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Yuan Z, Jiang S, Qin K, Sun L. New insights into the evolutionary dynamic and lineage divergence of gasdermin E in metazoa. Front Cell Dev Biol 2022; 10:952015. [PMID: 35938154 PMCID: PMC9355259 DOI: 10.3389/fcell.2022.952015] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gasdermin (GSDM) is a family of pore-forming proteins that induce pyroptosis. To date, the origin and evolution of GSDM in Metazoa remain elusive. Here, we found that GSDM emerged early in Placozoa but is absent in a large number of invertebrates. In the lower vertebrate, fish, three types of GSDME, i.e., GSDMEa, GSDMEb, and a previously unreported type (designated GSDMEc), were idenitied. Evolutionarily, the three GSDMEs are distinctly separated: GSDMEa is closely related to tetrapod GSDME; GSDMEb exists exclusively in fish; GSDMEc forms the lineage root of tetrapod GSDMA/B/C/D. GSDMEc shares conserved genomic features with and is probably the prototype of GSDMA, which we found existing in all tetrapod classes. GSDMEc displays fast evolutionary dynamics, likely as a result of genomic transposition. A cross-metazoan analysis of GSDME revealed that GSDMEa shares a conserved caspase recognition motif with the GSDME of tetrapods and cnidarians, whereas GSDMEb has a unique caspase recognition motif similar to that of mammalian GSDMD, and GSDMEc exhibits no apparent caspase recognition motif. Through functional test, four highly conserved residues in vertebrate GSDME proved to be essential to auto-inhibition. Together our results provide new insights into the origin, evolution, and function of metazoan GSDMs.
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Affiliation(s)
- Zihao Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shuai Jiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Shuai Jiang, ; Li Sun,
| | - Kunpeng Qin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Shuai Jiang, ; Li Sun,
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Irving K, Wellenreuther M, Ritchie PA. Description of the growth hormone gene of the Australasian snapper, Chrysophrys auratus, and associated intra- and interspecific genetic variation. JOURNAL OF FISH BIOLOGY 2021; 99:1060-1070. [PMID: 34036582 DOI: 10.1111/jfb.14810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/23/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
The growth hormone (GH) gene of the marine teleost, the Australasian snapper (Chrysophrys auratus), was identified and characterized from the reference genome showing it was approximately 5577 bp in length and consisted of six exons and five introns. Large polymorphic repeat regions were found in the first and third introns, and putative transcription factor binding sites were identified. Phylogenetic analysis of the GH genes of perciform fish showed largely conserved coding regions and highly variable noncoding regions among species. Despite some exon sequence variation and an amino acid deletion identified between C. auratus and its sister species Chrysophrys/Pagrus major, the amino acid sequences and putative secondary structures were largely conserved across the Sparidae. A population-level assessment of 99 samples caught at five separate coastal locations in New Zealand revealed six variable alleles at the intron 1 site of the C. auratus GH gene. A population genetic analysis suggested that C. auratus from the five sample locations were largely panmictic, with no evidence for departure from the Hardy-Weinberg equilibrium, and have a high level of heterozygosity. Overall these results suggest that the GH gene is largely conserved across the coding regions, but some variability could be detected.
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Affiliation(s)
- Kate Irving
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Limited, Nelson, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Peter A Ritchie
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Ji SC, Kim JH, Jung MH, Kim JH, Kim HW, Kim MS, Myeong JI, Kim DJ. The complete mitochondrial genome analysis and phylogenetic position of the short barbeled grunter Hapalogenys nigripinnis (Lobotiformes: Hapalogenyidae) from Jeju island, Korea. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3706-3707. [PMID: 33367068 PMCID: PMC7655029 DOI: 10.1080/23802359.2020.1831982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
This study analyzed the complete mitochondrial genome of the short barbeled grunter Hapalogenys nigripinnis (Accession number: MT374064). The complete mitogenome was 16,476 bp long and included 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Nucleotide composition of the genome was A: 28.70%, T:27.46%, G: 15.73%, and C: 28.11%. All genes were encoded on the H-strand, except for the NADH dehydrogenase subunit (ND6) and 8 tRNA genes. When compared this sequence with the mitogenome of Chinese black grunt, Korean short barbeled grunter showed difference of 64 bp of nucleotide sequence in 20 genes. Phylogenetic tree was constructed using the neighbor-joining (NJ) method and showed the phylogenetic position of the short barbeled grunter in Korea.
