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Papadogiannis V, Hockman D, Mercurio S, Ramsay C, Hintze M, Patthey C, Streit A, Shimeld SM. Evolution of the expression and regulation of the nuclear hormone receptor ERR gene family in the chordate lineage. Dev Biol 2023; 504:12-24. [PMID: 37696353 DOI: 10.1016/j.ydbio.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/01/2023] [Accepted: 09/09/2023] [Indexed: 09/13/2023]
Abstract
The Estrogen Related Receptor (ERR) nuclear hormone receptor genes have a wide diversity of roles in vertebrate development. In embryos, ERR genes are expressed in several tissues, including the central and peripheral nervous systems. Here we seek to establish the evolutionary history of chordate ERR genes, their expression and their regulation. We examine ERR expression in mollusc, amphioxus and sea squirt embryos, finding the single ERR orthologue is expressed in the nervous system in all three, with muscle expression also found in the two chordates. We show that most jawed vertebrates and lampreys have four ERR paralogues, and that vertebrate ERR genes were ancestrally linked to Estrogen Receptor genes. One of the lamprey paralogues shares conserved expression domains with jawed vertebrate ERRγ in the embryonic vestibuloacoustic ganglion, eye, brain and spinal cord. Hypothesising that conserved expression derives from conserved regulation, we identify a suite of pan-vertebrate conserved non-coding sequences in ERR introns. We use transgenesis in lamprey and chicken embryos to show that these sequences are regulatory and drive reporter gene expression in the nervous system. Our data suggest an ancient association between ERR and the nervous system, including expression in cells associated with photosensation and mechanosensation. This includes the origin in the vertebrate common ancestor of a suite of regulatory elements in the 3' introns that drove nervous system expression and have been conserved from this point onwards.
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Affiliation(s)
| | - Dorit Hockman
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Silvia Mercurio
- Department of Environmental Science and Policy, Università Degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Claire Ramsay
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Mark Hintze
- Centre for Craniofacial & Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Cedric Patthey
- Department of Radiosciences, Umeå University, 901 85, Umeå, Sweden
| | - Andrea Streit
- Centre for Craniofacial & Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Sebastian M Shimeld
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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2
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Abstract
Sabellida Levinsen, 1883 is a large morphologically uniform group of sedentary annelids commonly known as fanworms. These annelids live in tubes made either of calcareous carbonate or mucus with agglutinated sediment. They share the presence of an anterior crown consisting of radioles and the division of the body into thorax and abdomen marked by a chaetal and fecal groove inversion. This study synthesises the current state of knowledge about the diversity of fanworms in the broad sense (morphological, ecological, species richness), the species occurrences in the different biogeographic regions, highlights latest surveys, provides guidelines for identification of members of each group, and describe novel methodologies for species delimitation. As some members of this group are well-known introduced pests, we address information about these species and their current invasive status. In addition, an overview of the current evolutionary hypothesis and history of the classification of members of Sabellida is presented. The main aim of this review is to highlight the knowledge gaps to stimulate research in those directions.
