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Stephenson M, Hiley AS, Rouse GW, Mongiardino Koch N. The mitochondrial genome of the deep-sea pyramid urchin Echinocrepis rostrata (Echinoidea: Holasteroida: Pourtalesiidae). Mitochondrial DNA B Resour 2024; 9:390-393. [PMID: 38529110 PMCID: PMC10962292 DOI: 10.1080/23802359.2024.2333572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
We present the mitochondrial genome of the deep-sea, epibenthic, irregular echinoid Echinocrepis rostrata, representing the first sequenced mitogenome of the order Holasteroida. The length of the complete E. rostrata mitochondrial genome is 15,716 base pairs, and its GC content is 34.87%. It contains 13 protein-coding genes, two rRNA genes, and 22 tRNA genes, whose order is identical to that of all other available echinoid mitogenomes. Phylogenetic analysis of available mitochondrial genomes, based on all coding loci, places E. rostrata as the sister group to spatangoids (heart urchins).
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Affiliation(s)
- Matthew Stephenson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Avery S. Hiley
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Greg W. Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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2
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Park C, Kim EB, Ju SJ. The complete mitochondrial genome of deep-sea ophiuroid Ophioleila elegans (Echinodermata: Ophiuroidea) from the Shkolnik Guyot, a northwest Pacific seamount. Mitochondrial DNA B Resour 2023; 8:1334-1338. [PMID: 38189027 PMCID: PMC10768936 DOI: 10.1080/23802359.2023.2288441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024] Open
Abstract
Ophiuroids are a diversified benthic taxon in the deep sea. Given their various dispersal strategies, they are considered an adequate group to assess genetic connectivity, especially in the seamounts that function as islands. Ophioleila elegans A.H. Clark, 1949, in the family Ophiothamnidae, was previously reported from the Caiwei Guyot, a seamount in the northwest Pacific Ocean. Here, we described the mitochondrial genome of O. elegans collected from another seamount in the northwest Pacific. The whole mitogenome is 16,376 bp in length and encodes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis based on the mitogenome sequences showed that O. elegans was clustered with Histampica sp., the only species for which mitogenome sequence has been reported within the family Ophiothamnidae. The complete mitogenome of O. elegans first reported in the present study provides useful information for population genetics and evolutionary relationship of this taxon, especially in the northwest Pacific seamounts.
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Affiliation(s)
- Chailinn Park
- Ocean Georesources Research Department, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- Ocean Science Major, University of Science and Technology, Daejeon, Republic of Korea
| | - Eun-Bi Kim
- Ocean Georesources Research Department, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Se-Jong Ju
- Ocean Science Major, University of Science and Technology, Daejeon, Republic of Korea
- Marine Resources & Environment Research Division, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
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3
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Sun S, Xiao N, Sha Z. Mitogenomes provide insights into the phylogeny and evolution of brittle stars (Echinodermata, Ophiuroidea). ZOOL SCR 2022. [DOI: 10.1111/zsc.12576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Shao'e Sun
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- College of Biological Sciences University of Chinese Academy of Sciences Beijing China
| | - Ning Xiao
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- College of Biological Sciences University of Chinese Academy of Sciences Beijing China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- College of Biological Sciences University of Chinese Academy of Sciences Beijing China
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4
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Shin JS, Song CU, Choi H, Kwon KK, Kang DH, Eyun SI, Choi KS. The complete mitochondrial genome of the sand dollar Astriclypeus mannii (Verrill, 1867) (Echinoidea: Astriclypeidae) in the subtidal sand flat in Jeju Island off the south coast of Korea. Mitochondrial DNA B Resour 2022; 7:1602-1603. [PMID: 36106189 PMCID: PMC9467572 DOI: 10.1080/23802359.2022.2116946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Jong-Seop Shin
- Department of Marine Life Science (BK21 FOUR) and Marine Science Institute, Jeju National University, Jeju, Korea
| | - Chi-une Song
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Hyeongwoo Choi
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Korea
| | - Do-Hyung Kang
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology, Jeju, Korea
| | - Seong-il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Kwang-Sik Choi
- Department of Marine Life Science (BK21 FOUR) and Marine Science Institute, Jeju National University, Jeju, Korea
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Sun S, Xiao N, Sha Z. Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea. PeerJ 2022; 10:e13730. [PMID: 35919401 PMCID: PMC9339218 DOI: 10.7717/peerj.13730] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/23/2022] [Indexed: 01/17/2023] Open
Abstract
Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-Ser AGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-Ser AGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.
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Affiliation(s)
- Shao’e Sun
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ning Xiao
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
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Lessios HA, Hendler G. Mitochondrial phylogeny of the brittle star genus Ophioderma. Sci Rep 2022; 12:5304. [PMID: 35351912 PMCID: PMC8964800 DOI: 10.1038/s41598-022-08944-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/11/2022] [Indexed: 11/09/2022] Open
Abstract
We reconstructed the mitochondrial phylogeny of the species of the brittle star genus Ophioderma, using sequences of the Cytochrome Oxidase I gene (COI) to address four questions: (i) Are the species of Ophioderma described on morphological evidence reflected in mitochondrial genealogy? (ii) Which species separated from which? (iii) When did speciation events occur? (iv) What is the rate of COI evolution in ophiuroids? We found that most of the 22 described species we sampled coincide with monophyletic clusters of COI sequences, but there are exceptions, most notably in the eastern Pacific, in which three undescribed species were indicated. The COI phylogeny lacks resolution in the deeper nodes, but it does show that there are four species pairs, the members of which are found on either side of the central American Isthmus. Two pairs with a genetic distance of ~ 4% between Atlantic and Pacific members were probably split during the final stages of Isthmus completion roughly 3 million years ago. The rate of divergence provided by these pairs allowed the calibration of a relaxed molecular clock. Estimated dates of divergence indicate that the lineages leading to extant species coalesce at times much older than congeneric species in other classes of echinoderms, suggesting that low extinction rates may be one of the reasons that ophiuroids are species-rich. The mean rate of COI substitution in Ophioderma is three times slower than that of echinoids. Conclusions of previous mitochondrial DNA studies of ophiuroids that relied on echinoid calibrations to determine divergence times need to be revised.
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Affiliation(s)
- H A Lessios
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Panama.
| | - Gordon Hendler
- Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA, 90007, USA
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MOHAMMED-GEBA KHALED, ABBAS EMANM, AHMED HAMDYO, SHALABI MOHAMMEDA, HAMED ELSAYEDAE, RAZEK FATMAAABDEL, SOLIMAN TAHA. Comparing genetic markers’ efficiencies for discrimination between two commercially important holothuroids in the Mediterranean Sea, Holothuria polii and Holothuria sanctori. Zootaxa 2022; 5092:559-575. [DOI: 10.11646/zootaxa.5092.5.4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Indexed: 11/04/2022]
Abstract
Sea cucumber (bêche-de-mer, Echinodermata: Holothuroidea) is one of the top internationally traded seafood varieties. Besides its direct nutritional benefits, it is continuously used in the traditional medicine in different areas and cultures in the world. This world-wide interest triggered various issues related to stocks´ declining and risks of species extinction. For these reasons, the current study was designed to provide molecular tools for accurate discrimination between two sea cucumber species that prevail the Mediterranean of these echinoderms in Egypt, that are Holothuria polii and H. sanctori. The power of three gene markers, i.e., 16S rDNA, 28S rDNA, and Histone H3 in achieving accurate DNA-based identification, as well as elucidating clear phylogenetic and genetic diversity differences between those two species was assessed. Among the three genes, 16S rDNA showed the highest potentials as genetic and phylogenetic species discrimination marker. Both 28S rDNA and H3 exhibited the least number of holothuroid reference sequences in the GenBank database. For genetic diversity within each species population, 16S rDNA exhibited the best potentials, followed by H3. 28S rDNA showed no genetic polymorphism at all. Moreover, the collective data of both H3 and 16S rDNA suggested a possible role of asexual reproduction behavior in H. sanctori in the reduction of genetic diversity, as a possible response to overfishing. Hence, the current research can recommend the simultaneous application of both 16S rDNA and H3 as accurate markers for genetic discrimination among H. polii, H. sanctori and other different holothuroid species.