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Affiliation(s)
- Seung-Chul Ji
- Jeju Fisheries Research Institute, National Institute of Fisheries Science, Jeju, Korea
| | - Jae-Hoon Kim
- Jeju Fisheries Research Institute, National Institute of Fisheries Science, Jeju, Korea
| | - Min-Hwan Jung
- Jeju Fisheries Research Institute, National Institute of Fisheries Science, Jeju, Korea
| | - Jung-Hyun Kim
- Jeju Fisheries Research Institute, National Institute of Fisheries Science, Jeju, Korea
| | - Hyo-Won Kim
- Jeju Fisheries Research Institute, National Institute of Fisheries Science, Jeju, Korea
| | | | - Jeong-In Myeong
- Jeju Fisheries Research Institute, National Institute of Fisheries Science, Jeju, Korea
| | - Dae-Jung Kim
- Jeju Fisheries Research Institute, National Institute of Fisheries Science, Jeju, Korea
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Zheng Y, Feng L, Liu H, Song R, Xu S, Shi H, Gao T. The complete mitochondrial genome of Hapalogenys analis (Perciformes, Haemulidea) except for control region, obtained by whole genome sequencing. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2807-2808. [PMID: 33457955 PMCID: PMC7782058 DOI: 10.1080/23802359.2020.1788463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
In this study, we obtained the complete mitochondrial genome of Hapalogenys analis using whole genome sequencing. With the exception for control region, this mitochondrial genome, consisting of 16,355 base pairs (bp), contains 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), and 21 transfer RNAs (tRNAs). This mitochondrial genome also lacks a tRNA-Pro gene after tRNA-Thr gene. The overall base composition shows 25.45% of T, 29.73% of C, 28.68% of A and 16.14% of G, with a slight A + T rich feature (54.13%). Sanger sequencing is needed to confirm the accuracy of control region, as well as the lack of tRNA-Pro gene. The mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.
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Affiliation(s)
- Yunya Zheng
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Linxiao Feng
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Haoyu Liu
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Riyu Song
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Shengyong Xu
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Huilai Shi
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China.,Zhejiang Province Key Lab of Mariculture and Enhancement, Marine Fisheries Research Institute of Zhejiang, Zhoushan, Zhejiang, China
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
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Vialle RA, de Souza JES, Lopes KDP, Teixeira DG, Alves Sobrinho PDA, Ribeiro-dos-Santos AM, Furtado C, Sakamoto T, Oliveira Silva FA, Herculano Corrêa de Oliveira E, Hamoy IG, Assumpção PP, Ribeiro-dos-Santos Â, Santos Lima JPM, Seuánez HN, de Souza SJ, Santos S. Whole Genome Sequencing of the Pirarucu (Arapaima gigas) Supports Independent Emergence of Major Teleost Clades. Genome Biol Evol 2018; 10:2366-2379. [PMID: 29982381 PMCID: PMC6143160 DOI: 10.1093/gbe/evy130] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2018] [Indexed: 01/14/2023] Open
Abstract
The Pirarucu (Arapaima gigas) is one of the world's largest freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in an Illumina platform. The final draft genome assembly was ∼661 Mb, with a contig N50 equal to 51.23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21.69% of the whole genome, and a total of 24,655 protein-coding genes were predicted from the genome assembly, with an average of nine exons per gene. Phylogenomic analysis based on 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sister groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a period of ∼30 Myr in the Jurassic. The draft genome of A. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also offer a valuable data for economic applications.
