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Lavrov DV, Diaz MC, Maldonado M, Morrow CC, Perez T, Pomponi SA, Thacker RW. Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera). PLoS One 2023; 18:e0287281. [PMID: 38048310 PMCID: PMC10695373 DOI: 10.1371/journal.pone.0287281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/15/2023] [Indexed: 12/06/2023] Open
Abstract
Class Demospongiae is the largest in the phylum Porifera (Sponges) and encompasses nearly 8,000 accepted species in three subclasses: Keratosa, Verongimorpha, and Heteroscleromorpha. Subclass Heteroscleromorpha contains ∼90% of demosponge species and is subdivided into 17 orders. The higher level classification of demosponges underwent major revision as the result of nearly three decades of molecular studies. However, because most of the previous molecular work only utilized partial data from a small number of nuclear and mitochondrial (mt) genes, this classification scheme needs to be tested by larger datasets. Here we compiled a mt dataset for 136 demosponge species-including 64 complete or nearly complete and six partial mt-genome sequences determined or assembled for this study-and used it to test phylogenetic relationships among Demospongiae in general and Heteroscleromorpha in particular. We also investigated the phylogenetic position of Myceliospongia araneosa, a highly unusual demosponge without spicules and spongin fibers, currently classified as Demospongiae incertae sedis, for which molecular data were not available. Our results support the previously inferred sister-group relationship between Heteroscleromorpha and Keratosa + Verongimorpha and suggest five main clades within Heteroscleromorpha: Clade C0 composed of order Haplosclerida; Clade C1 composed of Scopalinida, Sphaerocladina, and Spongillida; Clade C2 composed of Axinellida, Biemnida, Bubarida; Clade C3 composed of Tetractinellida; and Clade C4 composed of Agelasida, Clionaida, Desmacellida, Merliida, Suberitida, Poecilosclerida, Polymastiida, and Tethyida. The inferred relationships among these clades were (C0(C1(C2(C3+C4)))). Analysis of molecular data from M. araneosa placed it in the C3 clade as a sister taxon to the highly skeletonized tetractinellids Microscleroderma sp. and Leiodermatium sp. Molecular clock analysis dated divergences among the major clades in Heteroscleromorpha from the Cambrian to the Early Silurian, the origins of most heteroscleromorph orders in the middle Paleozoic, and the most basal splits within these orders around the Paleozoic to Mesozoic transition. Overall, the results of this study are mostly congruent with the accepted classification of Heteroscleromorpha, but add temporal perspective and new resolution to phylogenetic relationships within this subclass.
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Affiliation(s)
- Dennis V. Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
| | - Maria C. Diaz
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
- Museo Marino de Margarita, Boca de Río, Nueva Esparta, Venezuela
| | - Manuel Maldonado
- Department of Marine Ecology, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Girona, Spain
| | - Christine C. Morrow
- Zoology Department, School of Natural Sciences & Ryan Institute, NUI Galway, University Road, Galway, Ireland
- Ireland and Queen’s University Marine Laboratory, Portaferry, Northern Ireland
| | - Thierry Perez
- Institut Méditerranéen de la Biodiversité et d’Ecologie marine et continentale (IMBE), CNRS, Aix-Marseille Université, IRD, Avignon Université City, Provence, France
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Robert W. Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, United States of America
- Smithsonian Tropical Research Institute, Balboa, Panama City, Republic of Panama