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Xiao J, Tian P, Guo F, Yu S, Wang W, Wang X, Niu W. Characterization of the complete mitochondrial genome of Diploastrea heliopora and phylogeny of the scleractinia species which have group I introns in their COI genes. Saudi J Biol Sci 2021; 28:7054-7060. [PMID: 34867006 PMCID: PMC8626255 DOI: 10.1016/j.sjbs.2021.07.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/04/2022] Open
Abstract
Mitochondrial genome DNA is a powerful marker for resolving phylogenetic relationships among scleractinian corals. Here, we decode the complete mitochondrial genome of Diploastrea heliopora (Lamarck, 1816) for the first time. The general features are 18 363 bp in length, and conventionally, with 13 protein coding genes, two ribosomal RNAs, and two transfer RNAs. Gene arrangement and distribution are similar to other scleractinian corals. Moreover, the COI gene of D. heliopora is broken up into two parts by a complex group I intron. This intron is 1076 bases in length and contains helical structures (P1-P10, except P2) and four conserved regions (P, Q, R, and S). The mitochondrial genome of D. heliopora has asymmetric base composition (13.03% C, 20.29% G, 25.91% A, and 40.77% for T). Based on concatenated protein coding genes, ML and BI trees show similar phylogenetic relationship: D. heliopora clustered closely with Sclerophyllia maxima and Echinophyllia aspera into the robust branch. The data and conclusion in this study are reference for further phylogenetic studies of corals.
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Affiliation(s)
- Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Feng Guo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Shuangen Yu
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Wei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xiaolei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
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9
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Sun S, Sha Z, Xiao N. The first two complete mitogenomes of the order Apodida from deep-sea chemoautotrophic environments: New insights into the gene rearrangement, origin and evolution of the deep-sea sea cucumbers. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100839. [PMID: 33933835 DOI: 10.1016/j.cbd.2021.100839] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
The deep-sea ecosystem is considered as the largest and most remote biome of the world. It is meaningful and important to elucidate the life origins by exploring the origin and adaptive genetic mechanisms of the large deep-sea organisms. Sea cucumbers (Holothuroidea) are abundant and economically important group of echinoderms, living from the shallow-waters to deep-sea. In this study, we present the mitochondrial genomes of the sea cucumber Chiridota heheva and Chiridota sp. collected from the deep-sea cold seep and hydrothermal vent, respectively. This is the first reported mitochondrial genomes from the order Apodida. The mitochondrial genomes of C. heheva (17,200 bp) and Chiridota sp. (17,199 bp) display novel gene arrangements with the first protein-coding gene rearrangements in the class Holothuroidea. Bases composition analysis showed that the A + T content of deep-sea holothurians were significantly higher than that of the shallow-water groups. We compared the arrangement of genes from the 24 available holothurian mitogenomes and found that the transposition, reverse transposition and tandem-duplication-random-losses (TDRL) may be involved in the evolution of mitochondrial gene arrangements in Holothuroidea. Phylogenetic analysis revealed that the Apodida clustered with Elasipodida, forming two basal deep-sea holothurian clades. The divergence between the deep-sea and shallow-water holothurians was located at 386.93 Mya, during the Late Devonian. Mitochondrial protein-coding genes of deep-sea holothurians underwent relaxed purifying selection. There are 57 positive selected amino acids sites for some mitochondrial genes of the three deep-sea clades, implying they may involve in the adaption of deep-sea sea cucumbers.
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Affiliation(s)
- Shao'e Sun
- Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Zhongli Sha
- Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Xiao
- Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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Medina-Feliciano JG, Pirro S, García-Arrarás JE, Mashanov V, Ryan JF. Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration. FRONTIERS IN MARINE SCIENCE 2021; 8:603410. [PMID: 38741925 PMCID: PMC11090492 DOI: 10.3389/fmars.2021.603410] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Regeneration is one of the most fascinating and yet least understood biological processes. Echinoderms, one of the closest related invertebrate groups to humans, can contribute to our understanding of the genetic basis of regenerative processes. Among echinoderms, sea cucumbers have the ability to grow back most of their body parts following injury, including the intestine and nervous tissue. The cellular and molecular events underlying these abilities in sea cucumbers have been most extensively studied in the species Holothuria glaberrima. However, research into the regenerative abilities of this species has been impeded due to the lack of adequate genomic resources. Here, we report the first draft genome assembly of H. glaberrima and demonstrate its value for future genetic studies. Using only short sequencing reads, we assembled the genome into 89,105 scaffolds totaling 1.1 gigabases with an N50 of 25 kilobases. Our BUSCO assessment of the genome resulted in 894 (91.4%) complete and partial genes from 978 genes queried. We incorporated transcriptomic data from several different life history stages to annotate 51,415 genes in our final assembly. To demonstrate the usefulness of the genome, we fully annotated the melanotransferrin (Mtf) gene family, which have a potential role in the regeneration of the sea cucumber intestine. Using these same data, we extracted the mitochondrial genome, which showed high conservation to that of other holothuroids. Thus, these data will be a critical resource for ongoing studies of regeneration and other studies in sea cucumbers.
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Affiliation(s)
| | - Stacy Pirro
- Iridian Genomes, Inc., Bethesda, MD, United States
| | - Jose E. García-Arrarás
- Biology Department, University of Puerto Rico, Río Piedras Campus, San Juan, PR, United States
| | - Vladimir Mashanov
- Wake Forest Institute for Regenerative Medicine, Winston Salem, NC, United States
| | - Joseph F. Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, United States
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Yang F, Zhou C, Tran NT, Sun Z, Wu J, Ge H, Lu Z, Zhong C, Zhu Z, Yang Q, Lin Q. Comparison of the complete mitochondrial genome of Phyllophorus liuwutiensis (Echinodermata: Holothuroidea: Phyllophoridae) to that of other sea cucumbers. FEBS Open Bio 2020; 10:1587-1600. [PMID: 32573974 PMCID: PMC7396427 DOI: 10.1002/2211-5463.12914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/31/2020] [Accepted: 06/17/2020] [Indexed: 12/25/2022] Open
Abstract
Sea cucumber species are abundant (>1400 species) and widely distributed globally. mtDNA sequencing is frequently used to identify the phylogenetic and evolutionary relationships among species. However, there are no reports on the mitochondrial genome of Phyllophorus liuwutiensis. Here, we performed mtDNA sequencing of P. liuwutiensis to examine its phylogenetic relationships with other echinoderms. Its mitochondrial genome (15 969 bp) contains 37 coding genes, including 13 protein‐coding genes, 22 tRNA genes and 2 rRNA genes. Except for one protein‐coding gene (nad6) and five tRNA genes encoded on the negative strand, all other genes were encoded on the positive strand. The mitochondrial bases of P. liuwutiensis were composed of 29.55% T, 22.16% C, 35.64% A and 12.64% G. The putative control region was 703 bp in length. Seven overlapping regions (1–10 bp) were found. The noncoding region between the genes ranged from 1 to 130 bp in length. One putative control region has been found in the P. liuwutiensis mitogenome. All of the tRNA genes were predicted to fold into a cloverleaf structure. In addition, we compared the gene arrangements of six echinoderms, revealing that the gene order of P. liuwutiensis was a new arrangement.
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Affiliation(s)
- Fuyuan Yang
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,College of Fisheries and Life Science, Shanghai Ocean University, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Ngoc Tuan Tran
- Institute of Marine Sciences, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, China
| | - Zaiqiao Sun
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Hui Ge
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhen Lu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Chenhui Zhong
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhihuang Zhu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Qiuhua Yang
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,College of Fisheries and Life Science, Shanghai Ocean University, China
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12
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Lin JP, Tsai MH, Kroh A, Trautman A, Machado DJ, Chang LY, Reid R, Lin KT, Bronstein O, Lee SJ, Janies D. The first complete mitochondrial genome of the sand dollar Sinaechinocyamus mai (Echinoidea: Clypeasteroida). Genomics 2020; 112:1686-1693. [PMID: 31629878 PMCID: PMC7032948 DOI: 10.1016/j.ygeno.2019.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/18/2019] [Accepted: 10/08/2019] [Indexed: 11/26/2022]
Abstract
Morphologic and molecular data often lead to different hypotheses of phylogenetic relationships. Such incongruence has been found in the echinoderm class Echinoidea. In particular, the phylogenetic status of the order Clypeasteroida is not well resolved. Complete mitochondrial genomes are currently available for 29 echinoid species, but no clypeasteroid had been sequenced to date. DNA extracted from a single live individual of Sinaechinocyamus mai was sequenced with 10× Genomics technology. This first complete mitochondrial genome (mitogenome) for the order Clypeasteroida is 15,756 base pairs in length. Phylogenomic analysis based on 34 ingroup taxa belonging to nine orders of the class Echinoidea show congruence between our new genetic inference and published trees based on morphologic characters, but also includes some intriguing differences that imply the need for additional investigation.
