Gene duplications and the origins of vertebrate development

Development ◽  
1994 ◽  
Vol 1994 (Supplement) ◽  
pp. 125-133 ◽  
Author(s):  
Peter W. H. Holland ◽  
Jordi Garcia-Fernàndez ◽  
Nic A. Williams ◽  
Arend Sidow
Keyword(s):  
Gene Duplication ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Homeobox Gene ◽  
Gene Families ◽  
Gene Clusters ◽  
Second Phase ◽  
Genetic Changes ◽  
New Genes ◽  
Duplication Events

All vertebrates possess anatomical features not seen in their closest living relatives, the protochordates (tunicates and amphioxus). Some of these features depend on developmental processes or cellular behaviours that are again unique to vertebrates. We are interested in the genetic changes that may have permitted the origin of these innovations. Gene duplication, followed by functional divergence of new genes, may be one class of mutation that permits major evolutionary change. Here we examine the hypothesis that gene duplication events occurred close to the origin and early radiation of the vertebrates. Genome size comparisons are compatible with the occurrence of duplications close to vertebrate origins; more precise insight comes from cloning and phylogenetic analysis of gene families from amphioxus, tunicates and vertebrates. Comparisons of Hox gene clusters, other homeobox gene families, Wnt genes and insulin-related genes all indicate that there was a major phase of gene duplication close to vertebrate origins, after divergence from the amphioxus lineage; we suggest there was probably a second phase of duplication close to jawed vertebrate origins. From amphioxus and vertebrate homeobox gene expression patterns, we suggest that there are multiple routes by which new genes arising from gene duplication acquire new functions and permit the evolution of developmental innovations.

scholarly journals Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

2021 ◽  
Author(s):  
Laszlo G Nagy ◽  
Peter Jan Vonk ◽  
Markus Kunzler ◽  
Csenge Foldi ◽  
Mate Viragh ◽  
...  
Keyword(s):  
Cell Wall ◽  
Fruiting Body ◽  
Expression Patterns ◽  
Schizophyllum Commune ◽  
Gene Families ◽  
Second Phase ◽  
Fruiting Bodies ◽  
Body Development ◽  
Fruiting Body Development

Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates tissue differentiation, growth and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim to comprehensively identify conserved genes related to fruiting body morphogenesis and distill novel functional hypotheses for functionally poorly characterized genes. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide informed hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defense, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10% of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Key words: functional annotation; comparative genomics; cell wall remodeling; development; fruiting body morphogenesis; mushroom; transcriptome

scholarly journals Integrative Analysis of miRNA-mRNA and miRNA-miRNA Interactions

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Li Guo ◽  
Yang Zhao ◽  
Sheng Yang ◽  
Hui Zhang ◽  
Feng Chen
Keyword(s):  
Expression Patterns ◽  
Gene Families ◽  
Gene Clusters ◽  
Integrative Analysis ◽  
Biological Processes ◽  
Change Analysis ◽  
Functional Relationships ◽  
Collaborative Interactions ◽  
Or Gene ◽  
Fold Change Analysis

MicroRNAs (miRNAs) are small, noncoding regulatory molecules. They are involved in many essential biological processes and act by suppressing gene expression. The present work reports an integrative analysis of miRNA-mRNA and miRNA-miRNA interactions and their regulatory patterns using high-throughput miRNA and mRNA datasets. Aberrantly expressed miRNA and mRNA profiles were obtained based on fold change analysis, and qRT-PCR was used for further validation of deregulated miRNAs. miRNAs and target mRNAs were found to show various expression patterns. miRNA-miRNA interactions and clustered/homologous miRNAs were also found to contribute to the flexible and selective regulatory network. Interacting miRNAs (e.g., miRNA-103a and miR-103b) showed more pronounced differences in expression, which suggests the potential “restricted interaction” in the miRNA world. miRNAs from the same gene clusters (e.g., miR-23b gene cluster) or gene families (e.g., miR-10 gene family) always showed the same types of deregulation patterns, although they sometimes differed in expression levels. These clustered and homologous miRNAs may have close functional relationships, which may indicate collaborative interactions between miRNAs. The integrative analysis of miRNA-mRNA based on biological characteristics of miRNA will further enrich miRNA study.

scholarly journals Enhanced functional divergence of duplicate genes several million years after gene duplication in the Arabidopsis lineage

2016 ◽  
Author(s):  
Kousuke Hanada ◽  
Ayumi Tezuka ◽  
Masafumi Nozawa ◽  
Yutaka Suzuki ◽  
Sumio Sugano ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Synonymous Substitution ◽  
Duplicate Genes ◽  
Duplicated Genes ◽  
Highly Qualified ◽  
Duplication Events ◽  
Synonymous Substitution Rates

