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Russo A, Alessandrini M, El Baidouri M, Frei D, Galise TR, Gaidusch L, Oertel HF, Garcia Morales SE, Potente G, Tian Q, Smetanin D, Bertrand JAM, Onstein RE, Panaud O, Frey JE, Cozzolino S, Wicker T, Xu S, Grossniklaus U, Schlüter PM. Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation. Nat Commun 2024; 15:6308. [PMID: 39060266 PMCID: PMC11282089 DOI: 10.1038/s41467-024-50622-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Pollinator-driven evolution of floral traits is thought to be a major driver of angiosperm speciation and diversification. Ophrys orchids mimic female insects to lure male pollinators into pseudocopulation. This strategy, called sexual deception, is species-specific, thereby providing strong premating reproductive isolation. Identifying the genomic architecture underlying pollinator adaptation and speciation may shed light on the mechanisms of angiosperm diversification. Here, we report the 5.2 Gb chromosome-scale genome sequence of Ophrys sphegodes. We find evidence for transposable element expansion that preceded the radiation of the O. sphegodes group, and for gene duplication having contributed to the evolution of chemical mimicry. We report a highly differentiated genomic candidate region for pollinator-mediated evolution on chromosome 2. The Ophrys genome will prove useful for investigations into the repeated evolution of sexual deception, pollinator adaptation and the genomic architectures that facilitate evolutionary radiations.
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Affiliation(s)
- Alessia Russo
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland.
- Department of Systematic and Evolutionary Botany and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland.
| | - Mattia Alessandrini
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Moaine El Baidouri
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- EMR269 MANGO, Institut de Recherche pour le Développement, Perpignan, France
| | - Daniel Frei
- Department of Methods Development and Analytics, Agroscope, Wädenswil, Switzerland
| | | | - Lara Gaidusch
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Hannah F Oertel
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Sara E Garcia Morales
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Qin Tian
- Naturalis Biodiversity Centre, Leiden, The Netherlands
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Dmitry Smetanin
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Joris A M Bertrand
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- EMR269 MANGO, Institut de Recherche pour le Développement, Perpignan, France
| | - Renske E Onstein
- Naturalis Biodiversity Centre, Leiden, The Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle - Jena - Leipzig, Leipzig, Germany
| | - Olivier Panaud
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- EMR269 MANGO, Institut de Recherche pour le Développement, Perpignan, France
| | - Jürg E Frey
- Department of Methods Development and Analytics, Agroscope, Wädenswil, Switzerland
| | | | - Thomas Wicker
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Shuqing Xu
- Institute of Organismic and Molecular Evolution, University of Mainz, Mainz, Germany
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Philipp M Schlüter
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
- Department of Systematic and Evolutionary Botany and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland.
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Dallagnol LC, Cônsoli FL. Evolutionary and phylogenetic insights from the mitochondrial genomic analysis of Diceraeus melacanthus and D. furcatus (Hemiptera: Pentatomidae). Sci Rep 2024; 14:12861. [PMID: 38834792 DOI: 10.1038/s41598-024-63584-w] [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: 01/23/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
The mitochondrial genomes of D. melacanthus and D. furcatus were sequenced and used to investigate the phylogenetic relationships with 54 species of Pentatomidae. Their mitogenomes are 17,197 and 15,444 bp-long, respectively, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22/21 transfer RNA genes, with conserved gene arrangement. Leu, Lys, and Ser were the most common amino acids in their PCGs. PCGs evolutionary analysis indicated their mitogenomes are under purifying selection, and the most conserved genes are from the cytochrome complex, reinforcing their suitability as markers for molecular taxonomy. We identified 490 mtSSRs in 56 Pentatomidae species, with large variation and a positive correlation between mtSSR number and genome size. Three mtSSRs were identified in each Diceraeus species. Only the mtSSR in the nad6 (D. melacanthus) and nad4 (D. furcatus) appear to have application as molecular markers for species characterization. Phylogenetic analysis confirmed the monophyly of Pentatomidae. However, our analysis challenged the monophyly of Pentatominae and Podopinae. We also detected unexpected relationships among some tribes and genera, highlighting the complexity of the internal taxonomic structure of Pentatomidae. Both Diceraeus species were grouped in the same clade with the remaining Carpocorini analyzed.
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Affiliation(s)
- Lilian Cris Dallagnol
- Insect Interactions Laboratory, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Fernando Luís Cônsoli
- Insect Interactions Laboratory, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil.
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Gutiérrez EG, Ortega J, Savoie A, Baeza JA. The mitochondrial genome of the mountain wooly tapir, Tapirus pinchaque and a formal test of the effect of altitude on the adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates. BMC Genomics 2023; 24:527. [PMID: 37674108 PMCID: PMC10481570 DOI: 10.1186/s12864-023-09596-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND The harsh conditions of high-altitude environments are known to drive the evolution of physiological and morphological traits in endothermic animals. These conditions are expected to result in the adaptive evolution of protein coding genes encoded in mitochondrial genomes that are vital for the oxidative phosphorylation pathway. In this study, we formally tested for signatures of adaptive evolution on mitochondrial protein coding genes in Tapirus pinchaque and other odd-toed ungulates inhabiting high-elevation environments. RESULTS The AT-rich mitochondrial genome of T. pinchaque is 16,750 bp long. A phylomitogenomic analysis supports the monophyly of the genus Tapirus and families in the Perissodactyla. The ratio of non-synonymous to synonymous substitutions demonstrated that all mitochondrial genes undergo purifying selection in T. pinchaque and other odd ungulates living at high elevations. Over this negative background selection, Branch Models suggested that cox3 and nad6 might be undergoing stronger purifying selection than other mitochondrial protein coding genes. Furthermore, Site Models suggested that one and four sites in nad2 and nad5, respectively, could be experiencing positive selection. However, these results were supported by Likelihood Ratio Tests but not Bayesian Empirical Bayes posterior probabilities. Additional analyses (in DataMonkey) indicated a relaxation of selection strength in nad6, evidence of episodic diversifying selection in cob, and revealed episodic positive/diversifying selection signatures for two sites in nad1, and one site each in nad2 and nad4. CONCLUSION The mitochondrial genome of T. pinchaque is an important genomic resource for conservation of this species and this study contributes to the understanding of adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates inhabiting high-altitude environments.
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Affiliation(s)
- Edgar G Gutiérrez
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Químicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala S/N, Col. Santo Tomás, Ciudad de México, C.P. 11340, Mexico
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Químicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala S/N, Col. Santo Tomás, Ciudad de México, C.P. 11340, Mexico
| | - Avery Savoie
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA.
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL, 34949, USA.
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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Barrera CA, Ortega J, Gutierrez-Guerrero YT, Baeza JA. Comparative mitochondrial genomics of American nectar-feeding long-nosed bats Leptonycteris spp. with insights into the phylogeny of the family Phyllostomidae. Gene 2023:147588. [PMID: 37364695 DOI: 10.1016/j.gene.2023.147588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/05/2023] [Accepted: 06/21/2023] [Indexed: 06/28/2023]
Abstract
Among leaf-nosed bats (family Phyllostomidae), the genus Leptonycteris (subfamily Glossophaginae), contains three migratory and obligate nectar-dwelling species of great ecological and economic importance; the greater long-nosed bat L. nivalis, the lesser long-nosed bat L. yerbabuenae, and the southern long-nosed bat L. curasoae. According to the IUCN, the three species are categorized as 'vulnerable', 'endangered', and 'near threatened', respectively. In this study, we assembled and characterized in detail the mitochondrial genome of Leptonycteris spp. and examined the phylogenetic position of this genus in the family Phyllostomidae based on protein coding genes (PCGs). The mitogenomes of L. nivalis, L. curasoae, and L. yerbabuenae are 16,708, 16,758, and 16,729 bp in length and each encode 13 PCGs, 22 transfer RNA genes, 2 rRNA genes, and a putative control region (CR). Mitochondrial gene order is identical to that reported before for the family Phyllostomidae. All tRNAs exhibit a 'cloverleaf' secondary structure, except tRNA-Serine-1 that is missing the DHU arm in the three species. All PCGs are exposed to purifying selection with atp8 experiencing the most relaxed purifying selection as the ω ratio was higher for this gene compared to the other PCGs in each species. The CR of each species contains three functional domains: extended termination associated sequence (ETAS), Central, and conserved sequence block domain (CSB). A phylomitogenomic analysis revealed that Leptonycteris is monophyletic and most closely related to the genus Glossophaga. The analysis also supported the monophyly of the family Glossophaginae in the speciose family Phyllostomidae. The mitochondria characterization of these species provides relevant information to develop molecular markers for conservation purposes.