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Taite M, Fernández-Álvarez FÁ, Braid HE, Bush SL, Bolstad K, Drewery J, Mills S, Strugnell JM, Vecchione M, Villanueva R, Voight JR, Allcock AL. Genome skimming elucidates the evolutionary history of Octopoda. Mol Phylogenet Evol 2023; 182:107729. [PMID: 36773750 DOI: 10.1016/j.ympev.2023.107729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 12/10/2022] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Phylogenies for Octopoda have, until now, been based on morphological characters or a few genes. Here we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes of twenty Octopoda specimens, comprising 18 species of Cirrata and Incirrata, representing 13 genera and all five putative families of Cirrata (Cirroctopodidae, Cirroteuthidae, Grimpoteuthidae, Opisthoteuthidae and Stauroteuthidae) and six families of Incirrata (Amphitretidae, Argonautidae, Bathypolypodidae, Eledonidae, Enteroctopodidae, and Megaleledonidae) which were assembled using genome skimming. Phylogenetic trees were built using Maximum Likelihood and Bayesian Inference with several alignment matrices. All mitochondrial genomes had the 'typical' genome composition and gene order previously reported for octopodiforms, except Bathypolypus ergasticus, which appears to lack ND5, two tRNA genes that flank ND5 and two other tRNA genes. Argonautoidea was revealed as sister to Octopodidae by the mitochondrial protein-coding gene dataset, however, it was recovered as sister to all other incirrate octopods with strong support in an analysis using nuclear rRNA genes. Within Cirrata, our study supports two existing classifications suggesting neither is likely in conflict with the true evolutionary history of the suborder. Genome skimming is useful in the analysis of phylogenetic relationships within Octopoda; inclusion of both mitochondrial and nuclear data may be key.
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Affiliation(s)
- M Taite
- School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - F Á Fernández-Álvarez
- School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland; Institut de Ciències del Mar (CSIC), Passeig Marítim 37-49, E-08003 Barcelona, Spain.
| | - H E Braid
- AUT Lab for Cephalopod Ecology & Systematics, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - S L Bush
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington DC 20560, USA.
| | - K Bolstad
- AUT Lab for Cephalopod Ecology & Systematics, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand.
| | - J Drewery
- Marine Scotland, Marine Laboratory, 375 Victoria Road, Aberdeen AB11 9DB, UK.
| | - S Mills
- National Institute of Water and Atmospheric Research, 301 Evans Bay Parade, Wellington, New Zealand.
| | - J M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Qld, Australia.
| | - M Vecchione
- National Systematics Laboratory, Office of Science and Technology, NOAA Fisheries, Washington, DC, USA; Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA.
| | - R Villanueva
- Institut de Ciències del Mar (CSIC), Passeig Marítim 37-49, E-08003 Barcelona, Spain.
| | - J R Voight
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S DuSable Lake Shore Dr., Chicago, IL 60605, USA.
| | - A L Allcock
- School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland.
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Quek ZBR, Ng JY, Jain SS, Long JXS, Lim SC, Tun K, Huang D. Low genetic diversity and predation threaten a rediscovered marine sponge. Sci Rep 2022; 12:22499. [PMID: 36577798 PMCID: PMC9797562 DOI: 10.1038/s41598-022-26970-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Discovered in 1819 in the tropical waters off Singapore, the magnificent Neptune's cup sponge Cliona patera (Hardwicke, 1820) was harvested for museums and collectors until it was presumed extinct worldwide for over a century since 1907. Recently in 2011, seven living individuals were rediscovered in Singapore with six relocated to a marine protected area in an effort to better monitor and protect the population, as well as to enhance external fertilisation success. To determine genetic diversity within the population, we sequenced the complete mitochondrial genomes and nuclear ribosomal DNA of these six individuals and found extremely limited variability in their genes. The low genetic diversity of this rediscovered population is confirmed by comparisons with close relatives of C. patera and could compromise the population's ability to recover from environmental and anthropogenic pressures associated with the highly urbanised coastlines of Singapore. This lack of resilience is compounded by severe predation which has been shrinking sponge sizes by up to 5.6% every month. Recovery of this highly endangered population may require ex situ approaches and crossbreeding with other populations, which are also rare.