AbstractLineage-specifically duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selective pressures immediately after gene duplication is clear in the speciation process. Plants have substantially higher gene duplication rates than most other eukaryotes. Here, using Illumina short reads from Arabidopsis halleri, which has highly qualified plant genomes in close species (Brassica rapa, A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups among B. rapa, A. thaliana, A. lyrata and A. halleri. The frequency of duplication events in the Arabidopsis lineage was approximately 10 times higher than the frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss. Of the currently retained genes in A. halleri, 11–24% had undergone gene duplication in the Arabidopsis lineage. To examine the degree of selective pressure for duplicated genes, we calculated the ratios of nonsynonymous to synonymous substitution rates (KA/KS) in the A. halleri-lyrata and A. halleri lineages. Using a maximum-likelihood framework, we examined positive (KA/KS > 1) and purifying selection (KA/KS < 1) at a significant level (P < 0.01). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. More interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication at a higher proportion than immediately after gene duplication.

scholarly journals GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow

2016 ◽  
Author(s):  
Anil S. Thanki ◽  
Nicola Soranzo ◽  
Wilfried Haerty ◽  
Robert P. Davey
Keyword(s):  
Gene Duplication ◽  
Structural Changes ◽  
Gene Families ◽  
Vital Role ◽  
Software Project ◽  
Command Line ◽  
Gene Trees ◽  
Ancestral Gene ◽  
The Galaxy ◽  
Duplication Events

AbstractBackgroundGene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL and HomoloGene, to identify gene families and visualise syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families.FindingsA certain amount of expertise is required to configure and run the Ensembl Compara GeneTrees pipeline via command line. Therefore, we have converted the command line Ensembl Compara GeneTrees pipeline into a Galaxy workflow, called GeneSeqToFamily, and provided additional functionality. This workflow uses existing tools from the Galaxy ToolShed, as well as providing additional wrappers and tools that are required to run the workflow.ConclusionsGeneSeqToFamily represents the Ensembl Compara pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxy’s user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualise the gene families produced by the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project.

scholarly journals Comparative Phylogenomic Synteny Network Analysis of Mammalian and Angiosperm Genomes

2018 ◽  
Author(s):  
Tao Zhao ◽  
M. Eric Schranz
Keyword(s):  
Large Scale ◽  
Homeobox Gene ◽  
Gene Families ◽  
Gene Clusters ◽  
Parahox Gene ◽  
Family Networks ◽  
Plant Genomes ◽  
Eukaryotic Gene ◽  
Syntenic Gene ◽  
Phylogenetic Profiling

AbstractBackgroundSynteny analysis is a valuable approach for understanding eukaryotic gene and genome evolution, but still relies largely on pairwise or reference-based comparisons. Network approaches can be utilized to expand large-scale phylogenomic microsynteny studies. There is now a wealth of completed mammalian (animal) and angiosperm (plant) genomes, two very important lineages that have evolved and radiated over the last ~170 million years. Genomic organization and conservation differs greatly between these two groups; however, a systematic and comparative characterization of synteny between the two lineages using the same approaches and metrics has not been undertaken.ResultsWe have built complete microsynteny networks for 87 mammalian and 107 angiosperm genomes, which contain 1,464,753 nodes (genes) and 49,426,268 edges (syntenic connections between genes) for mammals, and 2,234,461 nodes and 46,938,272 edges for angiosperms, respectively. Exploiting network statistics, we present the functional characteristics of extremely conserved and diversified gene families. We summarize the features of all syntenic gene clusters and present lineage-wide phylogenetic profiling, revealing intriguing sub-clade lineage-specific clusters. We depict several representative clusters of important developmental genes in humans, such as CENPJ, p53 and NFE2. Finally, we present the complete homeobox gene family networks for both mammals (including Hox and ParaHox gene clusters) and angiosperms.ConclusionsOur results illustrate and quantify overall synteny conservation and diversification properties of all annotated genes for mammals and angiosperms and show that plant genomes are in general more dynamic.

scholarly journals Evolutionary Pattern and Regulation Analysis to Support Why Diversity Functions Existed within PPAR Gene Family Members

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Tianyu Zhou ◽  
Xiping Yan ◽  
Guosong Wang ◽  
Hehe Liu ◽  
Xiang Gan ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Hormone Receptors ◽  
Expression Patterns ◽  
Family Members ◽  
Duplication Event ◽  
Promoter Regions ◽  
Evolutionary Pattern ◽  
Duplication Events ◽  
Differential Transcription

Peroxisome proliferators-activated receptor (PPAR) gene family members exhibit distinct patterns of distribution in tissues and differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events. The conserved domains of HOLI (ligand binding domain of hormone receptors) domain and ZnF_C4 (C4 zinc finger in nuclear in hormone receptors) are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity functions. The evolutionary variants in the promoter regions and 3′ UTR regions of PPARs result into differential transcription factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions. These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3′ UTR are essential for PPARs evolution and diversity functions acquired.

scholarly journals Genome-Wide Identification and Characterization of the PERK Gene Family in Gossypium hirsutum Reveals Gene Duplication and Functional Divergence

2019 ◽  
Vol 20 (7) ◽  
pp. 1750 ◽  
Author(s):  
Ghulam Qanmber ◽  
Ji Liu ◽  
Daoqian Yu ◽  
Zhao Liu ◽  
Lili Lu ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Plant Species ◽  
Functional Divergence ◽  
Rapid Evolution ◽  
Purifying Selection ◽  
Gene Families ◽  
Promoter Regions ◽  
Large Gene ◽  
Receptor Kinases