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Affiliation(s)
- Jih-Pai Lin
- Department of Geosciences, National Taiwan University, Taipei, Taiwan.
| | - Mong-Hsun Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Andreas Kroh
- Department of Geology and Palaeontology, Natural History Museum Vienna, Vienna, Austria
| | - Aaron Trautman
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, USA
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, USA; Bioinformatics Graduate Program, University of São Paulo, Brazil
| | - Lo-Yu Chang
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - Robert Reid
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, USA
| | - Kuan-Ting Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Omri Bronstein
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel; Steinhardt Museum of Natural History, Tel-Aviv, Israel
| | - Shyh-Jye Lee
- Department of Life Science, National Taiwan University, Taipei, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, USA
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Zhong S, Liu Y, Zhao Y, Huang G. The complete mitochondrial genome of sea cucumber Stichopus monotuberculatus (aspidochirotida: Stichopodidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3305-3306. [PMID: 33365967 PMCID: PMC7707201 DOI: 10.1080/23802359.2019.1673244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The sea cucumber, Stichopus monotuberculatus, is an economically important holothuroid in China due to its larger body size and valuable nutrition. However, the taxonomic revision studies of Stichopodidae have been one of the most controversial issues in recent years. Moreover, there remain considerable doubts about a complex of cryptic species within S. monotuberculatus. In this study, we report the complete mitochondrial genome of S. monotuberculatus. The mitogenome has 16,274 base pairs (60.4% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study adds one more available complete mitogenomes of Stichopus and will provide useful genetic information for future evolutionary and taxonomic classification of Stichopodidae.
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Affiliation(s)
- Shengping Zhong
- Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Yonghong Liu
- Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Yanfei Zhao
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Guoqiang Huang
- Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, China
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Yang Q, Lin Q, Wu J, Yang F, Ge H, Qiu D, Li Z, Lu Z, Li S, Zhou C. The complete mitochondrial genome sequence of Stichopus variegatus (Echinodermata: Holothuroidea) and phylogenetic studies of Echinodermata. Mitochondrial DNA B Resour 2019; 4:3244-3245. [PMID: 33365938 PMCID: PMC7707333 DOI: 10.1080/23802359.2019.1669502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/16/2019] [Indexed: 11/16/2022] Open
Abstract
At present, there exist some confusing issues on the species classification and phylogeny in Echinodermata. In this study, we first determined and described the complete mitochondrial genome of Stichopus variegatus. The complete mitogenome sequence had a circular mapping molecular with the total length of 16,315 bp and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. To further validate the newly determined sequences, phylogenetic trees involving all the Holothuroidea and other Echinodermata species available in GenBank Database were constructed. These results would be used for the species identification and further phylogenetic studies of Echinodermata.
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Affiliation(s)
- Qiuhua Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, Guangdong, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Fuyuan Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Hui Ge
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Denggao Qiu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Zhongqin Li
- Fisheries College, Engineering Research Center on Eel Modern Industrial Technology of Ministry of Education, Jimei University, Xiamen, Fujian, China
| | - Zhen Lu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, Guangdong, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
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Yang M, Gong L, Sui J, Li X. The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): Insight into the deep-sea adaptive evolution of vesicomyids. PLoS One 2019; 14:e0217952. [PMID: 31536521 PMCID: PMC6752807 DOI: 10.1371/journal.pone.0217952] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022] Open
Abstract
The deep-sea chemosynthetic environment is one of the most extreme environments on the Earth, with low oxygen, high hydrostatic pressure and high levels of toxic substances. Species of the family Vesicomyidae are among the dominant chemosymbiotic bivalves found in this harsh habitat. Mitochondria play a vital role in oxygen usage and energy metabolism; thus, they may be under selection during the adaptive evolution of deep-sea vesicomyids. In this study, the mitochondrial genome (mitogenome) of the vesicomyid bivalve Calyptogena marissinica was sequenced with Illumina sequencing. The mitogenome of C. marissinica is 17,374 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes. All of these genes are encoded on the heavy strand. Some special elements, such as tandem repeat sequences, “G(A)nT” motifs and AT-rich sequences, were observed in the control region of the C. marissinica mitogenome, which is involved in the regulation of replication and transcription of the mitogenome and may be helpful in adjusting the mitochondrial energy metabolism of organisms to adapt to the deep-sea chemosynthetic environment. The gene arrangement of protein-coding genes was identical to that of other sequenced vesicomyids. Phylogenetic analyses clustered C. marissinica with previously reported vesicomyid bivalves with high support values. Positive selection analysis revealed evidence of adaptive change in the mitogenome of Vesicomyidae. Ten potentially important adaptive residues were identified, which were located in cox1, cox3, cob, nad2, nad4 and nad5. Overall, this study sheds light on the mitogenomic adaptation of vesicomyid bivalves that inhabit the deep-sea chemosynthetic environment.
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Affiliation(s)
- Mei Yang
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Gong
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jixing Sui
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinzheng Li
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
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16
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Yang Q, Lin Q, Yang F, Wu J, Lu Z, Li S, Zhou C. Characterization of the complete mitochondrial genome of a holothurians species: Holothuria hilla (Holothuroidea: Holothuriidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2847-2848. [PMID: 33365756 PMCID: PMC7706501 DOI: 10.1080/23802359.2019.1660267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Mitochondrial genome sequence is a great potential method to both resolve disputed taxonomic issues and to infer phylogenetic relationships among holothurians. In this study, we present the complete mitochondrial genome of Holothuria hilla which was 15,744 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. The gene content and arrangement were typical for Holothuroidea ground pattern. The overall base composition was 32.43% A, 27.20% T, 24.35% C and 16.02% G, showing a bias toward A + T (59.63%). The maximum-likelihood tree based on the concatenated 13 protein-coding genes revealed the phylogenetic relationships among the Holothuroidea species.
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Affiliation(s)
- Qiuhua Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Fuyuan Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhen Lu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
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Yang Q, Lin Q, Wu J, Tran NT, Huang R, Sun Z, Zhu Z, Lu Z, Li S, Zhou C. Complete mitochondrial genome of Holothuria leucospilata (Holothuroidea, Holothuriidae) and phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2751-2752. [PMID: 33365713 PMCID: PMC7706471 DOI: 10.1080/23802359.2019.1644226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The complete Holothuria leucospilata mitochondrial genome was determined and analyzed in this work. It had a circular mapping molecular with a total length of 15,904 bp and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 putative control region. Phylogenetic analysis showed that H. leucospilata clustered together with Holothuria scabra and Holothuria forskali. The complete mitochondrial genome provided in this work would be used for elucidation of Holothuroidea conservation genetics and evolutionary relationships.
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Affiliation(s)
- Qiuhua Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Ngoc Tuan Tran
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Ruifang Huang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zaiqiao Sun
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhihuang Zhu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhen Lu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
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18
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Li Y, Kocot KM, Tassia MG, Cannon JT, Bernt M, Halanych KM. Mitogenomics Reveals a Novel Genetic Code in Hemichordata. Genome Biol Evol 2019; 11:29-40. [PMID: 30476024 PMCID: PMC6319601 DOI: 10.1093/gbe/evy254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2018] [Indexed: 01/26/2023] Open
Abstract
The diverse array of codon reassignments demonstrate that the genetic code is not universal in nature. Exploring mechanisms underlying codon reassignment is critical for understanding the evolution of the genetic code during translation. Hemichordata, comprising worm-like Enteropneusta and colonial filter-feeding Pterobranchia, is the sister taxon of echinoderms and is more distantly related to chordates. However, only a few hemichordate mitochondrial genomes have been sequenced, hindering our understanding of mitochondrial genome evolution within Deuterostomia. In this study, we sequenced four mitochondrial genomes and two transcriptomes, including representatives of both major hemichordate lineages and analyzed together with public available data. Contrary to the current understanding of the mitochondrial genetic code in hemichordates, our comparative analyses suggest that UAA encodes Tyr instead of a "Stop" codon in the pterobranch lineage Cephalodiscidae. We also predict that AAA encodes Lys in pterobranch and enteropneust mitochondrial genomes, contradicting the previous assumption that hemichordates share the same genetic code with echinoderms for which AAA encodes Asn. Thus, we propose a new mitochondrial genetic code for Cephalodiscus and a revised code for enteropneusts. Moreover, our phylogenetic analyses are largely consistent with previous phylogenomic studies. The only exception is the phylogenetic position of the enteropneust Stereobalanus, whose placement as sister to all other described enteropneusts. With broader taxonomic sampling, we provide evidence that evolution of mitochondrial gene order and genetic codes in Hemichordata are more dynamic than previously thought and these findings provide insights into mitochondrial genome evolution within this clade.
