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.

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 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 Evolution of Lysine-Specific Demethylase 1 and REST Corepressor Gene Families and Their Molecular Interaction

2021 ◽  
Author(s):  
Montserrat Olivares ◽  
Gianluca Merello ◽  
Daniel Verbel ◽  
Marcela Gonzalez ◽  
María Andrés ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Molecular Biology ◽  
Gene Families ◽  
Whole Genome ◽  
Model Species ◽  
Whole Genome Duplications ◽  
Lysine Specific Demethylase ◽  
Genome Duplications ◽  
History Of ◽  
The Common

Abstract Lysine-specific demethylase 1A (LSD1) binds to RCOR gene family of corepressors to erase transcriptionally active marks on histones. Functional diversity in these complexes depends on the type of RCOR included, which modulates the complex´s catalytic activity. We studied the duplicative history of RCOR and LSD gene families, and analyzed the evolution of their interaction. We found that RCOR genes are the product of the two rounds of whole-genome duplications that occurred early in vertebrate evolution. In contrast, the origin of the LSD genes traces back before to the divergence of animals and plants. Coimmunoprecipitation experiments using resurrected RCOR and LSD1 proteins of the jawed vertebrate ancestor, and the common hop, date the origin of LSD1-RCOR interaction to the ancestor of animals, fungi, and plants. Overall, we trace LSD1-RCOR complex evolution and propose that animal, fungi, and plant non-model species offer advantages in addressing questions about the molecular biology of this epigenetic complex.

scholarly journals The power of synteny : deep evolutionary insights from comparative genomics

2021 ◽  
Author(s):  
◽  
Richard Shawn Abrahams
Keyword(s):  
Sequence Data ◽  
Sequence Similarity ◽  
Gene Tree ◽  
Evolutionary Mechanisms ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Orthologous Locus ◽  
Orthology Detection ◽  
Insight Into

Synteny, or the order of genes in a given genome, is an emergent property of individuals and species that has only, with the implementation of next gen-sequencing, become available for evolutionary consideration. In this dissertation, I leverage syntenic information in concert with sequence data to draw connections between evolutionary mechanisms, species divergence, and trait innovation. In Chapter I, I review the major themes that ties my dissertation research together, highlighting important mechanisms at work in evolutionary complexity and introducing the system of which it will be a part. In Chapter II, I use a phylogenomic approach to better understand species relationships within the tribe. I utilize transcriptome sequences and genome derived synteny information to improve orthology detection over standard sequence similarity approaches and gain greater insight into the relationships of the tribe. I also implement differential fractionation rate orthology inference information to address gene tree-species tree incongruence. In Chapter III, as published in Abrahams et al., 2020, I utilize a microsynteny network and phylogenetic inference to investigate the origin and diversification of the MAM/IPMS gene family. I uncover unique MAM-like genes found at the orthologous locus in the Cleomaceae that shed light on the transition from IPMS to MAM. In the Brassicaceae, I identify six distinct MAM clades across Lineages I, II, and III. I characterize the evolutionary impact and consequences of local duplications, transpositions, whole genome duplications, and gene fusion events, generating several new hypotheses on the function and diversity of the MAM locus.

scholarly journals Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome

Nature Plants ◽  
2021 ◽  
Author(s):  
Liuyu Qin ◽  
Yiheng Hu ◽  
Jinpeng Wang ◽  
Xiaoliang Wang ◽  
Ran Zhao ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Sequence Data ◽  
Expression Patterns ◽  
Whole Genome ◽  
Angiosperm Evolution ◽  
Aristolochic Acids ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
High Quality Genome ◽  
Angiosperm Genome

AbstractAristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.

scholarly journals Widespread retention of ohnologs in key developmental gene families following whole genome duplication in arachnopulmonates

2020 ◽  
Author(s):  
Amber Harper ◽  
Luis Baudouin Gonzalez ◽  
Anna Schönauer ◽  
Michael Seiter ◽  
Michaela Holzem ◽  
...  
Keyword(s):  
Genetic Material ◽  
Gene Families ◽  
Comparative Approach ◽  
Whole Genome ◽  
Developmental Gene ◽  
Spider Species ◽  
Transcriptomic Data ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Horseshoe Crabs