Proline-rich extensin-like receptor kinases (PERKs) are an important class of receptor kinases in plants. Receptor kinases comprise large gene families in many plant species, including the 15 PERK genes in Arabidopsis. At present, there is no comprehensive published study of PERK genes in G. hirsutum. Our study identified 33 PERK genes in G. hirsutum. Phylogenetic analysis of conserved PERK protein sequences from 15 plant species grouped them into four well defined clades. The GhPERK gene family is an evolutionarily advanced gene family that lost its introns over time. Several cis-elements were identified in the promoter regions of the GhPERK genes that are important in regulating growth, development, light responses and the response to several stresses. In addition, we found evidence for gene loss or addition through segmental or whole genome duplication in cotton. Gene duplication and synteny analysis identified 149 orthologous/paralogous gene pairs. Ka/Ks values show that most GhPERK genes experienced strong purifying selection during the rapid evolution of the gene family. GhPERK genes showed high expression levels in leaves and during ovule development. Furthermore, the expression of GhPERK genes can be regulated by abiotic stresses and phytohormone treatments. Additionally, PERK genes could be involved in several molecular, biological and physiological processes that might be the result of functional divergence.

scholarly journals Population genomics of two closely related anhydrobiotic midges reveals differences in adaptation to extreme desiccation

2020 ◽  
Author(s):  
N.M. Shaykhutdinov ◽  
G.V. Klink ◽  
S.K. Garushyants ◽  
O.S. Kozlova ◽  
A.V. Cherkasov ◽  
...  
Keyword(s):  
Population Genomics ◽  
Expression Profiles ◽  
Gene Families ◽  
Genomic Region ◽  
Ancestral Gene ◽  
New Genes ◽  
Protective Genes ◽  
Duplication Events ◽  
Polypedilum Vanderplanki ◽  
The Sleeping Chironomid

AbstractThe sleeping chironomid Polypedilum vanderplanki is capable of anhydrobiosis, a striking example of adaptation to extreme desiccation. Tolerance to complete desiccation in this species is associated with the emergence of multiple paralogs of protective genes. One of the gene families highly expressed under anhydrobiosis and involved in this process are protein-L-isoaspartate (D-aspartate) O-methyltransferases (PIMTs). Recently, a closely related anhydrobiotic midge from Malawi, P. pembai, showing the ability to tolerate complete desiccation similar to that of P. vanderplanki, but experiences more frequent desiccation-rehydration cycles due to differences in ecology, was discovered. Here, we sequenced and assembled the genome of P. pembai and performed a population genomics analysis of several populations of P. vanderplanki and a population of P. pembai. We observe positive selection and radical changes in the genetic architecture of the PIMT locus between the two species, including multiple duplication events in the P. pembai lineage. In particular, PIMT-4, the most highly expressed of these PIMTs, is present in six copies in the P. pembai; these copies differ in expression profiles, suggesting possible sub- or neofunctionalization. The nucleotide diversity (π) of the genomic region carrying these new genes is decreased in P. pembai, but not in the orthologous region carrying the ancestral gene in P. vanderplanki, providing evidence for a selective sweep associated with post-duplication adaptation in the former. Overall, our results suggest an extensive recent and likely ongoing, adaptation of the mechanisms of anhydrobiosis.

scholarly journals Genome-Wide Prediction, Functional Divergence, and Characterization of Stress-Responsive BZR Transcription Factors in B. napus

2022 ◽  
Vol 12 ◽  
Author(s):  
Rehman Sarwar ◽  
Rui Geng ◽  
Lei Li ◽  
Yue Shan ◽  
Ke-Ming Zhu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Future Research ◽  
Plant Tolerance ◽  
Specific Expression ◽  
Biotic Stresses ◽  
Organ Specific ◽  
Duplication Events

BRASSINAZOLE RESISTANT (BZR) are transcriptional factors that bind to the DNA of targeted genes to regulate several plant growth and physiological processes in response to abiotic and biotic stresses. However, information on such genes in Brassica napus is minimal. Furthermore, the new reference Brassica napus genome offers an excellent opportunity to systematically characterize this gene family in B. napus. In our study, 21 BnaBZR genes were distributed across 19 chromosomes of B. napus and clustered into four subgroups based on Arabidopsis thaliana orthologs. Functional divergence analysis among these groups evident the shifting of evolutionary rate after the duplication events. In terms of structural analysis, the BnaBZR genes within each subgroup are highly conserved but are distinctive within groups. Organ-specific expression analyses of BnaBZR genes using RNA-seq data and quantitative real-time polymerase chain reaction (qRT-PCR) revealed complex expression patterns in plant tissues during stress conditions. In which genes belonging to subgroups III and IV were identified to play central roles in plant tolerance to salt, drought, and Sclerotinia sclerotiorum stress. The insights from this study enrich our understanding of the B. napus BZR gene family and lay a foundation for future research in improving rape seed environmental adaptability.

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