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Affiliation(s)
- Z. B. Randolph Quek
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Yale-NUS College, National University of Singapore, Singapore, Singapore
| | - Juat Ying Ng
- grid.4280.e0000 0001 2180 6431School of Design and Environment, National University of Singapore, Singapore, Singapore ,grid.467827.80000 0004 0620 8814National Biodiversity Centre, National Parks Board, Singapore, Singapore
| | - Sudhanshi S. Jain
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - J. X. Sean Long
- grid.462738.c0000 0000 9091 4551Republic Polytechnic, Singapore, Singapore
| | - Swee Cheng Lim
- grid.4280.e0000 0001 2180 6431Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Karenne Tun
- grid.467827.80000 0004 0620 8814National Biodiversity Centre, National Parks Board, Singapore, Singapore
| | - Danwei Huang
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Centre for Nature-Based Climate Solutions, National University of Singapore, Singapore, Singapore
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Gornik SG, Flores V, Reinhardt F, Erber L, Salas-Leiva DE, Douvropoulou O, Lassadi I, Einarsson E, Mörl M, Git A, Stadler PF, Pain A, Waller RF. Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes. Mol Biol Evol 2022; 39:6701636. [PMID: 36108082 PMCID: PMC9550989 DOI: 10.1093/molbev/msac191] [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] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial genomes of apicomplexans, dinoflagellates, and chrompodellids that collectively make up the Myzozoa, encode only three proteins (Cytochrome b [COB], Cytochrome c oxidase subunit 1 [COX1], Cytochrome c oxidase subunit 3 [COX3]), contain fragmented ribosomal RNAs, and display extensive recombination, RNA trans-splicing, and RNA-editing. The early-diverging Perkinsozoa is the final major myzozoan lineage whose mitochondrial genomes remained poorly characterized. Previous reports of Perkinsus genes indicated independent acquisition of non-canonical features, namely the occurrence of multiple frameshifts. To determine both ancestral myzozoan and novel perkinsozoan mitochondrial genome features, we sequenced and assembled mitochondrial genomes of four Perkinsus species. These data show a simple ancestral genome with the common reduced coding capacity but disposition for rearrangement. We identified 75 frameshifts across the four species that occur as distinct types and that are highly conserved in gene location. A decoding mechanism apparently employs unused codons at the frameshift sites that advance translation either +1 or +2 frames to the next used codon. The locations of frameshifts are seemingly positioned to regulate protein folding of the nascent protein as it emerges from the ribosome. The cox3 gene is distinct in containing only one frameshift and showing strong selection against residues that are otherwise frequently encoded at the frameshift positions in cox1 and cob. All genes lack cysteine codons implying a reduction to 19 amino acids in these genomes. Furthermore, mitochondrion-encoded rRNA fragment complements are incomplete in Perkinsus spp. but some are found in the nuclear DNA suggesting import into the organelle. Perkinsus demonstrates further remarkable trajectories of organelle genome evolution including pervasive integration of frameshift translation into genome expression.
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Affiliation(s)
| | - Victor Flores
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Franziska Reinhardt
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Lieselotte Erber
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Dayana E Salas-Leiva
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Olga Douvropoulou
- Pathogen Genomics Group, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Elin Einarsson
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Anna Git
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany,Discrete Biomathematics, Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany,Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, Währinger Str. 17, Alsergrund, Vienna 1090, Austria,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Arnab Pain
- Pathogen Genomics Group, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia,International Institute for Zoonosis Control, Hokkaido University, 001-0020 North 20, West 10 Kita-ku, Sapporo 001-0020, Japan
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Yang C, Hou X, Liu BY, Gong HS, Yuan H, Li XJ, Tang J, Wang Y. The mitogenome of common snipe, Gallinago gallinago gallinago Linnaeus, 1758 and evolutionary implications for the family Scolopacidae. Mitochondrial DNA B Resour 2021; 6:2886-2889. [PMID: 34532579 PMCID: PMC8439222 DOI: 10.1080/23802359.2021.1972870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The mitochondrial genome (mitogenome) of Gallinago gallinago gallinago Linnaeus, 1758 was determined by the high-throughput data. The assembled mitogenome was 16,919 bp in length, with a 58.7% A + T content and GC skew of −0.3850. Among 13 PCGs, an unusual start codon (GTG) was identified for the COX1 gene, and incomplete stop codons (T-) were found in the COX3, ND2 and ND4 genes. The function of a cytosine insertion at site 174 in the ND3 gene and its phylogenetic significance are worthy of further scrutiny. In the control region (CR), thirteen 15-bp simple sequence repeats were found in G. g. gallinago. Phylogenetic analysis indicated that Gallinago was clustered at the basal position of the Scolopax clade and that the monophyly of Gallinago was also recovered. The mitogenome data of G. g. gallinago provides useful resources for further studying the evolution of Scolopacidae.