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Affiliation(s)
- Yuanning Li
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
| | - Kevin M Kocot
- Department of Biological Sciences & Alabama Museum of Natural History, The University of Alabama
| | - Michael G Tassia
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
| | - Johanna T Cannon
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara
| | - Matthias Bernt
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Kenneth M Halanych
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
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Mu W, Liu J, Zhang H. Complete mitochondrial genome of Benthodytes marianensis (Holothuroidea: Elasipodida: Psychropotidae): Insight into deep sea adaptation in the sea cucumber. PLoS One 2018; 13:e0208051. [PMID: 30500836 PMCID: PMC6267960 DOI: 10.1371/journal.pone.0208051] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/09/2018] [Indexed: 01/01/2023] Open
Abstract
Complete mitochondrial genomes play important roles in studying genome evolution, phylogenetic relationships, and species identification. Sea cucumbers (Holothuroidea) are ecologically important and diverse members, living from the shallow waters to the hadal trench. In this study, we present the mitochondrial genome sequence of the sea cucumber Benthodytes marianensis collected from the Mariana Trench. To our knowledge, this is the first reported mitochondrial genome from the genus Benthodytes. This complete mitochondrial genome is 17567 bp in length and consists of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes (duplication of two tRNAs: trnL and trnS). Most of these genes are coded on the positive strand except for one protein-coding gene (nad6) and five tRNA genes which are coded on the negative strand. Two putative control regions (CRs) have been found in the B. marianensis mitogenome. We compared the order of genes from the 10 available holothurian mitogenomes and found a novel gene arrangement in B. marianensis. Phylogenetic analysis revealed that B. marianensis clustered with Peniagone sp. YYH-2013, forming the deep-sea Elasipodida clade. Positive selection analysis showed that eleven residues (24 S, 45 S, 185 S, 201 G, 211 F and 313 N in nad2; 108 S, 114 S, 322 C, 400 T and 427 S in nad4) were positively selected sites with high posterior probabilities. We predict that nad2 and nad4 may be the important candidate genes for the further investigation of the adaptation of B. marianensis to the deep-sea environment.
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Affiliation(s)
- Wendan Mu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- * E-mail:
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20
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Mu W, Liu J, Zhang H. The first complete mitochondrial genome of the Mariana Trench Freyastera benthophila (Asteroidea: Brisingida: Brisingidae) allows insights into the deep-sea adaptive evolution of Brisingida. Ecol Evol 2018; 8:10673-10686. [PMID: 30519397 PMCID: PMC6262923 DOI: 10.1002/ece3.4427] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/27/2018] [Accepted: 07/10/2018] [Indexed: 01/13/2023] Open
Abstract
Starfish (phylum Echinodermata) are ecologically important and diverse members of marine ecosystems in all of the world's oceans, from the shallow water to the hadal zone. The deep sea is recognized as an extremely harsh environment on earth. In this study, we present the mitochondrial genome sequence of Mariana Trench starfish Freyastera benthophila, and this study is the first to explore in detail the mitochondrial genome of a deep-sea member of the order Brisingida. Similar to other starfish, it contained 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes (duplication of two tRNAs: trnL and trnS). Twenty-two of these genes are encoded on the positive strand, while the other 15 are encoded on the negative strand. The gene arrangement was identical to those of sequenced starfish. Phylogenetic analysis showed the deep-sea Brisingida as a sister taxon to the traditional members of the Asteriidae. Positive selection analysis indicated that five residues (8 N and 16 I in atp8, 47 D and 196 V in nad2, 599 N in nad5) were positively selected sites with high posterior probabilities. Compared these features with shallow sea starfish, we predict that variation specifically in atp8, nad2, and nad5 may play an important role in F. benthophila's adaptation to deep-sea environment.
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Affiliation(s)
- Wendan Mu
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jun Liu
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
| | - Haibin Zhang
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
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21
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Galaska MP, Li Y, Kocot KM, Mahon AR, Halanych KM. Conservation of mitochondrial genome arrangements in brittle stars (Echinodermata, Ophiuroidea). Mol Phylogenet Evol 2018; 130:115-120. [PMID: 30316947 DOI: 10.1016/j.ympev.2018.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 11/18/2022]
Abstract
Brittle stars are conspicuous members of benthic ecosystems, fill many ecological niches and are the most speciose of all classes of echinoderms. With high levels of biodiversity, elucidating the evolutionary history of this group is important. Understanding of higher-level relationships within Ophiuroidea has been aided by multilocus nuclear data and DNA barcoding. However, the degree of consistency between mitochondrial and nuclear data within ophiuroids remains unclear and deserves further assessment. In this study, 17 mitochondrial genomes spanning the taxonomic breadth of Ophiuroidea were utilized to explore evolutionary relationships through maximum likelihood analyses, Bayesian inference and comparative assessment of gene order. Our phylogenetic analyses, based on both nucleotide and amino acid residues, support recent findings based on multilocus nuclear data and morphology, in that the brittle star clades Ophintegrida and Euryophiurida were recovered as monophyletic with the latter comprising Euyalida, Ophiuridae and Ophiopyrgidae. Only three different arrangements of the 13 protein coding and 2 ribosomal RNA genes were observed. As expected, tRNA genes were more likely to have undergone rearrangement but the order of all 37 genes was found to be conserved in all sampled Euryalida and Ophiuridae. Both Euryalida and the clade comprised of Ophiuridae and Ophiopyrgidae, each had their own conserved rearrangement of protein coding genes and ribosomal genes, after divergence from their last common ancestor. Euryalida has a rearrangement of the two ribosomal RNA genes, rrnS and rrnL, in contrast to Ophiuridae and Ophiopyrgidae, which had an inversion of the genes nad1, nad2, and cob relative to Ophintegrida. Further, our data support the gene order found in all sampled Euryalida as the most likely ancestral order for all Ophiuroidea.
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Affiliation(s)
- Matthew P Galaska
- Department of Biological Sciences, Auburn University, Molette Biology Laboratory for Environmental and Climate Change Studies, 101 Rouse Life Science Building, Auburn, AL 36849, USA; Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA.
| | - Yuanning Li
- Department of Biological Sciences, Auburn University, Molette Biology Laboratory for Environmental and Climate Change Studies, 101 Rouse Life Science Building, Auburn, AL 36849, USA
| | - Kevin M Kocot
- Department of Biological Sciences and Alabama Museum of Natural History, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Andrew R Mahon
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Kenneth M Halanych
- Department of Biological Sciences, Auburn University, Molette Biology Laboratory for Environmental and Climate Change Studies, 101 Rouse Life Science Building, Auburn, AL 36849, USA.
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22
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A complete logical approach to resolve the evolution and dynamics of mitochondrial genome in bilaterians. PLoS One 2018; 13:e0194334. [PMID: 29547666 PMCID: PMC5856267 DOI: 10.1371/journal.pone.0194334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/01/2018] [Indexed: 01/12/2023] Open
Abstract
Investigating how recombination might modify gene order during the evolution has become a routine part of mitochondrial genome analysis. A new method of genomic maps analysis based on formal logic is described. The purpose of this method is to 1) use mitochondrial gene order of current taxa as datasets 2) calculate rearrangements between all mitochondrial gene orders and 3) reconstruct phylogenetic relationships according to these calculated rearrangements within a tree under the assumption of maximum parsimony. Unlike existing methods mainly based on the probabilistic approach, the main strength of this new approach is that it calculates all the exact tree solutions with completeness and provides logical consequences as highly robust results. Moreover, this method infers all possible hypothetical ancestors and reconstructs character states for all internal nodes of the trees. We started by testing our method using the deuterostomes as a study case. Then, with sponges as an outgroup, we investigated the evolutionary history of mitochondrial genomes of 47 bilaterian phyla and emphasised the peculiar case of chaetognaths. This pilot work showed that the use of formal logic in a hypothetico-deductive background such as phylogeny (where experimental testing of hypotheses is impossible) is very promising to explore mitochondrial gene order in deuterostomes and should be applied to many other bilaterian clades.