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Affiliation(s)
- Carlos A Barrera
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico City, Mexico.
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico City, Mexico.
| | - Yocelyn T Gutierrez-Guerrero
- Museum of Vertebrate Zoology, Department of Integrative Biology, University of California Berkeley, Berkeley, CA, US.
| | - J A Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634, USA; Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL 34949, USA; Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, Coquimbo 1281, Chile.
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Comparative analysis of mitochondrial genomes reveals family-specific architectures and molecular features in scorpions (Arthropoda: Arachnida: Scorpiones). Gene 2023; 859:147189. [PMID: 36657651 DOI: 10.1016/j.gene.2023.147189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/19/2022] [Accepted: 01/06/2023] [Indexed: 01/17/2023]
Abstract
Scorpions are a group of arachnids with great evolutionary success that comprise more than 2,000 described species. Mitochondrial genomes have been little studied in this clade. We describe and compare different scorpion mitochondrial genomes and analyze their architecture and molecular characteristics. We assembled eight new scorpion mitochondrial genomes from transcriptomic datasets, annotated them, predicted the secondary structures of tRNAs, and compared the nucleotide composition, codon usage, and relative synonymous codon usage of 16 complete scorpion mitochondrial genomes. Lastly, we provided a phylogeny based on all mitochondrial protein coding genes. We characterized the mitogenomes in detail and reported particularities such as dissimilar synteny in the family Buthidae compared to other scorpions, unusual tRNA secondary structures, and unconventional start and stop codons in all scorpions. Our comparative analysis revealed that scorpion mitochondrial genomes exhibit different architectures and features depending on taxonomic identity. We highlight the parvorder Buthida, particularly the family Buthidae, as it invariably exhibited different mitogenome features such as synteny, codon usage, and AT-skew compared to the parvorder Iurida that included the rest of the scorpion families we analyzed in this study. Our results provide a better understanding of the evolution of mitogenome features and phylogenetic relationships in scorpions.
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Baeza JA, Macdonald-Shedd A, Latorre-Cárdenas MC, Griffin E, Gutiérrez-Rodríguez C. The first genomic resource for the ‘near threatened’ Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae. J NAT HIST 2023. [DOI: 10.1080/00222933.2023.2186809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Colín A, Galván-Tirado C, Carreón-Palau L, Bracken-Grissom HD, Baeza JA. Mitochondrial genomes of the land hermit crab Coenobita clypeatus (Anomura: Paguroidea) and the mole crab Emerita talpoida (Anomura: Hippoidea) with insights into phylogenetic relationships in the Anomura (Crustacea: Decapoda). Gene X 2023; 849:146896. [DOI: 10.1016/j.gene.2022.146896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/31/2022] [Accepted: 09/12/2022] [Indexed: 11/28/2022] Open
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Baeza JA. Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica. PeerJ 2022; 10:e14428. [PMID: 36523460 PMCID: PMC9745948 DOI: 10.7717/peerj.14428] [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: 06/23/2022] [Accepted: 10/30/2022] [Indexed: 12/12/2022] Open
Abstract
The Amur or Siberian tiger Panthera tigris altaica (Temminck, 1844) is currently restricted to a small region of its original geographical range in northwestern Asia and is considered 'endangered' by the IUCN Red List of Threatened Species. This solitary, territorial, and large top predator is in major need of genomic resources to inform conservation management strategies. This study formally tested if complete mitochondrial genomes of P. tigris altaica can be assembled from non-enriched metagenomic libraries generated from scat eDNA samples using the Illumina sequencing platform and open-access bioinformatics pipelines. The mitogenome of P. tigris altaica was assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 322.7x to 17.6x in four different scat eDNA samples. A nearly complete mitochondrial genome (101x) was retrieved from a fifth scat eDNA sample. The complete or nearly complete mitochondrial genomes of P. tigris altaica were AT-rich and composed of 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Synteny observed in all assembled mitogenomes was identical to that reported before for P. tigris altaica and other felids. A phylogenomic analysis based on all PCGs demonstrated that the mitochondrial genomes assembled from scat eDNA reliably identify the sequenced samples as belonging to P. tigris and distinguished the same samples from closely and distantly related congeneric species. This study demonstrates that it is viable to retrieve accurate whole and nearly complete mitochondrial genomes of P. tigris altaica (and probably other felids) from scat eDNA samples without library enrichment protocols and using open-access bioinformatics workflows. This new genomic resource represents a new tool to support conservation strategies (bio-prospecting and bio-monitoring) in this iconic cat.
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Affiliation(s)
- J. Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, United States,Smithsonian Marine Station at Fort Pierce, Fort Pierce, Florida, United States,Departamento de Biologia Marina, Universidad Catolica del Norte, Coquimbo, IV Region, Chile
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Luis Molina-Quirós J, Hernández-Muñoz S, Antonio Baeza J. The complete mitochondrial genome of the roosterfish Nematistius pectoralis Gill 1862: purifying selection in protein coding genes, organization of the control region, and insights into family-level phylogenomic relationships in the recently erected order Carangiformes. Gene 2022; 845:146847. [PMID: 36058495 DOI: 10.1016/j.gene.2022.146847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/26/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022]
Abstract
The roosterfish Nematistius pectoralis is considered as one of the most magnificent sportfishes worldwide. This study developed the first genomic resource for this trophy-fish that is heavily targeted by the fly-fishing industry. The complete mitochondrial genome of N. pectoralis was assembled using short read sequences and analyzed in detail. The mitochondrial genome of N. pectoralis is 16,537 bp in length and comprises 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (12S and 16S), and 22 transfer RNA genes. A long intergenic space 770 bp in length was assumed to be the D-loop or Control Region (CR). Most of the PCGs and tRNA genes are encoded in the L-strand. All PCGs are under purifying selection and atp8 and nad6 experienced the least selective pressure. All tRNAs exhibit a cloverleaf secondary structure except tRNA-Serine 1 that lacked the D-arm loop. The D-loop of N. pectoralis exhibits three domains commonly described in other fishes; extended terminal associated sequences (ETAS), central, and conserved sequence block (CSB). A ML phylogenetic reconstruction of the newly recognized order Carangiformes based on all 13 mitochondrial PCGs did not support the monophyly of this clade but recognized several families as monophyletic, including Bothidae, Carangidae, Istiophoridae, Latidae, Paralichthyidae, Polynemidae, and Rhombosoleidae. Nematistius pectoralis was sister to a clade composed of Toxotes chatareus (fam. Toxotidae) + Lactarius lactarius (fam. Lactariidae). This genomic resource developed for N. pectoralis will aid in improving our understanding of the population genomics of and strengthen conservation and management strategies in this remarkable trophy-fish.
