly journals Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications

2020 ◽  
Author(s):  
Elise Parey ◽  
Alexandra Louis ◽  
Cédric Cabau ◽  
Yann Guiguen ◽  
Hugues Roest Crollius ◽  
...  
Keyword(s):  
Gene Families ◽  
Sequence Evolution ◽  
Whole Genome ◽  
Gene Trees ◽  
Ensembl Database ◽  
Whole Genome Duplications ◽  
Gene Copies ◽  
Genome Duplications ◽  
Phenotypic Robustness ◽  
New Gene

AbstractWhole genome duplications (WGD) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-descended species, which hinders the exploration of functional consequences of WGDs. Here we present SCORPiOs, a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-million-year-old WGD at the origin of teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,391) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art methods. Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade.

scholarly journals Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences

2021 ◽  
Vol 9 ◽  
Author(s):  
Madeleine E. Aase-Remedios ◽  
David E. K. Ferrier
Keyword(s):  
Chromosomal Rearrangements ◽  
Expression Patterns ◽  
Gene Families ◽  
Evolutionary Transitions ◽  
Whole Genome Duplications ◽  
Chordate Evolution ◽  
Genome Duplications ◽  
The Many ◽  
Genome Assemblies ◽  
The Impact

Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.

scholarly journals Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 259 ◽  
Author(s):  
Karolina Susek ◽  
Wojciech Bielski ◽  
Katarzyna B. Czyż ◽  
Robert Hasterok ◽  
Scott A. Jackson ◽  
...  
Keyword(s):  
Karyotype Evolution ◽  
Chromosomal Rearrangements ◽  
Chromosome Mapping ◽  
Artificial Chromosome ◽  
Basic Chromosome Number ◽  
Plant Genome ◽  
Old World ◽  
Whole Genome Duplications ◽  
Genome Duplications

Plant genome evolution can be very complex and challenging to describe, even within a genus. Mechanisms that underlie genome variation are complex and can include whole-genome duplications, gene duplication and/or loss, and, importantly, multiple chromosomal rearrangements. Lupins (Lupinus) diverged from other legumes approximately 60 mya. In contrast to New World lupins, Old World lupins show high variability not only for chromosome numbers (2n = 32–52), but also for the basic chromosome number (x = 5–9, 13) and genome size. The evolutionary basis that underlies the karyotype evolution in lupins remains unknown, as it has so far been impossible to identify individual chromosomes. To shed light on chromosome changes and evolution, we used comparative chromosome mapping among 11 Old World lupins, with Lupinus angustifolius as the reference species. We applied set of L. angustifolius-derived bacterial artificial chromosome clones for fluorescence in situ hybridization. We demonstrate that chromosome variations in the species analyzed might have arisen from multiple changes in chromosome structure and number. We hypothesize about lupin karyotype evolution through polyploidy and subsequent aneuploidy. Additionally, we have established a cytogenomic map of L. angustifolius along with chromosome markers that can be used for related species to further improve comparative studies of crops and wild lupins.

scholarly journals Cotton genome evolution and features of its structural and functional organization

2020 ◽  
Vol 65 (1) ◽  
Author(s):  
Ksenia Strygina ◽  
Elena Khlestkina ◽  
Larisa Podolnaya
Keyword(s):  
Genome Evolution ◽  
Functional Organization ◽  
Functional Divergence ◽  
Model Organism ◽  
Plant Genome ◽  
Individual Species ◽  
Expression Of Genes ◽  
Genome Duplications ◽  
Allotetraploid Species ◽  
Allotetraploid Cotton

Allotetraploid cotton Gossypium hirsutum L. is not only an important crop, but also a model organism used to study such processes as polyploidization, plant genome evolution and the influence of polyploidy on gene expression. The present article provides a review of studies devoted to the taxonomy of the genus Gossypium, the evolution of the genomes of its representatives (including 45 diploid and 7 allotetraploid species), and the functional divergence of duplicated copies of the same genes in allotetraploid species. The discussion concerns the areas of individual species’ origin, as well as the reasons of the high variation in genome size (from ~880 Mb to ~2400 Mb), which was influenced by both full-genome duplications and the spread of mobile genetic elements. The data support the fact that the expression of genes in allotetraploid cotton changes as a result of polyploidization, and that one of the two subgenomes dominates in the formation of one or another trait. The considered data shed light on the features of the evolution of plant genes and genomes.

scholarly journals New Insights into Ligand-Receptor Pairing and Coevolution of Relaxin Family Peptides and Their Receptors in Teleosts

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Sara Good ◽  
Sergey Yegorov ◽  
Joran Martijn ◽  
Jens Franck ◽  
Jan Bogerd
Keyword(s):  
Sequence Data ◽  
Gene Families ◽  
Theoretical Background ◽  
Whole Genome Duplications ◽  
Relaxin Family ◽  
Receptor Interactions ◽  
Genome Duplications ◽  
Show Evidence ◽  
Specific Receptors ◽  
Respective Function

Relaxin-like peptides (RLN/INSL) play diverse roles in reproductive and neuroendocrine processes in placental mammals and are functionally associated with two distinct types of receptors (RXFP) for each respective function. The diversification of RLN/INSL and RXFP gene families in vertebrates was predominantly driven by whole genome duplications (2R and 3R). Teleosts preferentially retained duplicates of genes putatively involved in neuroendocrine regulation, harboring a total of 10-11 receptors and 6 ligand genes, while most mammals have equal numbers of ligands and receptors. To date, the ligand-receptor relationships of teleost Rln/Insl peptides and their receptors have largely remained unexplored. Here, we use selection analyses based on sequence data from 5 teleosts and qPCR expression data from zebrafish to explore possible ligand-receptor pairings in teleosts. We find support for the hypothesis that, with the exception of RLN, which has undergone strong positive selection in mammalian lineages, the ligand and receptor genes shared between mammals and teleosts appear to have similar pairings. On the other hand, the teleost-specific receptors show evidence of subfunctionalization. Overall, this study underscores the complexity of RLN/INSL and RXFP ligand-receptor interactions in teleosts and establishes theoretical background for further experimental work in nonmammals.

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