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Article ; Online: Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences

Madeleine E. Aase-Remedios / David E. K. Ferrier

Frontiers in Ecology and Evolution, Vol

2021 Volume 9

Abstract: 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 ... ...

Abstract	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.
Keywords	amphioxus ; tunicates ; lamprey ; ohnologues ; subfunctionalisation ; rediploidization ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
Subject code	572
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Horizons in evolutionary genomics

David E. K. Ferrier

BMC Biology, Vol 16, Iss 1, Pp 1-

an interview with David Ferrier

2018 Volume 3

Abstract: Abstract David Ferrier is a Reader at the University of St Andrews and Deputy Director of the Scottish Oceans Institute, where his lab studies how the diversity of form in the animal kingdom evolved, with an emphasis on using comparative genomics. In ... ...

Abstract	Abstract David Ferrier is a Reader at the University of St Andrews and Deputy Director of the Scottish Oceans Institute, where his lab studies how the diversity of form in the animal kingdom evolved, with an emphasis on using comparative genomics. In this interview, David shares his thoughts on how to escape the ‘straitjacket’ of traditional model systems, transparency in peer review, and the past and future of genome sequencing.
Keywords	Evolution ; Development ; Genomics ; Homeobox ; Genome organization ; Phylogenetics ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2018-11-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Recent advances in understanding the roles of whole genome duplications in evolution [version 2; referees

Carol MacKintosh / David E.K. Ferrier

F1000Research, Vol

2 approved]

2018 Volume 6

Abstract: Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors ... ...

Abstract	Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life.
Keywords	Agriculture & Biotechnology ; Community Ecology & Biodiversity ; Developmental Evolution ; Evolutionary/Comparative Genetics ; Evolutionary Ecology ; Genomics ; Microbial Evolution & Genomics ; Plant Biochemistry & Physiology ; Plant-Biotic Interactions ; Plant Genetics & Gene Expression ; Plant Genomes & Evolution ; Plant Growth & Development ; Medicine ; R ; Science ; Q
Subject code	570 ; 580
Language	English
Publishing date	2018-03-01T00:00:00Z
Publisher	F1000 Research Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Recent advances in understanding the roles of whole genome duplications in evolution [version 1; referees

Carol MacKintosh / David E.K. Ferrier

F1000Research, Vol

2 approved]

2017 Volume 6

Abstract	Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life.
Keywords	Agriculture & Biotechnology ; Community Ecology & Biodiversity ; Developmental Evolution ; Evolutionary/Comparative Genetics ; Evolutionary Ecology ; Genomics ; Microbial Evolution & Genomics ; Plant Biochemistry & Physiology ; Plant-Biotic Interactions ; Plant Genetics & Gene Expression ; Plant Genomes & Evolution ; Plant Growth & Development ; Medicine ; R ; Science ; Q
Subject code	570 ; 580
Language	English
Publishing date	2017-08-01T00:00:00Z
Publisher	F1000 Research Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Amphioxus SYCP1: a case of retrogene replacement and co-option of regulatory elements adjacent to the ParaHox cluster

Garstang, MylesG / David E. K. Ferrier

Development genes and evolution. 2018 Jan., v. 228, no. 1

2018

Abstract: Retrogenes are formed when an mRNA is reverse-transcribed and reinserted into the genome in a location unrelated to the original locus. If this retrocopy inserts into a transcriptionally favourable locus and is able to carry out its original function, it ...