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Ponz-Segrelles G, Ribeiro RP, Bleidorn C, Aguado Molina MT. Sex-specific gene expression differences in reproducing Syllis prolifera and Nudisyllis pulligera (Annelida, Syllidae). Mar Genomics 2020; 54:100772. [DOI: 10.1016/j.margen.2020.100772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/02/2020] [Accepted: 04/02/2020] [Indexed: 01/22/2023]
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Jiang L, Bi D, Ding H, Wu X, Zhu R, Zeng J, Yang X, Kan X. Systematic Identification and Evolution Analysis of Sox Genes in Coturnix japonica Based on Comparative Genomics. Genes (Basel) 2019; 10:genes10040314. [PMID: 31013663 PMCID: PMC6523956 DOI: 10.3390/genes10040314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/16/2019] [Accepted: 04/20/2019] [Indexed: 01/04/2023] Open
Abstract
Coturnix japonica (Japanese quail) has been extensively used as a model animal for biological studies. The Sox gene family, which was systematically characterized by a high-mobility group (HMG-box) in many animal species, encodes transcription factors that play central roles during multiple developmental processes. However, genome-wide investigations on the Sox gene family in birds are scarce. In the current study, we first performed a genome-wide study to explore the Sox gene family in galliform birds. Based on available genomic sequences retrieved from the NCBI database, we focused on the global identification of the Sox gene family in C. japonica and other species in Galliformes, and the evolutionary relationships of Sox genes. In our result, a total of 35 Sox genes in seven groups were identified in the C. japonica genome. Our results also revealed that dispersed gene duplications contributed the most to the expansion of the Sox gene family in Galliform birds. Evolutionary analyses indicated that Sox genes are an ancient gene family, and strong purifying selections played key roles in the evolution of CjSox genes of C. japonica. More interestingly, we observed that most Sox genes exhibited highly embryo-specific expression in both gonads. Our findings provided new insights into the molecular function and phylogeny of Sox gene family in birds.
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Affiliation(s)
- Lan Jiang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650000, China.
| | - De Bi
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Hengwu Ding
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, 241000, China.
| | - Xuan Wu
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Ran Zhu
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Juhua Zeng
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Xiaojun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650000, China.
| | - Xianzhao Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, 241000, China.
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Barton-Owen TB, Szabó R, Somorjai IML, Ferrier DEK. A Revised Spiralian Homeobox Gene Classification Incorporating New Polychaete Transcriptomes Reveals a Diverse TALE Class and a Divergent Hox Gene. Genome Biol Evol 2018; 10:2151-2167. [PMID: 29986009 PMCID: PMC6118893 DOI: 10.1093/gbe/evy144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2018] [Indexed: 11/13/2022] Open
Abstract
The diversity of mechanisms and capacity for regeneration across the Metazoa present an intriguing challenge in evolutionary biology, impacting on the burgeoning field of regenerative medicine. Broad taxonomic sampling is essential to improve our understanding of regeneration, and studies outside of the traditional model organisms have proved extremely informative. Within the historically understudied Spiralia, the Annelida have an impressive variety of tractable regenerative systems. The biomeralizing, blastema-less regeneration of the head appendage (operculum) of the serpulid polychaete keelworm Spirobranchus (formerly Pomatoceros) lamarcki is one such system. To profile potential regulatory mechanisms, we classified the homeobox gene content of opercular regeneration transcriptomes. As a result of retrieving several difficult-to-classify homeobox sequences, we performed an extensive search and phylogenetic analysis of the TALE and PRD-class homeobox gene content of a broad selection of lophotrochozoan genomes. These analyses contribute to our increasing understanding of the diversity, taxonomic extent, rapid evolution, and radical flexibility of these recently discovered homeobox gene radiations. Our expansion and integration of previous nomenclature systems helps to clarify their cryptic orthology. We also describe an unusual divergent S. lamarcki Antp gene, a previously unclassified lophotrochozoan orphan gene family (Lopx), and a number of novel Nk class orphan genes. The expression and potential involvement of many of these lineage- and clade-restricted homeobox genes in S. lamarcki operculum regeneration provides an example of diversity in regenerative mechanisms, as well as significantly improving our understanding of homeobox gene evolution.