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Affiliation(s)
- José Luis Molina-Quirós
- Biomolecular Laboratory, Center for International Programs, Universidad Veritas, San José, Costa Rica.
| | - Sebastián Hernández-Muñoz
- Biomolecular Laboratory, Center for International Programs, Universidad Veritas, San José, Costa Rica; Sala de Colecciones, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA; Departamento de Biología Marina, Universidad Catolica del Norte, Coquimbo, IV Región, Chile; Smithsonian Marine Station at Fort Pierce, Smithsonian Institution, Fort Pierce, FL, USA
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Ennis CC, Ortega J, Baeza JA. First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird's) tapir ( Tapirus bairdii). PeerJ 2022; 10:e13440. [PMID: 35669959 PMCID: PMC9166683 DOI: 10.7717/peerj.13440] [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: 12/02/2021] [Accepted: 04/25/2022] [Indexed: 01/14/2023] Open
Abstract
Baird's tapir, or the Central American Tapir Tapirus bairdii (family Tapiridae), is one of the largest mammals native to the forests and wetlands of southern North America and Central America, and is categorized as 'endangered' on the 2014 IUCN Red List of Threatened Species. This study reports, for the first time, the complete mitochondrial genome of T. bairdii and examines the phylogenetic position of T. bairdii amongst closely related species in the same family and order to which it belongs using mitochondrial protein-coding genes (PCG's). The circular, double-stranded, A-T rich mitochondrial genome of T. bairdii is 16,697 bp in length consisting of 13 protein-coding genes (PCG's), two ribosomal RNA genes (rrnS (12s ribosomal RNA and rrnL (16s ribosomal RNA)), and 22 transfer RNA (tRNA) genes. A 33 bp long region was identified to be the origin of replication for the light strand (OL), and a 1,247 bp long control region (CR) contains the origin of replication for the heavy strand (OH). A majority of the PCG's and tRNA genes are encoded on the positive, or heavy, strand. The gene order in T. baiirdi is identical to that of T. indicus and T. terrestris, the only two other species of extant tapirs with assembled mitochondrial genomes. An analysis of Ka/Ks ratios for all the PCG's show values <1, suggesting that all these PCGs experience strong purifying selection. A maximum-likelihood phylogenetic analysis supports the monophyly of the genus Tapirus and the order Perissodactyla. The complete annotation and analysis of the mitochondrial genome of T. bairdii will contribute to a better understanding of the population genomic diversity and structure of this species, and it will assist in the conservation and protection of its dwindling populations.
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Affiliation(s)
- Caroline C. Ennis
- Biological Sciences, Clemson University, Clemson, SC, United States of America
| | - Jorge Ortega
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de Mexico, Mexico DF, Mexico
| | - J. Antonio Baeza
- Biological Sciences, Clemson University, Clemson, SC, United States of America,Departamento de Biologia Marina, Universidad Catolica del Norte, Coquimbo, IV Region, Chile,Smithsonian Marine Station at Fort Pierce, Smithsonian Institute, Fort Pierce, FL, United States of America
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Lü J, Xia L, Liu X, Ma Y, Li J, Ye Y, Guo B. The mitochondrial genome of Grapsus albolineatus (Decapoda: Brachyura: Grapsidae) and phylogenetic associations in Brachyura. Sci Rep 2022; 12:2104. [PMID: 35136145 PMCID: PMC8826855 DOI: 10.1038/s41598-022-06080-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/11/2022] [Indexed: 11/09/2022] Open
Abstract
Complete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and evolutionary traits. In this study, we determined the complete mitochondrial DNA sequence of the herbivorous crab Grapsus albolineatus. It is a typical metazoan mitochondrial genome. The total size is 15,583 bp, contains the entire set of 37 genes, and has an AT-rich region. Then, 23 of the 37 genes were encoded by the heavy (+) strand while 14 are encoded by the light (−) strand. Compared with the pan-crustacean ground pattern, two tRNA genes (tRNA-His and tRNA-Gln) were rearranged and the tandem duplication/random loss model was used to explain the observed gene rearrangements. The phylogenetic results showed that all Grapsidae crabs clustered together as a group. Furthermore, the monophyly of each family was well supported, with the exception of Menippidae. In general, the results obtained in this study will contribute to the better understanding of gene rearrangements in Grapsidae crab mitogenomes and provide new insights into the phylogeny of Brachyura.
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Affiliation(s)
- Jiayin Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Liping Xia
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Xiaojuan Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
| | - Yanwen Ma
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
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Rodriguez-Pilco MA, Leśny P, Podsiadłowski L, Schubart CD, Baeza JA. Characterization of The Complete Mitochondrial Genome of the Bromeliad Crab Metopaulias depressus (Rathbun, 1896) (Crustacea: Decapoda: Brachyura: Sesarmidae). Genes (Basel) 2022; 13:genes13020299. [PMID: 35205344 PMCID: PMC8872168 DOI: 10.3390/genes13020299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
Metopaulias depressus is a non-marine crab endemic to Jamaica that dwells in rainforest bromeliads and exhibits elaborate active parental care behavior. Current genomic resources on M. depressus are rare, limiting the understanding of its adaptation to terrestrial life in species that evolved from marine ancestors. This study reports the complete mitochondrial genome of M. depressus assembled using Sanger sequencing. The AT-rich mitochondrial genome of M. depressus is 15,765 bp in length and comprises 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 691 bp-long intergenic space is assumed to be the control region (CR) or D-loop. A set of selective pressure analyses indicate that the entirety of the PCGs experience purifying selection. Cox1, cox2, nad5, cox3, and atp6 experience strong purifying selection, and atp8 experiences weak purifying selection compared to the rest of the PCGs. The secondary structures of most tRNA genes exhibit a standard ‘cloverleaf’ structure, with the exception of trnS1, which lacks the dihydroxyuridine (DHU) arm but not the loop, the trnH gene, which lacks the thymine pseudouracil cytosine (T) loop but not the arm, and trnM, which exhibits an overly developed T loop. A maximum likelihood phylogenetic analysis based on all PCGs indicated that M. depressus is more closely related to the genera Clistocoeloma, Nanosesarma, and Parasesarma than to Chiromantes, Geosesarma, and Orisarma. This study contributes to deciphering the phylogenetic relationships within the family Sesarmidae and represents a new genomic resource for this iconic crab species.
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Affiliation(s)
- Milena A. Rodriguez-Pilco
- Facultad de Ciencias Biológicas, Universidad Nacional de San Agustin, Av. Daniel Alcides Carreon s/n, Arequipa 04001, Peru;
| | - Peter Leśny
- Institute for Evolutionary Biology & Animal Ecology, University Bonn, 53121 Bonn, Germany;
| | - Lars Podsiadłowski
- Centre for Molecular Biodiversity Research (ZMB), Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), 53113 Bonn, Germany;
| | | | - Juan Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL 34949, USA
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, Coquimbo 1281, Chile
- Correspondence:
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13
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López-Cuamatzi IL, Ortega J, Baeza JA. The complete mitochondrial genome of the 'Zacatuche' Volcano rabbit (Romerolagus diazi), an endemic and endangered species from the Volcanic Belt of Central Mexico. Mol Biol Rep 2021; 49:1141-1149. [PMID: 34783988 DOI: 10.1007/s11033-021-06940-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/23/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND The 'Zacatuche', 'Teporingo', or Volcano rabbit (Romerolagus diazi) belongs to the family Leporidae, is an endemic species restricted to the Central part of the Trans-Mexican Volcanic Belt, and is considered 'endangered' by the IUCN Red List of Threatened Species. METHODS AND RESULTS This study reports, for the first time, the complete mitochondrial genome of R. diazi and examined the phylogenetic position of R. diazi among other closely related co-familiar species using mitochondrial protein-coding genes (PCGs). The mitogenome of R. diazi was assembled from short Illumina 150 bp pair-end reads with a coverage of 189x. The AT-rich mitochondrial genome of R. diazi is 17,400 bp in length and is comprised of 13 PCGs, two ribosomal RNA genes, and 22 transfer RNA genes. The gene order observed in the mitochondrial genome of R. diazi is identical to that reported for other leporids. Phylogenetic analyses based on PCGs support the basal position of Romerolagus within the Leporidae, at least when compared to the genera Oryctolagus and Lepus. Nonetheless, additional mitochondrial genomes from species belonging to the genera Bunolagus, Sylvilagus, and Pronolagus, among others, are needed before a more robust conclusion about the derived vs basal placement of Romerolagus within the family Leporidae can be reached based on mitochondrial PCGs. CONCLUSIONS This is the first genomic resource developed for R. diazi and it represents a tool to improve our understanding about the ecology and evolutionary biology of this iconic and endangered species.