AbstractWhole genome duplications (WGD) have occurred multiple times in the evolution of animals, including in the lineages leading to vertebrates, teleosts, horseshoe crabs and arachnopulmonates. These dramatic genomic events initially produce a wealth of new genetic material, which is generally followed by extensive gene loss. It appears that developmental genes such as homeobox genes, signalling pathway components and microRNAs, however, tend to be more frequently retained in duplicate following WGD (ohnologs). These not only provide the best evidence for the occurrence of WGD, but an opportunity to study its evolutionary implications. Although these genes are relatively well studied in the context of vertebrate WGD, genomic and transcriptomic data for independent comparison in other groups are scarce, with patchy sampling of only two of the five extant arachnopulmonate orders. To improve our knowledge of developmental gene repertoires, and their evolution since the arachnopulmonate WGD, we sequenced embryonic transcriptomes from two additional spider species and two whip spider species and surveyed them for three important gene families: Hox, Wnt and frizzled. We report extensive retention of ohnologs in all four species, further supporting the arachnopulmonate WGD hypothesis. Thanks to improved sampling we were able to identify patterns of likely ohnolog retention and loss within spiders, including apparent differences between major clades. The two amblypygid species have larger ohnolog repertoires of these genes than both spiders and scorpions; including the first reported duplicated Wnt1/wg, the first Wnt10 recovered in an arachnid, and broad retention of frizzled genes. These insights shed light on the evolution of the enigmatic whip spiders, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.

scholarly journals The unique genome architecture of the devastating West African cacao black pod pathogen Phytophthora megakarya

2019 ◽  
Author(s):  
Abraham Morales-Cruz ◽  
Shahin S. Ali ◽  
Andrea Minio ◽  
Rosa Figueroa-Balderas ◽  
Jadran F. García ◽  
...  
Keyword(s):  
Single Molecule ◽  
Central Africa ◽  
Gene Families ◽  
Genomic Diversity ◽  
Rxlr Effectors ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
West And Central Africa ◽  
Black Pod ◽  
Phytophthora Megakarya

ABSTRACTPhytophthora megakarya (Pmeg) and P. palmivora (Ppal) are oomycete pathogens that cause black pod rot of cacao (Theobroma cacao), the most economically important disease on cacao globally. While Ppal is a cosmopolitan pathogen, Pmeg, which is more aggressive on cacao than Ppal, has been reported only in West and Central Africa where it has been spreading and devastating cacao farms since the 1950s. In this study, we reconstructed the complete diploid genomes of multiple isolates of both species using single-molecule sequencing. Thirty-one additional genotypes were sequenced to analyze inter- and intra-species genomic diversity. These resources make it possible to better understand the molecular basis of virulence differences in closely related and consequential pathogens and study their evolutionary history. The Pmeg genome is exceptionally large (222 Mbp) and nearly twice the size Ppal (135 Mbp) and most known Phytophthora species (∼100 Mbp on average). We show that the genomes of both species recently expanded by independent whole-genome duplications (WGD). WGD and the dramatic transposable element associated expansion of a few gene families led to the exceptionally large genome and transcriptome of Pmeg and the diversification of virulence-related genes including secreted RxLR effectors. Finally, this study provides evidence of adaptive evolution among well-known effectors and discusses the implications of effector expansion and diversification.

scholarly journals Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage-specific whole-genome duplications

2014 ◽  
Vol 202 (3) ◽  
pp. 986-1000 ◽  
Author(s):  
Cyril Jourda ◽  
Céline Cardi ◽  
Didier Mbéguié-A-Mbéguié ◽  
Stéphanie Bocs ◽  
Olivier Garsmeur ◽  
...  
Keyword(s):  
Gene Families ◽  
Ethylene Biosynthesis ◽  
Musa Acuminata ◽  
Whole Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications
Sign in / Sign up

Export Citation Format

Share Document