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Affiliation(s)
- Chao Yang
- Shaanxi Institute of Zoology, Xi’an, China
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Xiang Hou
- Shaanxi Institute of Zoology, Xi’an, China
| | - Bo-Ye Liu
- Shaanxi Institute of Zoology, Xi’an, China
| | | | - Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- School of Basic Medical Sciences, Xi’an Medical University, Xi’an, China
| | - Xue-Juan Li
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Jie Tang
- Shaanxi Institute of Zoology, Xi’an, China
| | - Yan Wang
- Shaanxi Institute of Zoology, Xi’an, China
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Andreu-Sánchez S, Chen W, Stiller J, Zhang G. Multiple origins of a frameshift insertion in a mitochondrial gene in birds and turtles. Gigascience 2021; 10:giaa161. [PMID: 33463679 PMCID: PMC7814300 DOI: 10.1093/gigascience/giaa161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/05/2020] [Accepted: 12/18/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND During evolutionary history, molecular mechanisms have emerged to cope with deleterious mutations. Frameshift insertions in protein-coding sequences are extremely rare because they disrupt the reading frame. There are a few known examples of their correction through translational frameshifting, a process that enables ribosomes to skip nucleotides during translation to regain proper reading frame. Corrective frameshifting has been proposed to act on the single base pair insertion at position 174 of the mitochondrial NADH dehydrogenase subunit 3 gene (ND3) that has been observed in several turtles and birds. However, the relatively sparse taxonomic representation has hampered our understanding of the evolution of this insertion in vertebrates. RESULTS Here, we analyzed 87,707 ND3 sequences from 10,309 vertebrate taxa to reveal the evolutionary history of this insertion and its common genomic characteristics. We confirmed that the insertion only appears in turtles and birds and reconstructed that it evolved independently in both groups with complex patterns of gains and losses. The insertion was observed in almost all bird orders but was absent in all members of the diverse Passeriformes. We found strong conservation in the nucleotides surrounding the insertion in both turtles and birds, which implies that the insertion enforces structural constraints that could be involved in its correction. CONCLUSIONS Our study demonstrates that frameshifts can be widespread and can be retained for millions of years if they are embedded in a conserved sequence theme.
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Affiliation(s)
- Sergio Andreu-Sánchez
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- Present Address: University of Groningen, University Medical Center Groningen, Department of Pediatrics, 9700 RB Groningen, Netherlands
| | - Wanjun Chen
- China National Genebank, BGI-Shenzhen, Beishan Industrial Zone, 518083 Shenzhen, China
| | - Josefin Stiller
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen, Beishan Industrial Zone, 518083 Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China
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Schultz DT, Eizenga JM, Corbett-Detig RB, Francis WR, Christianson LM, Haddock SH. Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii. PeerJ 2020; 8:e8356. [PMID: 32025367 PMCID: PMC6991124 DOI: 10.7717/peerj.8356] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 12/04/2019] [Indexed: 11/20/2022] Open
Abstract
To date, five ctenophore species' mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.