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Affiliation(s)
- Issachar Leonardo López-Cuamatzi
- Posgrado en Ecología Tropical, Centro de Investigaciones Tropicales, Universidad Veracruzana, José María Morelos 44, Zona Centro, Centro, 91000, Xalapa-Enríquez, Mexico.
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Sto. Tomas, 11340, Ciudad de México, México
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA.,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL, 34949, USA.,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile
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14
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Jakovlić I, Zou H, Zhao XM, Zhang J, Wang GT, Zhang D. Evolutionary History of Inversions in Directional Mutational Pressures in Crustacean Mitochondrial Genomes: Implications for Evolutionary Studies. Mol Phylogenet Evol 2021; 164:107288. [PMID: 34365015 DOI: 10.1016/j.ympev.2021.107288] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 01/29/2023]
Abstract
Inversions of the origin of replication (ORI) in mitochondrial genomes produce asymmetrical mutational pressures that can cause strong base composition skews. Due to skews often being overlooked, the total number of crustacean lineages that underwent ORI events remains unknown. We analysed skews, cumulative skew plots, conserved sequence motifs, and mitochondrial architecture of all 965 available crustacean mitogenomes (699 unique species). We found indications of an ORI in 159 (22.7%) species, and mapped these to 23 ORI events: 16 identified with confidence and 7 putative (13 newly proposed, and for 5 we improved the resolution). Two ORIs occurred at or above the order level: Isopoda and Copepoda. Shifts in skew plots are not a precise tool for identifying the replication mechanism. We discuss how ORIs can produce mutational bursts in mitogenomes and show how these can interfere with various types of evolutionary studies. Phylogenetic analyses were plagued by artefactual clustering, and ORI lineages exhibited longer branches, a higher number of synonymous substitutions, higher mutational saturation, and higher compositional heterogeneity. ORI events also affected codon usage and protein properties. We discuss how this may have caused erroneous interpretation of data in previous studies that did not account for skew patterns.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xu-Mao Zhao
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China
| | - Jin Zhang
- Bio-Transduction Lab, Wuhan 430075, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China.
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15
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Ennis CC, Haeffner NN, Keyser CD, Leonard ST, Macdonald-Shedd AC, Savoie AM, Cronin TJ, Veldsman WP, Barden P, Chak STC, Baeza JA. Comparative mitochondrial genomics of sponge-dwelling snapping shrimps in the genus Synalpheus: Exploring differences between eusocial and non-eusocial species and insights into phylogenetic relationships in caridean shrimps. Gene 2021; 786:145624. [PMID: 33798681 DOI: 10.1016/j.gene.2021.145624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/18/2021] [Accepted: 03/26/2021] [Indexed: 11/29/2022]
Abstract
The genus Synalpheus is a cosmopolitan clade of marine shrimps found in most tropical regions. Species in this genus exhibit a range of social organizations, including pair-forming, communal breeding, and eusociality, the latter only known to have evolved within this genus in the marine realm. This study examines the complete mitochondrial genomes of seven species of Synalpheus and explores differences between eusocial and non-eusocial species considering that eusociality has been shown before to affect the strength of purifying selection in mitochondrial protein coding genes. The AT-rich mitochondrial genomes of Synalpheus range from 15,421 bp to 15,782 bp in length and comprise, invariably, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. A 648 bp to 994 bp long intergenic space is assumed to be the D-loop. Mitochondrial gene synteny is identical among the studied shrimps. No major differences occur between eusocial and non-eusocial species in nucleotide composition and codon usage profiles of PCGs and in the secondary structure of tRNA genes. Maximum likelihood phylogenetic analysis of the complete concatenated PCG complement of 90 species supports the monophyly of the genus Synalpheus and its family Alpheidae. Moreover, the monophyletic status of the caridean families Alvinocaridae, Atyidae, Thoridae, Lysmatidae, Palaemonidae, and Pandalidae within caridean shrimps are fully or highly supported by the analysis. We therefore conclude that mitochondrial genomes contain sufficient phylogenetic information to resolve relationships at high taxonomic levels within the Caridea. Our analysis of mitochondrial genomes in the genus Synalpheus contributes to the understanding of the coevolution between genomic architecture and sociality in caridean shrimps and other marine organisms.
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Affiliation(s)
- Caroline C Ennis
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Nariah N Haeffner
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Cameron D Keyser
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Shannon T Leonard
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | | | - Avery M Savoie
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Timothy J Cronin
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Werner P Veldsman
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, China
| | - Phillip Barden
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA.
| | - Solomon T C Chak
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA; Department of Biological Sciences, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA; Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida 34949, USA; Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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16
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Insights into the evolution of Brachyura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements. Int J Biol Macromol 2021; 170:717-727. [PMID: 33412200 DOI: 10.1016/j.ijbiomac.2020.12.210] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/29/2020] [Accepted: 12/29/2020] [Indexed: 11/23/2022]
Abstract
Brachyura is one of the most species rich and highly derived groups among extant crustaceans, with over 7250 known species. However, brachyuran phylogeny remains controversial and requires further study. Here, we combined 103 brachyuran mitogenomes from GenBank with 10 new mitogenomes to describe gene rearrangement patterns and explore the internal phylogenetic relationships of Brachyura. Most of the 10 novel mitogenomes had the typical 37 genes, except that of Longpotamon depressum, which lacked trnQ. We discovered 15 gene rearrangement patterns among Brachyura and preliminarily determined their rearrangement mechanisms with the help of CREx. We identified seven putative ancestral family gene orders among the 15 rearrangement patterns and expounded systematically upon the mechanisms of their rearrangement. In our phylogenetic analysis, Raninoida shared a sister relationship with an eubrachyuran clade ((Heterotremata [Potamoidea] + Thoracotremata) + Heterotremata) at maximum nodal support rather than Dromiacea, which did not support monophyly of Podotremata. In addition, Potamoidea (Parathelphusidae + Potamidae) retained a close relationship with Thoracotremata rather than their marine relatives in Heterotremata. Our study provides important information for the evolution of Brachyura by using the large taxon sampling currently available for systematic rearrangement and phylogenetic analyses.
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17
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Conrad I, Craft A, Thurman CL, Baeza JA. The complete mitochondrial genome of the red-jointed brackish-water fiddler crab Minuca minax (LeConte 1855) (Brachyura: Ocypodidae): New family gene order, and purifying selection and phylogenetic informativeness of protein coding genes. Genomics 2020; 113:565-572. [PMID: 32980522 DOI: 10.1016/j.ygeno.2020.09.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/10/2020] [Accepted: 09/22/2020] [Indexed: 10/23/2022]
Abstract
Minuca minax is a semi-terrestrial crustacean that commonly lives in low salinity, riverine habitats along the shores of the eastern United States. This study reports, for the first time, the complete mitochondrial genome of M. minax. The AT-rich mitochondrial genome of M. minax is 15,937 bp in length and comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 737 bp long intergenic space is assumed to be the D-loop. Most of the PCGs and tRNA genes are encoded in the L-strand. The gene order observed in the mitochondrial genome of M. minax is new although almost identical to that reported in confamiliar species. In all other confamiliar species to which M. minax is compared, the positions of the trnQ gene and the trnI gene are switched. KA/KS ratios calculated for all mitochondrial PCGs show values of <1, indicating that these PCGs are evolving under purifying selection. A maximum likelihood phylogenetic analysis (concatenated PCGs [n = 13], 15 species) supports the monophyly of the subfamilies Ocypodinae and Gelaminidae. Mitochondrial PCGs have enough phylogenetic information to reveal relationships supporting higher taxonomic levels within this family. The knowledge of a complete mitochondrial genome from the red-jointed brackish-water fiddler crab M. minax contributes to the better understanding of meta-population connectivity and the mechanisms involved in the adaptation of marine organisms to near-limnic conditions.