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Loeza-Quintana T, Adamowicz SJ. Iterative Calibration: A Novel Approach for Calibrating the Molecular Clock Using Complex Geological Events. J Mol Evol 2018; 86:118-137. [DOI: 10.1007/s00239-018-9831-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 02/02/2018] [Indexed: 01/04/2023]
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Ezhova OV, Egorova EA, Malakhov VV. Transformations of the axial complex of ophiuroids as a result of shifting of the madreporite to the oral side. BIOL BULL+ 2017. [DOI: 10.1134/s1062359016060091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Capel KCC, Migotto AE, Zilberberg C, Lin MF, Forsman Z, Miller DJ, Kitahara MV. Complete mitochondrial genome sequences of Atlantic representatives of the invasive Pacific coral species Tubastraea coccinea and T. tagusensis (Scleractinia, Dendrophylliidae): Implications for species identification. Gene 2016; 590:270-7. [PMID: 27234370 DOI: 10.1016/j.gene.2016.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
Members of the azooxanthellate coral genus Tubastraea are invasive species with particular concern because they have become established and are fierce competitors in the invaded areas in many parts of the world. Pacific Tubastraea species are spreading fast throughout the Atlantic Ocean, occupying over 95% of the available substrate in some areas and out-competing native endemic species. Approximately half of all known coral species are azooxanthellate but these are seriously under-represented compared to zooxanthellate corals in terms of the availability of mitochondrial (mt) genome data. In the present study, the complete mt DNA sequences of Atlantic individuals of the invasive scleractinian species Tubastraea coccinea and Tubastraea tagusensis were determined and compared to the GenBank reference sequence available for a Pacific "T. coccinea" individual. At 19,094bp (compared to 19,070bp for the GenBank specimen), the mt genomes assembled for the Atlantic T. coccinea and T. tagusensis were among the longest sequence determined to date for "Complex" scleractinians. Comparisons of genomes data showed that the "T. coccinea" sequence deposited on GenBank was more closely related to that from Dendrophyllia arbuscula than to the Atlantic Tubastraea spp., in terms of genome length and base pair similarities. This was confirmed by phylogenetic analysis, suggesting that the former was misidentified and might actually be a member from the genus Dendrophyllia. In addition, although in general the COX1 locus has a slow evolutionary rate in Scleractinia, it was the most variable region of the Tubastraea mt genome and can be used as markers for genus or species identification. Given the limited data available for azooxanthellate corals, the results presented here represent an important contribution to our understanding of phylogenetic relationships and the evolutionary history of the Scleractinia.
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Affiliation(s)
- K C C Capel
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - A E Migotto
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | - C Zilberberg
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M F Lin
- Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia; Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Z Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i, USA
| | - D J Miller
- Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - M V Kitahara
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil; Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil.
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Podlevsky JD, Li Y, Chen JJL. Structure and function of echinoderm telomerase RNA. RNA (NEW YORK, N.Y.) 2016; 22:204-215. [PMID: 26598712 PMCID: PMC4712671 DOI: 10.1261/rna.053280.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
Telomerase is a ribonucleoprotein (RNP) enzyme that requires an integral telomerase RNA (TR) subunit, in addition to the catalytic telomerase reverse transcriptase (TERT), for enzymatic function. The secondary structures of TRs from the three major groups of species, ciliates, fungi, and vertebrates, have been studied extensively and demonstrate dramatic diversity. Herein, we report the first comprehensive secondary structure of TR from echinoderms-marine invertebrates closely related to vertebrates-determined by phylogenetic comparative analysis of 16 TR sequences from three separate echinoderm classes. Similar to vertebrate TR, echinoderm TR contains the highly conserved template/pseudoknot and H/ACA domains. However, echinoderm TR lacks the ancestral CR4/5 structural domain found throughout vertebrate and fungal TRs. Instead, echinoderm TR contains a distinct simple helical region, termed eCR4/5, that is functionally equivalent to the CR4/5 domain. The urchin and brittle star eCR4/5 domains bind specifically to their respective TERT proteins and stimulate telomerase activity. Distinct from vertebrate telomerase, the echinoderm TR template/pseudoknot domain with the TERT protein is sufficient to reconstitute significant telomerase activity. This gain-of-function of the echinoderm template/pseudoknot domain for conferring telomerase activity presumably facilitated the rapid structural evolution of the eCR4/5 domain throughout the echinoderm lineage. Additionally, echinoderm TR utilizes the template-adjacent P1.1 helix as a physical template boundary element to prevent nontelomeric DNA synthesis, a mechanism used by ciliate and fungal TRs. Thus, the chimeric and eccentric structural features of echinoderm TR provide unparalleled insights into the rapid evolution of telomerase RNP structure and function.
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Affiliation(s)
- Joshua D Podlevsky
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Yang Li
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Julian J-L Chen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
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Shen X, Sun S, Zhao FQ, Zhang GT, Tian M, Tsang LM, Wang JF, Chu KH. Phylomitogenomic analyses strongly support the sister relationship of the Chaetognatha and Protostomia. ZOOL SCR 2015. [DOI: 10.1111/zsc.12140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology/Co-Innovation Center of Jiangsu Marine Bio-industry Technology; Huaihai Institute of Technology; Lianyungang 222005 China
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing 100101 China
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Shatin Hong Kong China
| | - Song Sun
- KLMEES and JBMERS; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
| | - Fang Qing Zhao
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing 100101 China
| | - Guang Tao Zhang
- KLMEES and JBMERS; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
| | - Mei Tian
- Jiangsu Key Laboratory of Marine Biotechnology/Co-Innovation Center of Jiangsu Marine Bio-industry Technology; Huaihai Institute of Technology; Lianyungang 222005 China
| | - Ling Ming Tsang
- Institute of Marine Biology; National Taiwan Ocean University; Keelung 20224 Taiwan
| | - Jin Feng Wang
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing 100101 China
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Shatin Hong Kong China
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Zhang Z, Bao X, Dong Y, Gao X, Gao L, Li S, Liu W, Hou H, Shi J, Pu H. Complete mitochondrial genome of Parastichopus californicus (Aspidochirotida: Stichopodidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3569-70. [PMID: 26260176 DOI: 10.3109/19401736.2015.1074222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we first determined and described the complete mitogenome sequence of Parastichopus californicus, which was 16 727 bp in length. The mitochondrial genome had the canonical mitochondrial gene content, including 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. The overall base composition of the heavy-strand was 31.5% A, 18 % G, 20.6% C and 29.9% T, with a high A + T content of 61.4%. ML phylogenetic tree indicated that P. californicus and P. nigripunctatus were clustered in one branch belonging to the genus Parastichopus. This conclusion was identical to the former result by the methods of morphological taxonomy.
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Affiliation(s)
- Zhenyu Zhang
- a School of Food Science and Technology, Dalian Polytechnic University , Dalian , Liaoning , P.R. China and
| | - Xiangbo Bao
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Ying Dong
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Xianggang Gao
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Lei Gao
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Shilei Li
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Weidong Liu
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Hongman Hou
- a School of Food Science and Technology, Dalian Polytechnic University , Dalian , Liaoning , P.R. China and
| | - Jingyun Shi
- a School of Food Science and Technology, Dalian Polytechnic University , Dalian , Liaoning , P.R. China and
| | - Hongshaung Pu
- a School of Food Science and Technology, Dalian Polytechnic University , Dalian , Liaoning , P.R. China and
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29
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Urata M. Molecular Identification of Ptychodera flava (Hemichordata: Enteropneusta): Reconsideration in Light of Nucleotide Polymorphism in the 18S Ribosomal RNA Gene. Zoolog Sci 2015; 32:307-13. [PMID: 26003987 DOI: 10.2108/zs140144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Seven nuclear and mitochondrial DNA markers were examined in 12 specimens of Ptychodera flava, a model acorn worm used in molecular biology, collected in Japan from three local populations with different modes of living. A comparison of intraspecific results did not show genetically isolated populations despite the species' enclave habitats and asexual reproduction. Moreover, both the nuclear 18S ribosomal RNA gene and mitochondrial 16S ribosomal RNA gene sequences were identical to those from Moorea in French Polynesia, nearly 10,000 kilometers away from Japan. I also provide the first definitive information regarding polymorphisms in 18S ribosomal RNA gene, the external transcribed spacer (ETS), internal transcribed spacers (ITS), and mitochondrial cytochrome c oxidase subunit 1 (mtCO1) sequence in hemichordates using newly designed primer sets, and I show both high larval vagility and certain criteria for the molecular identification of this species.