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Affiliation(s)
- Darrin T. Schultz
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Jordan M. Eizenga
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russell B. Corbett-Detig
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Warren R. Francis
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | | | - Steven H.D. Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
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Two new mitogenomes of Picidae (Aves, Piciformes): Sequence, structure and phylogenetic analyses. Int J Biol Macromol 2019; 133:683-692. [DOI: 10.1016/j.ijbiomac.2019.04.157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023]
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Partial Mitochondrial Genome Sequences of Two Abyssal Sponges (Porifera: Hexactinellida), Bathydorus laniger and Docosaccus maculatus. GENOME ANNOUNCEMENTS 2018; 6:6/16/e00234-18. [PMID: 29674536 PMCID: PMC5908954 DOI: 10.1128/genomea.00234-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We announce the nearly complete mitochondrial genome sequences of two hexactinellid sponges, Bathydorus laniger and Docosaccus maculatus. A contiguous region of over 15,000 bp was sequenced from each genome. An uncommon structural element was identified as a series of repetitive elements with sequences matching cob in the genome of D. maculatus.
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An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida). Front Zool 2017; 14:18. [PMID: 28331531 PMCID: PMC5359874 DOI: 10.1186/s12983-017-0191-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/20/2017] [Indexed: 11/24/2022] Open
Abstract
Background Glass sponges (Class Hexactinellida) are important components of deep-sea ecosystems and are of interest from geological and materials science perspectives. The reconstruction of their phylogeny with molecular data has only recently begun and shows a better agreement with morphology-based systematics than is typical for other sponge groups, likely because of a greater number of informative morphological characters. However, inconsistencies remain that have far-reaching implications for hypotheses about the evolution of their major skeletal construction types (body plans). Furthermore, less than half of all described extant genera have been sampled for molecular systematics, and several taxa important for understanding skeletal evolution are still missing. Increased taxon sampling for molecular phylogenetics of this group is therefore urgently needed. However, due to their remote habitat and often poorly preserved museum material, sequencing all 126 currently recognized extant genera will be difficult to achieve. Utilizing morphological data to incorporate unsequenced taxa into an integrative systematics framework therefore holds great promise, but it is unclear which methodological approach best suits this task. Results Here, we increase the taxon sampling of four previously established molecular markers (18S, 28S, and 16S ribosomal DNA, as well as cytochrome oxidase subunit I) by 12 genera, for the first time including representatives of the order Aulocalycoida and the type genus of Dactylocalycidae, taxa that are key to understanding hexactinellid body plan evolution. Phylogenetic analyses suggest that Aulocalycoida is diphyletic and provide further support for the paraphyly of order Hexactinosida; hence these orders are abolished from the Linnean classification. We further assembled morphological character matrices to integrate so far unsequenced genera into phylogenetic analyses in maximum parsimony (MP), maximum likelihood (ML), Bayesian, and morphology-based binning frameworks. We find that of these four approaches, total-evidence analysis using MP gave the most plausible results concerning congruence with existing phylogenetic and taxonomic hypotheses, whereas the other methods, especially ML and binning, performed more poorly. We use our total-evidence phylogeny of all extant glass sponge genera for ancestral state reconstruction of morphological characters in MP and ML frameworks, gaining new insights into the evolution of major hexactinellid body plans and other characters such as different spicule types. Conclusions Our study demonstrates how a comprehensive, albeit in some parts provisional, phylogeny of a larger taxon can be achieved with an integrative approach utilizing molecular and morphological data, and how this can be used as a basis for understanding phenotypic evolution. The datasets and associated trees presented here are intended as a resource and starting point for future work on glass sponge evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12983-017-0191-3) contains supplementary material, which is available to authorized users.
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Lavrov DV, Pett W. Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages. Genome Biol Evol 2016; 8:2896-2913. [PMID: 27557826 PMCID: PMC5633667 DOI: 10.1093/gbe/evw195] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2016] [Indexed: 12/11/2022] Open
Abstract
Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0-25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitution rates, and a large range of genome sizes. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes.