Abstract	Retrogenes are formed when an mRNA is reverse-transcribed and reinserted into the genome in a location unrelated to the original locus. If this retrocopy inserts into a transcriptionally favourable locus and is able to carry out its original function, it can, in rare cases, lead to retrogene replacement. This involves the original, often multi-exonic, parental copy being lost whilst the newer single-exon retrogene copy ‘replaces’ the role of the ancestral parent gene. One example of this is amphioxus SYCP1, a gene that encodes a protein used in synaptonemal complex formation during meiosis and which offers the opportunity to examine how a retrogene evolves after the retrogene replacement event. SYCP1 genes exist as large multi-exonic genes in most animals. AmphiSYCP1, however, contains a single coding exon of ~ 3200 bp and has inserted next to the ParaHox cluster of amphioxus, whilst the multi-exonic ancestral parental copy has been lost. Here, we show that AmphiSYCP1 has not only replaced its parental copy, but also has evolved additional regulatory function by co-opting a bidirectional promoter from the nearby AmphiCHIC gene. AmphiSYCP1 has also evolved a de novo, multi-exonic 5′untranslated region that displays distinct regulatory states, in the form of two different isoforms, and has evolved novel expression patterns during amphioxus embryogenesis in addition to its ancestral role in meiosis. The absence of ParaHox-like expression of AmphiSYCP1, despite its proximity to the ParaHox cluster, also suggests that this gene is not influenced by any potential pan-cluster regulatory mechanisms, which are seemingly restricted to only the ParaHox genes themselves.
Keywords	animals ; embryogenesis ; exons ; genes ; loci ; messenger RNA ; promoter regions ; synaptonemal complex ; transcription (genetics)
Language	English
Dates of publication	2018-01
Size	p. 13-30.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	1327962-2
ISSN	1432-041X ; 0949-944X
ISSN (online)	1432-041X
ISSN	0949-944X
DOI	10.1007/s00427-017-0600-9
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Pax3/7 duplicated and diverged independently in amphioxus, the basal chordate lineage

Thomas B. Barton-Owen / David E. K. Ferrier / Ildikó M. L. Somorjai

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 11

Abstract: Abstract The Pax3/7 transcription factor family is integral to developmental gene networks contributing to important innovations in vertebrate evolution, including the neural crest. The basal chordate lineage of amphioxus is ideally placed to understand ... ...

Abstract	Abstract The Pax3/7 transcription factor family is integral to developmental gene networks contributing to important innovations in vertebrate evolution, including the neural crest. The basal chordate lineage of amphioxus is ideally placed to understand the dynamics of the gene regulatory network evolution that produced these novelties. We report here the discovery that the cephalochordate lineage possesses two Pax3/7 genes, Pax3/7a and Pax3/7b. The tandem duplication is ancestral to all extant amphioxus, occurring in both Asymmetron and Branchiostoma, but originated after the split from the lineage leading to vertebrates. The two paralogues are differentially expressed during embryonic development, particularly in neural and somitic tissues, suggesting distinct regulation. Our results have implications for the study of amphioxus regeneration, neural plate and crest evolution, and differential tandem paralogue evolution.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2018-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mechanisms of Gene Duplication and Translocation and Progress towards Understanding Their Relative Contributions to Animal Genome Evolution

Olivia Mendivil Ramos / David E. K. Ferrier

International Journal of Evolutionary Biology, Vol

2012 Volume 2012

Keywords	Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Publishing date	2012-01-01T00:00:00Z
Publisher	Hindawi Publishing Corporation
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates

Michele Tinti / Catherine Johnson / Rachel Toth / David E. K. Ferrier / Carol MacKintosh

Open Biology, Vol 2, Iss

2012 Volume 7

Abstract: 14-3-3 proteins regulate cellular responses to stimuli by docking onto pairs of phosphorylated residues on target proteins. The present study shows that the human 14-3-3-binding phosphoproteome is highly enriched in 2R-ohnologues, which are proteins in ... ...

Abstract	14-3-3 proteins regulate cellular responses to stimuli by docking onto pairs of phosphorylated residues on target proteins. The present study shows that the human 14-3-3-binding phosphoproteome is highly enriched in 2R-ohnologues, which are proteins in families of two to four members that were generated by two rounds of whole genome duplication at the origin of the vertebrates. We identify 2R-ohnologue families whose members share a ‘lynchpin’, defined as a 14-3-3-binding phosphosite that is conserved across members of a given family, and aligns with a Ser/Thr residue in pro-orthologues from the invertebrate chordates. For example, the human receptor expression enhancing protein (REEP) 1–4 family has the commonest type of lynchpin motif in current datasets, with a phosphorylatable serine in the –2 position relative to the 14-3-3-binding phosphosite. In contrast, the second 14-3-3-binding sites of REEPs 1–4 differ and are phosphorylated by different kinases, and hence the REEPs display different affinities for 14-3-3 dimers. We suggest a conceptual model for intracellular regulation involving protein families whose evolution into signal multiplexing systems was facilitated by 14-3-3 dimer binding to lynchpins, which gave freedom for other regulatory sites to evolve. While increased signalling complexity was needed for vertebrate life, these systems also generate vulnerability to genetic disorders.
Keywords	branchiostoma ; ciona ; hereditary spastic paraplegia ; rab3gap1 ; rab3gap2 ; Biology (General) ; QH301-705.5
Subject code	500
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	The Royal Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Nereid on the rise