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Affiliation(s)
- Makoto Urata
- Takehara Marine Science Station, Setouchi Field Science Center, Graduate School of Biosphere Science, Hiroshima University, 5-8-1 Minato-machi, Takehara, Hiroshima 725-0024, Japan
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Feuda R, Smith AB. Phylogenetic signal dissection identifies the root of starfishes. PLoS One 2015; 10:e0123331. [PMID: 25955729 PMCID: PMC4425436 DOI: 10.1371/journal.pone.0123331] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/20/2015] [Indexed: 11/19/2022] Open
Abstract
Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors - Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution – have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented.
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Affiliation(s)
- Roberto Feuda
- Division of Biology and Biological Engineering, California Institute of Technology Pasadena, California, United States of America
| | - Andrew B Smith
- Department of Earth Sciences, The Natural History Museum, London, United Kingdom
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31
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Reich A, Dunn C, Akasaka K, Wessel G. Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa. PLoS One 2015; 10:e0119627. [PMID: 25794146 PMCID: PMC4368666 DOI: 10.1371/journal.pone.0119627] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/12/2015] [Indexed: 12/01/2022] Open
Abstract
Echinoderms (sea urchins, sea stars, brittle stars, sea lilies and sea cucumbers) are a group of diverse organisms, second in number within deuterostome species to only the chordates. Echinoderms serve as excellent model systems for developmental biology due to their diverse developmental mechanisms, tractable laboratory use, and close phylogenetic distance to chordates. In addition, echinoderms are very well represented in the fossil record, including some larval features, making echinoderms a valuable system for studying evolutionary development. The internal relationships of Echinodermata have not been consistently supported across phylogenetic analyses, however, and this has hindered the study of other aspects of their biology. In order to test echinoderm phylogenetic relationships, we sequenced 23 de novo transcriptomes from all five clades of echinoderms. Using multiple phylogenetic methods at a variety of sampling depths we have constructed a well-supported phylogenetic tree of Echinodermata, including support for the sister groups of Asterozoa (sea stars and brittle stars) and Echinozoa (sea urchins and sea cucumbers). These results will help inform developmental and evolutionary studies specifically in echinoderms and deuterostomes in general.
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Affiliation(s)
- Adrian Reich
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Casey Dunn
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Koji Akasaka
- Misaki Marine Biological Station, University of Tokyo, Miura, Japan
| | - Gary Wessel
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
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32
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Xia J, Ren C, Yu Z, Wu X, Qian J, Hu C. Complete mitochondrial genome of the sandfish Holothuria scabra (Holothuroidea, Holothuriidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4174-4175. [PMID: 25629485 DOI: 10.3109/19401736.2014.1003899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mitogenome) sequence of Holothuria scabra, an economically and ecologically important tropical sea cucumber, was first sequenced and annotated. The mitochondrial DNA is 15,779 bp in length and contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a 456 bp putative control region, of which gene order is identical to the echinoderm ground pattern. Comparative analyses between H. scabra and other holothurians revealed three new findings: (1) the mitogenome of H. scabra is highly compact having five regions with overlapping genes and least intergenic nucleotides among the sequenced holothurians, only accounting for 3.58% of its mitogenome; (2) the genus Holothuria mitogenomes show a pattern of high interspecies divergence at the 13 PCGs, and the genetic p-distance reaches 25.68% between H. scabra and H. forskali; (3) the incomplete stop codon T of cox2 shared with H. forskali may be a common feature in the genus Holothuria.
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Affiliation(s)
- Jianjun Xia
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Chunhua Ren
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Zonghe Yu
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Xiangyun Wu
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Jing Qian
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Chaoqun Hu
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
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Telford MJ, Lowe CJ, Cameron CB, Ortega-Martinez O, Aronowicz J, Oliveri P, Copley RR. Phylogenomic analysis of echinoderm class relationships supports Asterozoa. Proc Biol Sci 2015; 281:rspb.2014.0479. [PMID: 24850925 DOI: 10.1098/rspb.2014.0479] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
While some aspects of the phylogeny of the five living echinoderm classes are clear, the position of the ophiuroids (brittlestars) relative to asteroids (starfish), echinoids (sea urchins) and holothurians (sea cucumbers) is controversial. Ophiuroids have a pluteus-type larva in common with echinoids giving some support to an ophiuroid/echinoid/holothurian clade named Cryptosyringida. Most molecular phylogenetic studies, however, support an ophiuroid/asteroid clade (Asterozoa) implying either convergent evolution of the pluteus or reversals to an auricularia-type larva in asteroids and holothurians. A recent study of 10 genes from four of the five echinoderm classes used 'phylogenetic signal dissection' to separate alignment positions into subsets of (i) suboptimal, heterogeneously evolving sites (invariant plus rapidly changing) and (ii) the remaining optimal, homogeneously evolving sites. Along with most previous molecular phylogenetic studies, their set of heterogeneous sites, expected to be more prone to systematic error, support Asterozoa. The homogeneous sites, in contrast, support an ophiuroid/echinoid grouping, consistent with the cryptosyringid clade, leading them to posit homology of the ophiopluteus and echinopluteus. Our new dataset comprises 219 genes from all echinoderm classes; analyses using probabilistic Bayesian phylogenetic methods strongly support Asterozoa. The most reliable, slowly evolving quartile of genes also gives highest support for Asterozoa; this support diminishes in second and third quartiles and the fastest changing quartile places the ophiuroids close to the root. Using phylogenetic signal dissection, we find heterogenous sites support an unlikely grouping of Ophiuroidea + Holothuria while homogeneous sites again strongly support Asterozoa. Our large and taxonomically complete dataset finds no support for the cryptosyringid hypothesis; in showing strong support for the Asterozoa, our preferred topology leaves the question of homology of pluteus larvae open.
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Affiliation(s)
- Maximilian J Telford
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Christopher J Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Oceanview Boulevard, Pacific Grove, CA 93950, USA
| | - Christopher B Cameron
- Départment de Sciences Biologiques, Université de Montréal, Pavillion Marie-Victorin, C.P. 6128, Succ. Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Olga Ortega-Martinez
- Department of Biological and Environmental Sciences, Sven Lovén Centre for Marine Sciences, University of Gothenburg, Kristineberg 566, Fiskebäckskil 451 78, Sweden
| | - Jochanan Aronowicz
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60650, USA
| | - Paola Oliveri
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Richard R Copley
- CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Observatoire Océanographique, Villefranche-sur-mer 06230, France Sorbonne Universites, UPMC Univ Paris 06, Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Observatoire Oceanographique, Villefranche-sur-mer 06230, France
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Complete mitogenome of the edible sea urchin Loxechinus albus: genetic structure and comparative genomics within Echinozoa. Mol Biol Rep 2014; 42:1081-9. [DOI: 10.1007/s11033-014-3847-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 11/25/2014] [Indexed: 10/24/2022]
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35
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Dilly GF, Gaitán-Espitia JD, Hofmann GE. Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: a molecular resource for phylogenetics, ecophysiology and global change biology. Mol Ecol Resour 2014; 15:425-36. [DOI: 10.1111/1755-0998.12316] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 06/24/2014] [Accepted: 07/21/2014] [Indexed: 11/30/2022]
Affiliation(s)
- G. F. Dilly
- Marine Science Institute; Department of Ecology, Evolution and Marine Biology; University of California; Santa Barbara CA USA
| | - J. D. Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Valdivia Chile
| | - G. E. Hofmann
- Marine Science Institute; Department of Ecology, Evolution and Marine Biology; University of California; Santa Barbara CA USA
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O'Hara TD, Hugall AF, Thuy B, Moussalli A. Phylogenomic resolution of the class Ophiuroidea unlocks a global microfossil record. Curr Biol 2014; 24:1874-9. [PMID: 25065752 DOI: 10.1016/j.cub.2014.06.060] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/23/2014] [Accepted: 06/23/2014] [Indexed: 11/17/2022]
Abstract
Our understanding of the origin, evolution, and biogeography of seafloor fauna is limited because we have insufficient spatial and temporal data to resolve underlying processes. The abundance and wide distribution of modern and disarticulated fossil Ophiuroidea, including brittle stars and basket stars, make them an ideal model system for global marine biogeography if we have the phylogenetic framework necessary to link extant and fossil morphology in an evolutionary context. Here we construct a phylogeny from a highly complete 425-gene, 61-taxa transcriptome-based data set covering 15 of the 18 ophiuroid families and representatives of all extant echinoderm classes. We calibrate our phylogeny with a series of novel fossil discoveries from the early Mesozoic. We confirm the traditional paleontological view that ophiuroids are sister to the asteroids and date the crown group Ophiuroidea to the mid-Permian (270 ± 30 mega-annum). We refute all historical classification schemes of the Ophiuroidea based on gross structural characters but find strong congruence with schemes based on lateral arm plate microstructure and the temporal appearance of various plate morphologies in the fossil record. The verification that these microfossils contain phylogenetically informative characters unlocks their potential to advance our understanding of marine biogeographical processes.