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Affiliation(s)
- Isabelle Conrad
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Abby Craft
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Carl L Thurman
- Department of Biology, University of Northern Iowa, Cedar Falls, IA 50614-0421, USA
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA; Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida 34949, USA; Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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18
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González-Castellano I, Pons J, González-Ortegón E, Martínez-Lage A. Mitogenome phylogenetics in the genus Palaemon (Crustacea: Decapoda) sheds light on species crypticism in the rockpool shrimp P. elegans. PLoS One 2020; 15:e0237037. [PMID: 32810189 PMCID: PMC7444591 DOI: 10.1371/journal.pone.0237037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
The genus Palaemon comprises worldwide marine and freshwater shrimps and prawns, and some of them are ecologically or commercially important species. Palaemon is not currently a monophyletic group, so phylogenetics and systematics are constantly changing. Species crypticism has been pointed out in several Palaemon species, being the clearest evidence in the European rockpool shrimp P. elegans. Here we sequenced and described seven European Palaemon mitochondrial genomes. The mitochondrial protein-coding genes were used, along with those of three other Palaemon species, to perform mitogenome phylogenetic analyses to clarify the evolutionary relationships within the genus, and particularly to shed light on the cryptic species found within P. elegans. The Messinian Salinity Crisis (5.3-5.9 Ma, late Miocene) was proposed to be the origin of this cryptic species and it was used as aged constraint for calibration analysis. We provide the largest and the first time-calibrated mitogenome phylogeny of the genus Palaemon and mitogenome substitution rate was estimated (1.59% per million years) in Decapoda for the first time. Our results highlighted the need for future systematics changes in Palaemon and crypticism in P. elegans was confirmed. Mitochondrial genome and cox1 (1.41%) substitution rate estimates matched those published elsewhere, arguing that the Messinian Salinity Crisis was a plausible event driving the split between P. elegans and its cryptic species. Molecular dating suggested that Pleistocene glaciations were likely involved in the differentiation between the Atlantic and Mediterranean populations of P. elegans. On the contrary, the divergence between the Atlantic and Mediterranean populations of the common littoral shrimp P. serratus was greater and dated to be much older (4.5-12.3 Ma, Plio-Miocene), so we considered that they could represent two separated species. Therefore, species crypticism in the genus Palaemon seems to be a common phenomenon.
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Affiliation(s)
- Inés González-Castellano
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain
| | - Joan Pons
- Instituto Mediterráneo de Estudios Avanzados (IMEDEA), Consejo Superior de Investigaciones Científicas (CSIC) and Universitat de les Illes Balears, Esporles, Spain
| | - Enrique González-Ortegón
- Instituto de Ciencias Marinas de Andalucía (ICMAN), Consejo Superior de Investigaciones Científicas (CSIC), Puerto Real, Spain
| | - Andrés Martínez-Lage
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain
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19
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Chak STC, Barden P, Baeza JA. The complete mitochondrial genome of the eusocial sponge-dwelling snapping shrimp Synalpheus microneptunus. Sci Rep 2020; 10:7744. [PMID: 32385299 PMCID: PMC7210941 DOI: 10.1038/s41598-020-64269-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/13/2020] [Indexed: 01/10/2023] Open
Abstract
In the marine realm, eusociality is only known to have evolved within a clade of sponge-dwelling snapping shrimps in the genus Synalpheus. Deciphering the genomic underpinnings of eusociality in these marine shrimps has been limited by the sparse genomic resources in this genus. Here, we report, for a eusocial shrimp Synalpheus microneptunus, a complete mitochondrial genome (22X coverage) assembled from short Illumina 150 bp paired-end reads. The 15,603 bp long mitochondrial genome of S. microneptunus is AT-rich and includes 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and an 834 bp intergenic region assumed to be the D-loop. The gene order is identical to that reported for most caridean shrimps and corresponds to the presumed Pancrustacean ground pattern. All PCGs showed signs of purifying selection, with KA/KS <<1 across the whole PCGs and most sliding windows within PCGs. Maximum-likelihood and Bayesian inference phylogenetic analyses of 13 PCGs and 68 terminals supports the monophyly of the Caridea and the family Alpheidae. The complete mitochondrial genome of the eusocial shrimp Synalpheus microneptunus will contribute to a better understanding of the selective pressures and rates of molecular evolution in marine eusocial animals.
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Affiliation(s)
- Solomon T C Chak
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
| | - Phillip Barden
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA. .,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA. .,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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20
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Cappa R, de Campos C, Maxwell AP, McKnight AJ. "Mitochondrial Toolbox" - A Review of Online Resources to Explore Mitochondrial Genomics. Front Genet 2020; 11:439. [PMID: 32457801 PMCID: PMC7225359 DOI: 10.3389/fgene.2020.00439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Mitochondria play a significant role in many biological systems. There is emerging evidence that differences in the mitochondrial genome may contribute to multiple common diseases, leading to an increasing number of studies exploring mitochondrial genomics. There is often a large amount of complex data generated (for example via next generation sequencing), which requires optimised bioinformatics tools to efficiently and effectively generate robust outcomes from these large datasets. Twenty-four online resources dedicated to mitochondrial genomics were reviewed. This 'mitochondrial toolbox' summary resource will enable researchers to rapidly identify the resource(s) most suitable for their needs. These resources fulfil a variety of functions, with some being highly specialised. No single tool will provide all users with the resources they require; therefore, the most suitable tool will vary between users depending on the nature of the work they aim to carry out. Genetics resources are well established for phylogeny and DNA sequence changes, but further epigenetic and gene expression resources need to be developed for mitochondrial genomics.
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Affiliation(s)
- Ruaidhri Cappa
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
| | - Cassio de Campos
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, United Kingdom
| | - Alexander P Maxwell
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
| | - Amy J McKnight
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
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21
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Gan HM, Wengert P, Barton HA, Hudson AO, Savka MA. Insight into the resistome and quorum sensing system of a divergent Acinetobacter pittii isolate from an untouched site of the Lechuguilla Cave. Access Microbiol 2020; 2:acmi000089. [PMID: 34568753 PMCID: PMC8459101 DOI: 10.1099/acmi.0.000089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/11/2019] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter are Gram-negative bacteria belonging to the sub-phyla Gammaproteobacteria, commonly associated with soils, animal feeds and water. Some members of the Acinetobacter have been implicated in hospital-acquired infections, with broad-spectrum antibiotic resistance. Here we report the whole-genome sequence of LC510, an Acinetobacter species isolated from deep within a pristine location of the Lechuguilla Cave. Pairwise nucleotide comparison to three type strains within the genus Acinetobacter assigned LC510 as an Acinetobacter pittii isolate. Scanning of the LC510 genome identified two genes coding for b-lactamase resistance, despite the fact that LC510 was isolated from a portion of the cave not previously visited by humans and protected from anthropogenic input. The ability to produce acyl-homoserine lactone (AHL) signal in culture medium, an observation that is consistent with the identification of the luxI and luxR homologues in its genome, suggests that cell-to-cell communication remains important in an isolated cave ecosystem.