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Affiliation(s)
- Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - Walker Pett
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, Villeurbanne, France
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Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res 2016; 44:7007-78. [PMID: 27436286 PMCID: PMC5009743 DOI: 10.1093/nar/gkw530] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
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Affiliation(s)
- John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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Extensive Mitochondrial mRNA Editing and Unusual Mitochondrial Genome Organization in Calcaronean Sponges. Curr Biol 2015; 26:86-92. [PMID: 26725199 DOI: 10.1016/j.cub.2015.11.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/03/2015] [Accepted: 11/05/2015] [Indexed: 10/22/2022]
Abstract
One of the unusual features of DNA-containing organelles in general and mitochondria in particular is the frequent occurrence of RNA editing [1]. The term "RNA editing" refers to a variety of mechanistically unrelated biochemical processes that alter RNA sequence during or after transcription [2]. The editing can be insertional, deletional, or substitutional and has been found in all major types of RNAs [3, 4]. Although mitochondrial mRNA editing is widespread in some eukaryotic lineages [5-7], it is rare in animals, with reported cases limited both in their scope and in phylogenetic distribution [8-11] (see also [12]). While analyzing genomic data from calcaronean sponges Sycon ciliatum and Leucosolenia complicata, we were perplexed by the lack of recognizable mitochondrial coding sequences. Comparison of genomic and transcriptomic data from these species revealed the presence of mitochondrial cryptogenes whose transcripts undergo extensive editing. This editing consisted of single or double uridylate (U) insertions in pre-existing short poly(U) tracts. Subsequent analysis revealed the presence of similar editing in Sycon coactum and the loss of editing in Petrobiona massiliana, a hypercalcified calcaronean sponge. In addition, mitochondrial genomes of at least some calcaronean sponges were found to have a highly unusual architecture, with nearly all genes located on individual and likely linear chromosomes. Phylogenetic analysis of mitochondrial coding sequences revealed accelerated rates of sequence evolution in this group. The latter observation presents a challenge for the mutational-hazard hypothesis [13], which posits that mRNA editing should not occur in lineages with an elevated mutation rate.
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Zhang Y, Sun J, Li X, Qiu JW. The mitochondrial genome of the deep-sea glass sponge Lophophysema eversa (Porifera, Hexacinellida, Hyalonematidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:1273-4. [PMID: 25082454 DOI: 10.3109/19401736.2014.945552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We reported a nearly complete mitochondrial genome (mitogenome) from the glass sponge Lophophysema eversa, the second mitogenome in the order Amphidiscosida and the ninth in the class Hexactinellida. It is 20,651 base pairs in length and contains 39 genes including 13 protein-coding genes, 2 ribosomal RNA subunit genes and 24 tRNA genes. The gene content and order of L. eversa are identical to those of Tabachnickia sp., the other species with a sequenced mitogenome in Amphidiscosida, except with two additional tRNAs and three tRNA translocations. The cob gene has a +1 translational frameshift. These results will contribute to a better understanding of the phylogeny of glass sponges.
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Affiliation(s)
- Yanjie Zhang
- a Department of Biology , Hong Kong Baptist University , Hong Kong , P.R. China and
| | - Jin Sun
- a Department of Biology , Hong Kong Baptist University , Hong Kong , P.R. China and
| | - Xinzheng Li
- b Institute of Oceanology, Chinese Academy of Sciences , Qingdao , P.R. China
| | - Jian-Wen Qiu
- a Department of Biology , Hong Kong Baptist University , Hong Kong , P.R. China and
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Abstract
We report the complete mitochondrial genome sequence of the Mediterranean glass sponge Oopsacas minuta. This 19-kb mitochondrial genome has 24 noncoding genes (22 tRNAs and 2 rRNAs) and 14 protein-encoding genes coding for 11 subunits of respiratory chain complexes and 3 ATP synthase subunits.