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Affiliation(s)
| | - Andrew F Hugall
- Museum Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Ben Thuy
- Section Paléontologie, Musée National d'Histoire Naturelle du Luxembourg, 24 Rue Münster, 2160 Luxembourg
| | - Adnan Moussalli
- Museum Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
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37
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Gaitán-Espitia JD, Hofmann GE. Mitochondrial genome architecture of the giant red sea urchinMesocentrotus franciscanus(Strongylocentrotidae, Echinoida). ACTA ACUST UNITED AC 2014; 27:591-2. [DOI: 10.3109/19401736.2014.908359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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38
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Brewer MS, Swafford L, Spruill CL, Bond JE. Arthropod phylogenetics in light of three novel millipede (myriapoda: diplopoda) mitochondrial genomes with comments on the appropriateness of mitochondrial genome sequence data for inferring deep level relationships. PLoS One 2013; 8:e68005. [PMID: 23869209 PMCID: PMC3712015 DOI: 10.1371/journal.pone.0068005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 05/27/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda. RESULTS The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly). As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic. CONCLUSIONS The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic signal renders the resulting tree topologies as suspect. As such, these data are likely inappropriate for investigating such ancient relationships.
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Affiliation(s)
- Michael S Brewer
- Department of Biology, East Carolina University, Greenville, North Carolina, USA.
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Kober KM, Bernardi G. Phylogenomics of strongylocentrotid sea urchins. BMC Evol Biol 2013; 13:88. [PMID: 23617542 PMCID: PMC3637829 DOI: 10.1186/1471-2148-13-88] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/09/2013] [Indexed: 11/10/2022] Open
Abstract
Background Strongylocentrotid sea urchins have a long tradition as model organisms for studying many fundamental processes in biology including fertilization, embryology, development and genome regulation but the phylogenetic relationships of the group remain largely unresolved. Although the differing isolating mechanisms of vicariance and rapidly evolving gamete recognition proteins have been proposed, a stable and robust phylogeny is unavailable. Results We used a phylogenomic approach with mitochondrial and nuclear genes taking advantage of the whole-genome sequencing of nine species in the group to establish a stable (i.e. concordance in tree topology among multiple lies of evidence) and robust (i.e. high nodal support) phylogenetic hypothesis for the family Strongylocentrotidae. We generated eight draft mitochondrial genome assemblies and obtained 13 complete mitochondrial genes for each species. Consistent with previous studies, mitochondrial sequences failed to provide a reliable phylogeny. In contrast, we obtained a very well-supported phylogeny from 2301 nuclear genes without evidence of positive Darwinian selection both from the majority of most-likely gene trees and the concatenated fourfold degenerate sites: ((P. depressus, (M. nudus, M. franciscanus), (H. pulcherrimus, (S. purpuratus, (S. fragilis, (S. pallidus, (S. droebachiensis, S. intermedius)). This phylogeny was consistent with a single invasion of deep-water environments followed by a holarctic expansion by Strongylocentrotus. Divergence times for each species estimated with reference to the divergence times between the two major clades of the group suggest a correspondence in the timing with the opening of the Bering Strait and the invasion of the holarctic regions. Conclusions Nuclear genome data contains phylogenetic signal informative for understanding the evolutionary history of this group. However, mitochondrial genome data does not. Vicariance can explain major patterns observed in the phylogeny. Other isolating mechanisms are appropriate to explore in this system to help explain divergence patterns not well supported by vicariance, such as the effects of rapidly evolving gamete recognition proteins on isolating populations. Our findings of a stable and robust phylogeny, with the increase in mitochondrial and nuclear comparative genomic data, provide a system in which we can enhance our understanding of molecular evolution and adaptation in this group of sea urchins.
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Affiliation(s)
- Kord M Kober
- Department of Ecology & Evolutionary Biology, University Of California Santa Cruz, Santa Cruz, CA, USA.
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40
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Smith AB, Reich M. Tracing the evolution of the holothurian body plan through stem-group fossils. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12073] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew B. Smith
- Department of Earth Sciences; The Natural History Museum; Cromwell Road; London; SW7 5BD; UK
| | - Mike Reich
- Geowissenschaftliches Zentrum der Universität Göttingen, Museum, Sammlungen & Geopark; Goldschmidtstrasse 1-5; D-37077; Göttingen; Germany
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41
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Perseke M, Golombek A, Schlegel M, Struck TH. The impact of mitochondrial genome analyses on the understanding of deuterostome phylogeny. Mol Phylogenet Evol 2013; 66:898-905. [DOI: 10.1016/j.ympev.2012.11.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 11/09/2012] [Accepted: 11/22/2012] [Indexed: 10/27/2022]
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42
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Dyachuk V, Odintsova N. Larval myogenesis in Echinodermata: conserved features and morphological diversity between class-specific larval forms of Echinoidae, Asteroidea, and Holothuroidea. Evol Dev 2013; 15:5-17. [DOI: 10.1111/ede.12010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vyacheslav Dyachuk
- A. V. Zhirmunsky Institute of Marine Biology; FEB RAS, Palchevsky 17; Vladivostok 17 Palchevsky Str. 690059 Vladivostok Russia
- Far Eastern Federal University; 8 Sukhanova Str. Vladivostok 690950 Russia
| | - Nelly Odintsova
- A. V. Zhirmunsky Institute of Marine Biology; FEB RAS, Palchevsky 17; Vladivostok 17 Palchevsky Str. 690059 Vladivostok Russia
- Far Eastern Federal University; 8 Sukhanova Str. Vladivostok 690950 Russia
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43
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Leese F, Brand P, Rozenberg A, Mayer C, Agrawal S, Dambach J, Dietz L, Doemel JS, Goodall-Copstake WP, Held C, Jackson JA, Lampert KP, Linse K, Macher JN, Nolzen J, Raupach MJ, Rivera NT, Schubart CD, Striewski S, Tollrian R, Sands CJ. Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology. PLoS One 2012. [PMID: 23185309 PMCID: PMC3504011 DOI: 10.1371/journal.pone.0049202] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
High throughput sequencing technologies are revolutionizing genetic research. With this “rise of the machines”, genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datasets from non-model species, it is possible that DNA from non-target contaminant species such as bacteria, viruses, fungi, or other eukaryotic organisms may complicate the interpretation of the results. In this study we analysed 14 genomic pyrosequencing libraries of aquatic non-model taxa from four major evolutionary lineages. We quantified the amount of suitable micro- and minisatellites, mitochondrial genomes, known nuclear genes and transposable elements and searched for contamination from various sources using bioinformatic approaches. Our results show that in all sequence libraries with estimated coverage of about 0.02–25%, many appropriate micro- and minisatellites, mitochondrial gene sequences and nuclear genes from different KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways could be identified and characterized. These can serve as markers for phylogenetic and population genetic analyses. A central finding of our study is that several genomic libraries suffered from different biases owing to non-target DNA or mobile elements. In particular, viruses, bacteria or eukaryote endosymbionts contributed significantly (up to 10%) to some of the libraries analysed. If not identified as such, genetic markers developed from high-throughput sequencing data for non-model organisms may bias evolutionary studies or fail completely in experimental tests. In conclusion, our study demonstrates the enormous potential of low-coverage genome survey sequences and suggests bioinformatic analysis workflows. The results also advise a more sophisticated filtering for problematic sequences and non-target genome sequences prior to developing markers.
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Affiliation(s)
- Florian Leese
- Ruhr University Bochum, Department of Animal Ecology, Evolution and Biodiversity, Bochum, Germany.