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Affiliation(s)
- Thomas B Barton-Owen
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St. Andrews, United Kingdom
- The Biomedical Sciences Research Complex, School of Biology, University of St. Andrews, United Kingdom
| | - Réka Szabó
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St. Andrews, United Kingdom
| | - Ildiko M L Somorjai
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St. Andrews, United Kingdom
- The Biomedical Sciences Research Complex, School of Biology, University of St. Andrews, United Kingdom
| | - David E K Ferrier
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St. Andrews, United Kingdom
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Kenny NJ, Namigai EKO, Marlétaz F, Hui JHL, Shimeld SM. Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). Mar Genomics 2015; 24 Pt 2:139-46. [PMID: 26319627 DOI: 10.1016/j.margen.2015.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 06/19/2015] [Accepted: 07/14/2015] [Indexed: 12/01/2022]
Abstract
MicroRNAs (miRNA) are small non-coding RNAs that act post-transcriptionally to regulate gene expression levels. Some studies have indicated that microRNAs may have low homoplasy, and as a consequence the phylogenetic distribution of microRNA families has been used to study animal evolutionary relationships. Limited levels of lineage sampling, however, may distort such analyses. Lophotrochozoa is an under-sampled taxon that includes molluscs, annelids and nemerteans, among other phyla. Here, we present two novel draft genomes, those of the limpet Patella vulgata and polychaete Spirobranchus (Pomatoceros) lamarcki. Surveying these genomes for known microRNAs identifies numerous potential orthologues, including a number that have been considered to be confined to other lineages. RT-PCR demonstrates that some of these (miR-1285, miR-1287, miR-1957, miR-1983 and miR-3533), previously thought to be found only in vertebrates, are expressed. This study provides genomic resources for two lophotrochozoans and reveals patterns of microRNA evolution that could be hidden by more restricted sampling.
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Affiliation(s)
- Nathan J Kenny
- Simon F.S. Li Marine Science Laboratory of School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | | | | | - Jerome H L Hui
- Simon F.S. Li Marine Science Laboratory of School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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Kenny NJ, Shen X, Chan TTH, Wong NWY, Chan TF, Chu KH, Lam HM, Hui JHL. Genome of the Rusty Millipede, Trigoniulus corallinus, Illuminates Diplopod, Myriapod, and Arthropod Evolution. Genome Biol Evol 2015; 7:1280-95. [PMID: 25900922 PMCID: PMC4453065 DOI: 10.1093/gbe/evv070] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2015] [Indexed: 12/21/2022] Open
Abstract
The increasing availability of genomic information from the Arthropoda continues to revolutionize our understanding of the biology of this most diverse animal phylum. However, our sampling of arthropod diversity remains uneven, and key clade such as the Myriapoda are severely underrepresented. Here we present the genome of the cosmopolitanly distributed Rusty Millipede Trigoniulus corallinus, which represents the first diplopod genome to be published, and the second example from the Myriapoda as a whole. This genomic resource contains the majority of core eukaryotic genes (94.3%), and key transcription factor classes that were thought to be lost in the Ecdysozoa. Mitochondrial genome and gene family (transcription factor, Dscam, circadian clock-driving protein, odorant receptor cassette, bioactive compound, and cuticular protein) analyses were also carried out to shed light on their states in the Diplopoda and Myriapoda. The ready availability of T. corallinus recommends it as a new model for evolutionary developmental biology, and the data set described here will be of widespread utility in investigating myriapod and arthropod genomics and evolution.