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Affiliation(s)
- Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong 3220, Victoria, Australia.,Deakin Genomics Centre, Deakin University, Geelong 3220, Victoria, Australia.,School of Science, Monash University Malaysia, Bandar Sunway, 47500 Petaling Jaya, Selangor, Malaysia
| | - Peter Wengert
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Hazel A Barton
- Department of Biology, University of Akron, Akron, OH, USA
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Michael A Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
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22
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Baeza JA, Sepúlveda FA, González MT. The complete mitochondrial genome and description of a new cryptic species of Benedenia Diesing, 1858 (Monogenea: Capsalidae), a major pathogen infecting the yellowtail kingfish Seriola lalandi Valenciennes in the South-East Pacific. Parasit Vectors 2019; 12:490. [PMID: 31623679 PMCID: PMC6798380 DOI: 10.1186/s13071-019-3711-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/11/2019] [Indexed: 01/19/2023] Open
Abstract
Background The monogenean Benedenia seriolae parasitizes fishes belonging to the genus Seriola, represents a species complex, and causes substantial impact on fish welfare in aquaculture systems worldwide. This study reports, for the first time, the complete mitochondrial genome of B. humboldti n. sp., a new cryptic species from the South-East Pacific (SEP). Methods The mitogenome of B. humboldti n. sp. was assembled from short Illumina 150 bp pair-end reads. The phylogenetic position of B. humboldti n. sp. among other closely related congeneric and confamiliar capsalids was examined using mitochondrial protein-coding genes (PCGs). Morphology of B. humboldti n. sp. was examined based on fixed and stained specimens. Results The AT-rich mitochondrial genome of B. humboldti is 13,455 bp in length and comprises 12 PCGs (atp8 was absent as in other monogenean genomes), 2 ribosomal RNA genes, and 22 transfer RNA genes. All protein-coding, ribosomal RNA, and transfer RNA genes are encoded on the H-strand. The gene order observed in the mitochondrial genome of B. humboldti n. sp. was identical to that of B. seriolae from Japan but different from that of B. seriolae from Australia. The genetic distance between B. humboldti n. sp. and B. seriolae from Japan was high. Minor but reliable differences in the shape of the penis were observed between Benedenia humboldti n. sp. and congeneric species. Conclusions Phylogenetic analyses based on PCGs in association with differences in the shape of the penis permitted us to conclude that the material from the South-East Pacific represents a new species of Benedenia infecting S. lalandi off the coast of Chile. The discovery of this parasite represents the first step to improving our understanding of infestation dynamics and to develop control strategies for this pathogen infecting the farmed yellowtail kingfish, Seriola lalandi, in the South-East Pacific.![]()
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA. .,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA. .,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
| | - Fabiola A Sepúlveda
- Laboratorio Eco-parasitologia y Epidemiologia Marina (LEPyEM), Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta, Angamos 601, Antofagasta, Chile
| | - M Teresa González
- Laboratorio Eco-parasitologia y Epidemiologia Marina (LEPyEM), Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta, Angamos 601, Antofagasta, Chile.
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Barchi L, Acquadro A, Alonso D, Aprea G, Bassolino L, Demurtas O, Ferrante P, Gramazio P, Mini P, Portis E, Scaglione D, Toppino L, Vilanova S, Díez MJ, Rotino GL, Lanteri S, Prohens J, Giuliano G. Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm. FRONTIERS IN PLANT SCIENCE 2019; 10:1005. [PMID: 31440267 PMCID: PMC6693525 DOI: 10.3389/fpls.2019.01005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/18/2019] [Indexed: 05/20/2023]
Abstract
Single primer enrichment technology (SPET) is a new, robust, and customizable solution for targeted genotyping. Unlike genotyping by sequencing (GBS), and like DNA chips, SPET is a targeted genotyping technology, relying on the sequencing of a region flanking a primer. Its reliance on single primers, rather than on primer pairs, greatly simplifies panel design, and allows higher levels of multiplexing than PCR-based genotyping. Thanks to the sequencing of the regions surrounding the target SNP, SPET allows the discovery of thousands of closely linked, novel SNPs. In order to assess the potential of SPET for high-throughput genotyping in plants, a panel comprising 5k target SNPs, designed both on coding regions and introns/UTRs, was developed for tomato and eggplant. Genotyping of two panels composed of 400 tomato and 422 eggplant accessions, comprising both domesticated material and wild relatives, generated a total of 12,002 and 30,731 high confidence SNPs, respectively, which comprised both target and novel SNPs in an approximate ratio of 1:1.6, and 1:5.5 in tomato and eggplant, respectively. The vast majority of the markers was transferrable to related species that diverged up to 3.4 million years ago (Solanum pennellii for tomato and S. macrocarpon for eggplant). Maximum Likelihood phylogenetic trees and PCA outputs obtained from the whole dataset highlighted genetic relationships among accessions and species which were congruent with what was previously reported in literature. Better discrimination among domesticated accessions was achieved by using the target SNPs, while better discrimination among wild species was achieved using the whole SNP dataset. Our results reveal that SPET genotyping is a robust, high-throughput technology for genetic fingerprinting, with a high degree of cross-transferability between crops and their cultivated and wild relatives, and allows identification of duplicates and mislabeled accessions in genebanks.
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Affiliation(s)
| | | | - David Alonso
- COMAV, Universitat Politècnica de Valencia, Valencia, Spain
| | - Giuseppe Aprea
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Laura Bassolino
- CREA-GB, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Olivia Demurtas
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Paola Ferrante
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | | | - Paola Mini
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | | | | | - Laura Toppino
- CREA-GB, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | | | | | | | | | - Jaime Prohens
- COMAV, Universitat Politècnica de Valencia, Valencia, Spain
| | - Giovanni Giuliano
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
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Tan MH, Gan HM, Lee YP, Bracken-Grissom H, Chan TY, Miller AD, Austin CM. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci Rep 2019; 9:10756. [PMID: 31341205 PMCID: PMC6656734 DOI: 10.1038/s41598-019-47145-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023] Open
Abstract
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
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Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia.
- Deakin Genomics Centre, Deakin University, Geelong, Australia.
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, North Miami, Florida, 33181, USA
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 20224, Taiwan
| | - Adam D Miller
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
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25
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Gan HM, Linton SM, Austin CM. Two reads to rule them all: Nanopore long read-guided assembly of the iconic Christmas Island red crab, Gecarcoidea natalis (Pocock, 1888), mitochondrial genome and the challenges of AT-rich mitogenomes. Mar Genomics 2019; 45:64-71. [DOI: 10.1016/j.margen.2019.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 01/01/2023]
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26
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Gan HM, Grandjean F, Jenkins TL, Austin CM. Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication. BMC Genomics 2019; 20:335. [PMID: 31053062 PMCID: PMC6500004 DOI: 10.1186/s12864-019-5704-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 04/16/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod crustaceans with strong implications in crustacean phylogenetics. Such atypical mitochondrial features will benefit greatly from validation with emerging long read sequencing technologies such as Oxford Nanopore that can more accurately identify structural variation. RESULTS We re-sequenced the H. gammarus mitogenome on an Oxford Nanopore Minion flowcell and performed a long-read only assembly, generating a complete mitogenome assembly for H. gammarus. In contrast to previous reporting, we found an intact mitochondrial nad2 gene in the H. gammarus mitogenome and showed that its gene organization is broadly similar to that of the American lobster (H. americanus) except for the presence of a large tandemly duplicated region with evidence of pseudogenization in one of each duplicated protein-coding genes. CONCLUSIONS Using the European lobster as an example, we demonstrate the value of Oxford Nanopore long read technology in resolving problematic mitogenome assemblies. The increasing accessibility of Oxford Nanopore technology will make it an attractive and useful tool for evolutionary biologists to verify new and existing unusual mitochondrial gene rearrangements recovered using first and second generation sequencing technologies, particularly those used to make phylogenetic inferences of evolutionary scenarios.