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Zamora S, Rahman IA, Smith AB. Plated Cambrian bilaterians reveal the earliest stages of echinoderm evolution. PLoS One 2012; 7:e38296. [PMID: 22701623 PMCID: PMC3368939 DOI: 10.1371/journal.pone.0038296] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 05/01/2012] [Indexed: 02/02/2023] Open
Abstract
Echinoderms are unique in being pentaradiate, having diverged from the ancestral bilaterian body plan more radically than any other animal phylum. This transformation arises during ontogeny, as echinoderm larvae are initially bilateral, then pass through an asymmetric phase, before giving rise to the pentaradiate adult. Many fossil echinoderms are radial and a few are asymmetric, but until now none have been described that show the original bilaterian stage in echinoderm evolution. Here we report new fossils from the early middle Cambrian of southern Europe that are the first echinoderms with a fully bilaterian body plan as adults. Morphologically they are intermediate between two of the most basal classes, the Ctenocystoidea and Cincta. This provides a root for all echinoderms and confirms that the earliest members were deposit feeders not suspension feeders.
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Affiliation(s)
- Samuel Zamora
- Department of Palaeontology, The Natural History Museum, London, United Kingdom
| | - Imran A. Rahman
- School of Geography, Earth & Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Andrew B. Smith
- Department of Palaeontology, The Natural History Museum, London, United Kingdom
- * E-mail:
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45
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Mah CL, Blake DB. Global diversity and phylogeny of the Asteroidea (Echinodermata). PLoS One 2012; 7:e35644. [PMID: 22563389 PMCID: PMC3338738 DOI: 10.1371/journal.pone.0035644] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 03/19/2012] [Indexed: 11/18/2022] Open
Abstract
Members of the Asteroidea (phylum Echinodermata), popularly known as starfish or sea stars, are ecologically important and diverse members of marine ecosystems in all of the world's oceans. We present a comprehensive overview of diversity and phylogeny as they have figured into the evolution of the Asteroidea from Paleozoic to the living fauna. Living post-Paleozoic asteroids, the Neoasteroidea, are morphologically separate from those in the Paleozoic. Early Paleozoic asteroid faunas were diverse and displayed morphology that foreshadowed later living taxa. Preservation presents significant difficulties, but fossil occurrence and current accounts suggests a diverse Paleozoic fauna, which underwent extinction around the Permian-Triassic interval was followed by re-diversification of at least one surviving lineage. Ongoing phylogenetic classification debates include the status of the Paxillosida and the Concentricycloidea. Fossil and molecular evidence has been and continues to be part of the ongoing evolution of asteroid phylogenetic research. The modern lineages of asteroids include the Valvatacea, the Forcipulatacea, the Spinlosida, and the Velatida. We present an overview of diversity in these taxa, as well as brief notes on broader significance, ecology, and functional morphology of each. Although much asteroid taxonomy is stable, many new taxa remain to be discovered with many new species currently awaiting description. The Goniasteridae is currently one of the most diverse families within the Asteroidea. New data from molecular phylogenetics and the advent of global biodiversity databases, such as the World Asteroidea Database (http://www.marinespecies.org/Asteroidea/) present important new springboards for understanding the global biodiversity and evolution of asteroids.
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Affiliation(s)
- Christopher L Mah
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America.
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46
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Kondo M, Akasaka K. Current Status of Echinoderm Genome Analysis - What do we Know? Curr Genomics 2012; 13:134-43. [PMID: 23024605 PMCID: PMC3308324 DOI: 10.2174/138920212799860643] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 09/20/2011] [Accepted: 09/30/2011] [Indexed: 11/22/2022] Open
Abstract
Echinoderms have long served as model organisms for a variety of biological research, especially in the field of developmental biology. Although the genome of the purple sea urchin Strongylocentrotus purpuratus has been sequenced, it is the only echinoderm whose whole genome sequence has been reported. Nevertheless, data is rapidly accumulating on the chromosomes and genomic sequences of all five classes of echinoderms, including the mitochondrial genomes and Hox genes. This blossoming new data will be essential for estimating the phylogenetic relationships among echinoderms, and also to examine the underlying mechanisms by which the diverse morphologies of echinoderms have arisen.
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Affiliation(s)
- Mariko Kondo
- Misaki Marine Biological Station, Graduate School of Science, and Center for Marine Biology, The University of Tokyo, Japan
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Stöhr S, O'Hara TD, Thuy B. Global diversity of brittle stars (Echinodermata: Ophiuroidea). PLoS One 2012; 7:e31940. [PMID: 22396744 PMCID: PMC3292557 DOI: 10.1371/journal.pone.0031940] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 01/19/2012] [Indexed: 11/18/2022] Open
Abstract
This review presents a comprehensive overview of the current status regarding the global diversity of the echinoderm class Ophiuroidea, focussing on taxonomy and distribution patterns, with brief introduction to their anatomy, biology, phylogeny, and palaeontological history. A glossary of terms is provided. Species names and taxonomic decisions have been extracted from the literature and compiled in The World Ophiuroidea Database, part of the World Register of Marine Species (WoRMS). Ophiuroidea, with 2064 known species, are the largest class of Echinodermata. A table presents 16 families with numbers of genera and species. The largest are Amphiuridae (467), Ophiuridae (344 species) and Ophiacanthidae (319 species). A biogeographic analysis for all world oceans and all accepted species was performed, based on published distribution records. Approximately similar numbers of species were recorded from the shelf (n = 1313) and bathyal depth strata (1297). The Indo-Pacific region had the highest species richness overall (825 species) and at all depths. Adjacent regions were also relatively species rich, including the North Pacific (398), South Pacific (355) and Indian (316) due to the presence of many Indo-Pacific species that partially extended into these regions. A secondary region of enhanced species richness was found in the West Atlantic (335). Regions of relatively low species richness include the Arctic (73 species), East Atlantic (118), South America (124) and Antarctic (126).
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Affiliation(s)
- Sabine Stöhr
- Department of Invertebrate Zoology, Swedish Museum of Natural History, Stockholm, Sweden.
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48
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Xu X, Wu X, Yu Z. Comparative studies of the complete mitochondrial genomes of four Paphia clams and reconsideration of subgenus Neotapes (Bivalvia: Veneridae). Gene 2012; 494:17-23. [DOI: 10.1016/j.gene.2011.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 11/09/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
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49
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Okanishi M, O’Hara TD, Fujita T. Molecular phylogeny of the order Euryalida (Echinodermata: Ophiuroidea), based on mitochondrial and nuclear ribosomal genes. Mol Phylogenet Evol 2011; 61:392-9. [DOI: 10.1016/j.ympev.2011.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 06/08/2011] [Accepted: 07/06/2011] [Indexed: 11/25/2022]
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50
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Pisani D, Feuda R, Peterson KJ, Smith AB. Resolving phylogenetic signal from noise when divergence is rapid: a new look at the old problem of echinoderm class relationships. Mol Phylogenet Evol 2011; 62:27-34. [PMID: 21945533 DOI: 10.1016/j.ympev.2011.08.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 07/08/2011] [Accepted: 08/31/2011] [Indexed: 10/17/2022]
Abstract
Resolving evolutionary relationships in groups that underwent fast radiation in deep time is a problem for molecular phylogeny, as the scant phylogenetic signal that characterises short internal branches is generally swamped by more recent substitutions. We implement an approach, that maps how the support for rival phylogenies changes when analysing subsets of sites with either faster and more heterogeneous rates or slower and more homogeneous rates, to address a long-standing problem in deuterostome phylogeny - the interrelationships of the eleutherozoan echinoderm classes. We show that miRNA genes are phylogenetically uninformative as to the relationships of asteroids, echinoids and ophiuroids, consistent with a rapid radiation of these groups as suggested by their fossil record. Using three nuclear rRNAs and seven nuclear housekeeping genes, we map the support for the three possible phylogenetic arrangements of asteroids, ophiuroids and echinoids when moving between subsets of the data with very similar or very different rates of evolution. Only one of the three possible topologies (asteroids (ophiuroids+echinoids)) strengthens when the most rate-homogeneous subset of data are analysed. The other two possible pairings become stronger in a less reliable data subset, which includes the fastest and thus homoplasy-rich data in our alignment. Thus, while superficial analysis of our concatenated alignment identifies asteroids and ophiuroids as sister taxa, more thorough analyses suggest that ophiuroids may be more closely related to echinoids. Divergence of these echinoderm groups, using a relaxed molecular clock, is estimated to have occurred within ≈ 5 million years. Our results illustrate that the analytic approach of phylogenetic signal dissection can be a powerful tool to investigate rapid radiations in deep geologic time.
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Affiliation(s)
- Davide Pisani
- The National University of Ireland, Maynooth, Co. Kildare, Ireland
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