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Affiliation(s)
- Nathan J Kenny
- Simon F.S. Li Marine Science Laboratory of School of Life Sciences and Center of Soybean Research of State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xin Shen
- Center of Soybean Research of State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Thomas T H Chan
- Simon F.S. Li Marine Science Laboratory of School of Life Sciences and Center of Soybean Research of State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Nicola W Y Wong
- Simon F.S. Li Marine Science Laboratory of School of Life Sciences and Center of Soybean Research of State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ting Fung Chan
- Center of Soybean Research of State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ka Hou Chu
- Simon F.S. Li Marine Science Laboratory of School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hon-Ming Lam
- Center of Soybean Research of State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jerome H L Hui
- Simon F.S. Li Marine Science Laboratory of School of Life Sciences and Center of Soybean Research of State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
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Mbandi SK, Hesse U, van Heusden P, Christoffels A. Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms. BMC Bioinformatics 2015; 16:58. [PMID: 25880035 PMCID: PMC4344733 DOI: 10.1186/s12859-015-0492-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 02/06/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND De novo transcriptome assembly of short transcribed fragments (transfrags) produced from sequencing-by-synthesis technologies often results in redundant datasets with differing levels of unassembled, partially assembled or mis-assembled transcripts. Post-assembly processing intended to reduce redundancy typically involves reassembly or clustering of assembled sequences. However, these approaches are mostly based on common word heuristics and often create clusters of biologically unrelated sequences, resulting in loss of unique transfrags annotations and propagation of mis-assemblies. RESULTS Here, we propose a structured framework that consists of a few steps in pipeline architecture for Inferring Functionally Relevant Assembly-derived Transcripts (IFRAT). IFRAT combines 1) removal of identical subsequences, 2) error tolerant CDS prediction, 3) identification of coding potential, and 4) complements BLAST with a multiple domain architecture annotation that reduces non-specific domain annotation. We demonstrate that independent of the assembler, IFRAT selects bona fide transfrags (with CDS and coding potential) from the transcriptome assembly of a model organism without relying on post-assembly clustering or reassembly. The robustness of IFRAT is inferred on RNA-Seq data of Neurospora crassa assembled using de Bruijn graph-based assemblers, in single (Trinity and Oases-25) and multiple (Oases-Merge and additive or pooled) k-mer modes. Single k-mer assemblies contained fewer transfrags compared to the multiple k-mer assemblies. However, Trinity identified a comparable number of predicted coding sequence and gene loci to Oases pooled assembly. IFRAT selects bona fide transfrags representing over 94% of cumulative BLAST-derived functional annotations of the unfiltered assemblies. Between 4-6% are lost when orphan transfrags are excluded and this represents only a tiny fraction of annotation derived from functional transference by sequence similarity. The median length of bona fide transfrags ranged from 1.5kb (Trinity) to 2kb (Oases), which is consistent with the average coding sequence length in fungi. The fraction of transfrags that could be associated with gene ontology terms ranged from 33-50%, which is also high for domain based annotation. We showed that unselected transfrags were mostly truncated and represent sequences from intronic, untranslated (5' and 3') regions and non-coding gene loci. CONCLUSIONS IFRAT simplifies post-assembly processing providing a reference transcriptome enriched with functionally relevant assembly-derived transcripts for non-model organism.
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Affiliation(s)
- Stanley Kimbung Mbandi
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
| | - Uljana Hesse
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
| | - Peter van Heusden
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
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Genomic sequence and experimental tractability of a new decapod shrimp model, Neocaridina denticulata. Mar Drugs 2014; 12:1419-37. [PMID: 24619275 PMCID: PMC3967219 DOI: 10.3390/md12031419] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/23/2014] [Accepted: 02/28/2014] [Indexed: 12/14/2022] Open
Abstract
The speciose Crustacea is the largest subphylum of arthropods on the planet after the Insecta. To date, however, the only publically available sequenced crustacean genome is that of the water flea, Daphnia pulex, a member of the Branchiopoda. While Daphnia is a well-established ecotoxicological model, previous study showed that one-third of genes contained in its genome are lineage-specific and could not be identified in any other metazoan genomes. To better understand the genomic evolution of crustaceans and arthropods, we have sequenced the genome of a novel shrimp model, Neocaridina denticulata, and tested its experimental malleability. A library of 170-bp nominal fragment size was constructed from DNA of a starved single adult and sequenced using the Illumina HiSeq2000 platform. Core eukaryotic genes, the mitochondrial genome, developmental patterning genes (such as Hox) and microRNA processing pathway genes are all present in this animal, suggesting it has not undergone massive genomic loss. Comparison with the published genome of Daphnia pulex has allowed us to reveal 3750 genes that are indeed specific to the lineage containing malacostracans and branchiopods, rather than Daphnia-specific (E-value: 10⁻⁶). We also show the experimental tractability of N. denticulata, which, together with the genomic resources presented here, make it an ideal model for a wide range of further aquacultural, developmental, ecotoxicological, food safety, genetic, hormonal, physiological and reproductive research, allowing better understanding of the evolution of crustaceans and other arthropods.
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