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Affiliation(s)
- Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220 Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3220 Australia
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Petaling Jaya, Malaysia
- Monash University Malaysia Genomics Facility, Monash University, Bandar Sunway, 47500 Petaling Jaya, Malaysia
| | - Frederic Grandjean
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267 Equipe Ecologie Evolution Symbiose 5 rue Albert Turpin, 86073 Poitiers, Cedex, France
| | - Tom L. Jenkins
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Christopher Mervyn Austin
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220 Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3220 Australia
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Petaling Jaya, Malaysia
- Monash University Malaysia Genomics Facility, Monash University, Bandar Sunway, 47500 Petaling Jaya, Malaysia
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Gan HM, Lee MVL, Savka MA. Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4. PeerJ 2019; 7:e6366. [PMID: 30775173 PMCID: PMC6369824 DOI: 10.7717/peerj.6366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/20/2018] [Indexed: 12/21/2022] Open
Abstract
The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.
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Affiliation(s)
- Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Melvin V L Lee
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Michael A Savka
- College of Science, The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
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Chen J, Xing Y, Yao W, Xu X, Zhang C, Zhang Z, Liu Q. Phylomitogenomics reconfirm the phylogenetic position of the genus Metaplax inferred from the two grapsid crabs (Decapoda: Brachyura: Grapsoidea). PLoS One 2019; 14:e0210763. [PMID: 30682071 PMCID: PMC6347246 DOI: 10.1371/journal.pone.0210763] [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: 09/22/2018] [Accepted: 01/01/2019] [Indexed: 12/22/2022] Open
Abstract
Two new complete mitogenomes of the grapsids, Metaplax longipes Stimpson, 1858 and Nanosesarma minutum (De Man, 1887) were sequenced using next-generation sequencing (NGS). By analyzing a combination of 75 Brachyura taxa, our phylomitogenomic inferences suggested that Metaplax crab seperated earlier from the sesarmid crabs and closely related to the varunids with respect to Nanosesarma crab. It reconfirmed that the Metaplax should be removed from the Sesarmidae and assinged to the Varunidae. Additional mitogenomic comparisons including gene rearrangement and genomic organization were conducted among the 33 taxa of Grapsoidea and Ocypodoidea, and a shared rearrangement pattern between Metaplax longipes and the varunids were recovered, which also strongly supported the inference for the phylogenetic position of the Metaplax.
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Affiliation(s)
- Jianqin Chen
- Institute of Aquatic Biology, Jiangsu Key Laboratory of Biofunctional Molecule, School of Life Sciences, Chemistry & Chemical Engineering, Jiangsu Second Normal University, Nanjing, China
- * E-mail:
| | - Yuhui Xing
- Nanjing Normal University Zhongbei College, Nanjing, China
| | - Wenjia Yao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xue Xu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chenling Zhang
- Institute of Aquatic Biology, Jiangsu Key Laboratory of Biofunctional Molecule, School of Life Sciences, Chemistry & Chemical Engineering, Jiangsu Second Normal University, Nanjing, China
| | - Zhenhua Zhang
- Institute of Aquatic Biology, Jiangsu Key Laboratory of Biofunctional Molecule, School of Life Sciences, Chemistry & Chemical Engineering, Jiangsu Second Normal University, Nanjing, China
| | - Qing Liu
- Institute of Aquatic Biology, Jiangsu Key Laboratory of Biofunctional Molecule, School of Life Sciences, Chemistry & Chemical Engineering, Jiangsu Second Normal University, Nanjing, China
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Gan HM, John Wasserman R, Dalu T, Christopher Rogers D. The complete mitogenome of a South African cryptic species of tadpole shrimp within the Triops granarius (Lucas, 1864) species group. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1547145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Ryan John Wasserman
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Tatenda Dalu
- Ecology and Resource Management, University of Venda, Thohoyandou, South Africa
| | - D. Christopher Rogers
- Kansas Biological Survey and the Natural History Museum (Biodiversity Institute), Kansas University, Lawrence, KS, USA
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Gan HM, Nur Ilham Syahadah MY, Vilasri V, Tun Nurul Aimi MJ, Tan MP. Four whole mitogenome sequences of yellowtail stargazers ( Uranoscopus cognatus cantor 1849) from East Peninsular Malaysia and West Coast of Thailand. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1536473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | | | - Veera Vilasri
- Natural History Museum, National Science Museum, Pathumthani, Thailand
| | | | - Min Pau Tan
- School of Fisheries and Aquaculture Sciences, Universiti Malaysia Terengganu, Terengganu, Malaysia
- Institute of Marine Biotechnology (IMB) Universiti Malaysia Terengganu, Terengganu, Malaysia
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Baeza JA. The complete mitochondrial genome of the Caribbean spiny lobster Panulirus argus. Sci Rep 2018; 8:17690. [PMID: 30523272 PMCID: PMC6283867 DOI: 10.1038/s41598-018-36132-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/16/2018] [Indexed: 12/12/2022] Open
Abstract
Panulirus argus is a keystone species and target of the most lucrative fishery in the Caribbean region. This study reports, for the first time, the complete mitochondrial genome of Panulirus argus (average coverage depth nucleotide-1 = 70×) assembled from short Illumina 150 bp PE reads. The AT-rich mitochondrial genome of Panulirus argus was 15 739 bp in length and comprised 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 801 bp long intergenic space was assumed to be the D-loop. Most of the PCGs were encoded on the H-strand. The gene order observed in the mitochondrial genome of Panulirus argus corresponds to the presumed Pancrustacean ground pattern. KA/KS ratios calculated for all mitochondrial PCGs showed values < 1, indicating that all these PCGs are evolving under purifying selection. A maximum likelihood phylogenetic analysis (concatenated PCGs [n = 13], 154 arthropods) supported the monophyly of the Achelata and other infraorders within the Decapoda. Mitochondrial PCGs have enough phylogenetic informativeness to explore high-level genealogical relationships in the Pancrustacea. The complete mitochondrial genome of the Caribbean spiny lobster Panulirus argus will contribute to the better understanding of meta-population connectivity in this keystone overexploited species.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA.
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA.
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements. Mol Phylogenet Evol 2018; 127:320-331. [DOI: 10.1016/j.ympev.2018.05.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/03/2018] [Accepted: 05/13/2018] [Indexed: 01/08/2023]
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Characterization of four new mitogenomes from Ocypodoidea & Grapsoidea, and phylomitogenomic insights into thoracotreme evolution. Gene 2018; 675:27-35. [PMID: 29960073 DOI: 10.1016/j.gene.2018.06.088] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/01/2018] [Accepted: 06/25/2018] [Indexed: 11/24/2022]
Abstract
Four new complete mitochondrial genomes (mitogenomes) from the two superfamilies Ocypodoidea and Grapsoidea were sequenced, which represented Uca (Gelasimus) borealis (Ocypodidae: Ucinae), Dotilla wichmani (Dotillidae), Metopograpsus quadridentatus (Grapsidae: Grapsinae), and Gaetice depressus (Varunidae: Gaeticinae). All of the mitogenomes shared the complete set of 37 mitochondrial genes. Mitogenome lengths were 15,659, 15,600, 15,517, and 16,288 bp, respectively, with A + T contents of 69.41%, 68.46%, 70.30%, and 72.96%, respectively. Comparative genomic analyses suggested that they exhibited different genomic rearrangements. In particular, G. depressus shared a major rearrangement pattern present in Eriocheir crabs, while the remainder shared the brachyuran ground genomic rearrangement patterns. Phylomitogenomic inferences provided new evidence for the strongly supported nesting of Thoracotremata within Heterotremata clades. A close phylogenetic relationship was observed between Varunidae and Macrophthalmidae crabs, and between Dotillidae and Grapsidae crabs, which was consistent with mitochondrial genomic rearrangement similarities. Altogether, these results suggest the presence of reciprocal paraphyly for Ocypodoidea and Grapsoidea.