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Pett W, Lavrov DV. Cytonuclear Interactions in the Evolution of Animal Mitochondrial tRNA Metabolism. Genome Biol Evol 2015; 7:2089-101. [PMID: 26116918 PMCID: PMC4558845 DOI: 10.1093/gbe/evv124] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The evolution of mitochondrial information processing pathways, including replication, transcription and translation, is characterized by the gradual replacement of mitochondrial-encoded proteins with nuclear-encoded counterparts of diverse evolutionary origins. Although the ancestral enzymes involved in mitochondrial transcription and replication have been replaced early in eukaryotic evolution, mitochondrial translation is still carried out by an apparatus largely inherited from the α-proteobacterial ancestor. However, variation in the complement of mitochondrial-encoded molecules involved in translation, including transfer RNAs (tRNAs), provides evidence for the ongoing evolution of mitochondrial protein synthesis. Here, we investigate the evolution of the mitochondrial translational machinery using recent genomic and transcriptomic data from animals that have experienced the loss of mt-tRNAs, including phyla Cnidaria and Ctenophora, as well as some representatives of all four classes of Porifera. We focus on four sets of mitochondrial enzymes that directly interact with tRNAs: Aminoacyl-tRNA synthetases, glutamyl-tRNA amidotransferase, tRNAIle lysidine synthetase, and RNase P. Our results support the observation that the fate of nuclear-encoded mitochondrial proteins is influenced by the evolution of molecules encoded in mitochondrial DNA, but in a more complex manner than appreciated previously. The data also suggest that relaxed selection on mitochondrial translation rather than coevolution between mitochondrial and nuclear subunits is responsible for elevated rates of evolution in mitochondrial translational proteins.
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Affiliation(s)
- Walker Pett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University Present address: Laboratoire de Biométrie et Biologie Évolutive CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
| | - Dennis V Lavrov
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
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Wang Y, Zhou S, Qian L, Pan T, Zhang B. The mitochondrial genome of Ixobrychus flavicollis (Ardeidae: Ixobrychus). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:921-2. [PMID: 24960564 DOI: 10.3109/19401736.2014.926486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Ixobrychus flavicollis is the largest bittern in Ixobrychus which has very wide geographical range. In our results, the complete mitochondrial genome of I. flavicollis is 17,016 bp in length. Thirteen protein-coding genes, two rRNA genes, twenty-two tRNA genes and one non-coding region (D-loop) are present in this mitochondrial genome. No special arrangement when compared with other typical mitochondrial of vertebrates. The percentage of A and T (56.7%) was slightly higher than G and C.
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Affiliation(s)
- Yupeng Wang
- a School of Life Science, Anhui Normal University , Anhui , Wuhu , P.R China .,b School of Resources and Environment, Anhui Agricultural University , Hefei , Anhui , P.R China , and
| | - Shoubiao Zhou
- a School of Life Science, Anhui Normal University , Anhui , Wuhu , P.R China
| | - Lifu Qian
- c School of Life Science, Anhui University , Anhui , Hefei , P.R China
| | - Tao Pan
- c School of Life Science, Anhui University , Anhui , Hefei , P.R China
| | - Baowei Zhang
- c School of Life Science, Anhui University , Anhui , Hefei , P.R China
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Reiswig HM, Dohrmann M. Three new species of glass sponges (Porifera: Hexactinellida) from the West Indies, and molecular phylogenetics of Euretidae and Auloplacidae (Sceptrulophora). Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12138] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Henry M. Reiswig
- Natural History Section; Royal British Columbia Museum; 675 Belleville Street Victoria BC V8W 9W2 Canada
- Department of Biology; University of Victoria; 3800 Finnerty Road Victoria BC V8P 4H9 Canada
| | - Martin Dohrmann
- Department of Earth & Environmental Sciences, Palaeontology & Geobiology, Molecular Geo- & Palaeobiology Lab; Ludwig-Maximilians-University Munich; Richard-Wagner-Str. 10 80333 Munich Germany
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