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Affiliation(s)
- Ricardo Assunção Vialle
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | | | - Katia de Paiva Lopes
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Diego Gomes Teixeira
- Bioinformatics Multidisciplinary Environment – BioME, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | | | - André M Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
- Departmento de Genética, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Carolina Furtado
- Programa de Genética, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | - Tetsu Sakamoto
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | - Igor Guerreiro Hamoy
- Laboratório de Genética Aplicada, Universidade Federal Rural da Amazônia, Belém, PA, Brazil
| | | | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
| | - João Paulo Matos Santos Lima
- Bioinformatics Multidisciplinary Environment – BioME, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Héctor N Seuánez
- Programa de Genética, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Sandro José de Souza
- Bioinformatics Multidisciplinary Environment – BioME, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Sidney Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
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Gorzelak P, Rahman IA, Zamora S, Gąsiński A, Trzciński J, Brachaniec T, Salamon MA. Towards a Better Understanding of the Origins of Microlens Arrays in Mesozoic Ophiuroids and Asteroids. Evol Biol 2017. [DOI: 10.1007/s11692-017-9411-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sanciangco MD, Carpenter KE, Betancur-R R. Phylogenetic placement of enigmatic percomorph families (Teleostei: Percomorphaceae). Mol Phylogenet Evol 2015; 94:565-576. [PMID: 26493227 DOI: 10.1016/j.ympev.2015.10.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 11/26/2022]
Abstract
Percomorphs are a large and diverse group of spiny-finned fishes that have come to be known as the "bush at the top" due to their persistent lack of phylogenetic resolution. Recently, the broader Euteleost Tree of Life project (EToL) inferred a well-supported phylogenetic hypothesis that groups the diversity of percomorphs into nine well-supported series (supraordinal groups): Ophidiaria, Batrachoidaria, Gobiaria, Syngnatharia, Pelagiaria, Anabantaria, Carangaria, Ovalentaria, and Eupercaria. The EToL also provided, for the first time, a monophyletic definition of Perciformes - the largest order of vertebrates. Despite significant progress made in accommodating the diversity of percomorph taxa into major clades, some 62 families (most previously placed in "Perciformes", as traditionally defined) were not examined by the EToL. Here, we provide evidence for the phylogenetic affinities of 10 of those 62 families, seven of which have largely remained enigmatic. This expanded taxonomic sampling also provides further support for the nine EToL supraordinal series. We examined sequences from 21 genes previously used by the EToL and added two fast-evolving mitochondrial markers in an attempt to increase resolution within the rapid percomorph radiations. We restricted the taxonomic sampling to 1229 percomorph species, including expanded sampling from recent studies. Results of maximum likelihood analysis revealed that bathyclupeids (Bathyclupeidae), galjoen fishes (Dichistiidae), kelpfishes (Chironemidae), marblefishes (Aplodactylidae), trumpeters (Latridae), barbeled grunters (Hapalogenyidae), slopefishes (Symphysanodontidae), and picarel porgies (formerly Centracanthidae) are members of the series Eupercaria ("new bush at the top"). The picarel porgies and porgies (Sparidae) are now placed in the same family (Sparidae). Our analyses suggest a close affinity between the orders Spariformes (including Lethrinidae, Nemipteridae and Sparidae) and Lobotiformes (including the tripletails or Lobotidae, the barbeled grunters, and tigerperches or Datnioididae), albeit support for this group is low. None of the newly examined families belong in the order Perciformes, as recently defined. Finally, we confirm results from other recent studies that place the Australasian salmons (Arripidae) within Pelagiaria, and the false trevallies (Lactariidae) close to flatfishes, jacks, and trevallies, within Carangaria.
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Affiliation(s)
| | - Kent E Carpenter
- Department of Biology, Old Dominion University, Norfolk, VA 23529, USA
| | - Ricardo Betancur-R
- Department of Biology, University of Puerto Rico - Río Piedras, P.O. Box 23360, San Juan 00931, Puerto Rico.
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