B. Duygu Özpolat / Nadine Randel / Elizabeth A. Williams / Luis Alberto Bezares-Calderón / Gabriele Andreatta / Guillaume Balavoine / Paola Y. Bertucci / David E. K. Ferrier / Maria Cristina Gambi / Eve Gazave / Mette Handberg-Thorsager / Jörg Hardege / Cameron Hird / Yu-Wen Hsieh / Jerome Hui / Kevin Nzumbi Mutemi / Stephan Q. Schneider / Oleg Simakov / Hernando M. Vergara /

Michel Vervoort / Gáspár Jékely / Kristin Tessmar-Raible / Florian Raible / Detlev Arendt

EvoDevo, Vol 12, Iss 1, Pp 1-

Platynereis as a model system

2021 Volume 22

Abstract: Abstract The Nereid Platynereis dumerilii (Audouin and Milne Edwards (Annales des Sciences Naturelles 1:195–269, 1833) is a marine annelid that belongs to the Nereididae, a family of errant polychaete worms. The Nereid shows a pelago-benthic life cycle: ... ...

Abstract	Abstract The Nereid Platynereis dumerilii (Audouin and Milne Edwards (Annales des Sciences Naturelles 1:195–269, 1833) is a marine annelid that belongs to the Nereididae, a family of errant polychaete worms. The Nereid shows a pelago-benthic life cycle: as a general characteristic for the superphylum of Lophotrochozoa/Spiralia, it has spirally cleaving embryos developing into swimming trochophore larvae. The larvae then metamorphose into benthic worms living in self-spun tubes on macroalgae. Platynereis is used as a model for genetics, regeneration, reproduction biology, development, evolution, chronobiology, neurobiology, ecology, ecotoxicology, and most recently also for connectomics and single-cell genomics. Research on the Nereid started with studies on eye development and spiralian embryogenesis in the nineteenth and early twentieth centuries. Transitioning into the molecular era, Platynereis research focused on posterior growth and regeneration, neuroendocrinology, circadian and lunar cycles, fertilization, and oocyte maturation. Other work covered segmentation, photoreceptors and other sensory cells, nephridia, and population dynamics. Most recently, the unique advantages of the Nereid young worm for whole-body volume electron microscopy and single-cell sequencing became apparent, enabling the tracing of all neurons in its rope-ladder-like central nervous system, and the construction of multimodal cellular atlases. Here, we provide an overview of current topics and methodologies for P. dumerilii, with the aim of stimulating further interest into our unique model and expanding the active and vibrant Platynereis community.
Keywords	Annelida ; Spiralia ; Marine model species ; Evo-devo ; Integrative biology ; Evolution ; QH359-425
Subject code	612
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Hox genes are not always Colinear

Ana Sara Monteiro, David E.K. Ferrier

International Journal of Biological Sciences, Vol 2, Iss 3, Pp 95-

2006 Volume 103

Abstract: The deuterostomes are the clade of animals for which we have the most detailed understanding of Hox cluster organisation. With the Hox cluster of amphioxus ( Branchiostoma floridae ) we have the best prototypical, least derived Hox cluster for the group, ...

Abstract	The deuterostomes are the clade of animals for which we have the most detailed understanding of Hox cluster organisation. With the Hox cluster of amphioxus ( Branchiostoma floridae ) we have the best prototypical, least derived Hox cluster for the group, whilst the urochordates present us with some of the most highly derived and disintegrated clusters. Combined with the detailed mechanistic understanding of vertebrate Hox regulation, the deuterostomes provide much of the most useful data for understanding Hox cluster evolution. Considering both the prototypical and derived deuterostome Hox clusters leads us to hypothesize that Temporal Colinearity is the main constraining force on Hox cluster organisation, but until we have a much deeper understanding of the mechanistic basis for this phenomenon, and know how widespread across the Bilateria the mechanism(s) is/are, then we cannot know how the Hox cluster of the last common bilaterian operated and what have been the major evolutionary forces operating upon the Hox gene cluster.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2006-01-01T00:00:00Z
Publisher	Ivyspring International Publisher
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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