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Tan MH, Gan HM, Dally G, Horner S, Moreno PAR, Rahman S, Austin CM. More limbs on the tree: mitogenome characterisation and systematic position of ‘living fossil’ species Neoglyphea inopinata and Laurentaeglyphea neocaledonica (Decapoda : Glypheidea : Glypheidae). INVERTEBR SYST 2018. [DOI: 10.1071/is17050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Glypheids first appeared in the Lower Triassic period and were believed to be extinct until specimens of Neoglyphea inopinata Forest & Saint Laurent and Laurentaeglyphea neocaledonica Richer de Forges were described in 1975 and 2006, respectively. The finding of extant species has meant that molecular data can now be used to complement morphological and fossil-based studies to investigate the relationships of Glypheidea within the Decapoda. However, despite several molecular studies, the placement of this infraorder within the decapod phylogenetic tree is not resolved. One limitation is that molecular resources available for glypheids have been limited to a few nuclear and mitochondrial gene fragments. Many of the more recent large-scale studies of decapod phylogeny have used information from complete mitogenomes, but have excluded the infraorder Glypheidea due to the unavailability of complete mitogenome sequences. Using next-generation sequencing, we successfully sequenced and assembled complete mitogenome sequences from museum specimens of N. inopinata and L. neocaledonica, the only two extant species of glypheids. With these sequences, we constructed the first decapod phylogenetic tree based on whole mitogenome sequences that includes Glypheidea as one of 10 decapod infraorders positioned within the suborder Pleocyemata. From this, the Glypheidea appears to be a relatively derived lineage related to the Polychelida and Astacidea. Also in our study, we conducted a survey on currently available decapod mitogenome resources available on National Center for Biotechnology Information (NCBI) and identified infraorders that would benefit from more strategic and expanded taxonomic sampling.
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Yuhui X, Lijun Z, Yue H, Xiaoqi W, Chen Z, Zhang Huilun, Ruoran W, Da P, Hongying S. Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae). Zookeys 2017; 705:41-60. [PMID: 29118611 PMCID: PMC5674035 DOI: 10.3897/zookeys.705.11852] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/04/2017] [Indexed: 01/26/2023] Open
Abstract
Recent morphological and molecular evidence has challenged classical interpretations of eubrachyuran phylogeny and evolution. Complete mitochondrial genomes of two species of potamid freshwater crabs, Sinopotamon yaanense and Sinopotamon yangtsekiense were obtained using next-generation sequencing. The results revealed a novel gene order with translocations of a five-gene block and a tRNA gene in comparison to available brachyuran mitochondrial genomes. DNA sequence comparisons position the Potamidae, a primary freshwater crab family, outside of the clade for the traditional heterotreme families, and closer to the clade that includes the thoracotreme families of grapsoid and ocypodoid crabs. Mitogenomic comparisons using rapid next-generation sequencing and a much wider taxonomic sample are required for a high-resolution examination of the phylogenetic relationships within the Eubrachyura.
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Affiliation(s)
- Xing Yuhui
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Zhou Lijun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Hou Yue
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Wang Xiaoqi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Zhang Chen
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhang Huilun
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wang Ruoran
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Pan Da
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Sun Hongying
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
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More evolution underground: Accelerated mitochondrial substitution rate in Australian burrowing freshwater crayfishes (Decapoda: Parastacidae). Mol Phylogenet Evol 2017; 118:88-98. [PMID: 28966124 DOI: 10.1016/j.ympev.2017.09.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/18/2017] [Accepted: 09/26/2017] [Indexed: 12/11/2022]
Abstract
To further understand the evolutionary history and mitogenomic features of Australia's highly distinctive freshwater crayfish fauna, we utilized a recently described rapid mitogenome sequencing pipeline to generate 24 new crayfish mitogenomes including a diversity of burrowing crayfish species and the first for Astacopsis gouldi, the world's largest freshwater invertebrate. Whole mitogenome-based phylogeny estimates using both Bayesian and Maximum Likelihood methods substantially strengthen existing hypotheses for systematic relationships among Australian freshwater crayfish with evidence of pervasive diversifying selection and accelerated mitochondrial substitution rate among the members of the clade representing strongly burrowing crayfish that may reflect selection pressures for increased energy requirement for adaptation to terrestrial environment and a burrowing lifestyle. Further, gene rearrangements are prevalent in the burrowing crayfish mitogenomes involving both tRNA and protein coding genes. In addition, duplicated control regions were observed in two closely related Engaeus species, together with evidence for concerted evolution. This study significantly adds to the understanding of Australian freshwater crayfish evolutionary relationships and suggests a link between mitogenome evolution and adaptation to terrestrial environments and a burrowing lifestyle in freshwater crayfish.
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Ghiselli F, Milani L, Iannello M, Procopio E, Chang PL, Nuzhdin SV, Passamonti M. The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae). PeerJ 2017; 5:e3692. [PMID: 28848689 PMCID: PMC5571815 DOI: 10.7717/peerj.3692] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/25/2017] [Indexed: 12/30/2022] Open
Abstract
Despite the large number of animal complete mitochondrial genomes currently available in public databases, knowledge about mitochondrial genomics in invertebrates is uneven. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus, also known as the European clam. Ruditapes decussatus is morphologically and ecologically similar to the Manila clam Ruditapes philippinarum, which has been recently introduced for aquaculture in the very same habitats of Ruditapes decussatus, and that is replacing the native species. Currently the production of the European clam is almost insignificant, nonetheless it is considered a high value product, and therefore it is an economically important species, especially in Portugal, Spain and Italy. In this work we: (i) assembled Ruditapes decussatus mitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing; (ii) analyzed and characterized the Ruditapes decussatus mitochondrial genome, comparing its features with those of other venerid bivalves; (iii) assessed mitochondrial sequence polymorphism (SP) and copy number variation (CNV) of tandem repeats across 26 samples. Despite using high-throughput approaches we did not find evidence for the presence of two sex-linked mitochondrial genomes, typical of the doubly uniparental inheritance of mitochondria, a phenomenon known in ∼100 bivalve species. According to our analyses, Ruditapes decussatus is more genetically similar to species of the Genus Paphia than to the congeneric Ruditapes philippinarum, a finding that bolsters the already-proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with few SPs and little variability of the sequences flanking the control region (Largest Unassigned Regions (LURs). Strikingly, although we found low nucleotide variability along the entire mitochondrial genome, we observed high levels of length polymorphism in the LUR due to CNV of tandem repeats, and even a LUR length heteroplasmy in two samples. It is not clear if the lack of genetic variability in the mitochondrial genome of Ruditapes decussatus is a cause or an effect of the ongoing replacement of Ruditapes decussatus with the invasive Ruditapes philippinarum, and more analyses, especially on nuclear sequences, are required to assess this point.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
| | - Emanuele Procopio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
| | - Peter L Chang
- Department of Biological Sciences, Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
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Grandjean F, Tan MH, Gan HM, Lee YP, Kawai T, Distefano RJ, Blaha M, Roles AJ, Austin CM. Rapid recovery of nuclear and mitochondrial genes by genome skimming from Northern Hemisphere freshwater crayfish. ZOOL SCR 2017. [DOI: 10.1111/zsc.12247] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Frederic Grandjean
- UMR CNRS 7267 Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions; 5 rue Albert Turpin Poitiers Cedex France
| | - Mun Hua Tan
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
| | - Han Ming Gan
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
| | - Yin Peng Lee
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
| | - Tadashi Kawai
- Fisheries Research Department; Wakkanai Fisheries Research Institute; 4-5-15 Suehiro Wakkanai-shi 097-0001 Hokkaido Japan
| | - Robert J. Distefano
- Missouri Department of Conservation; East Gans Road Columbia Missouri 65201 USA
| | - Martin Blaha
- Faculty of Fisheries and Protection of Waters; South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses; University of South Bohemia in České Budějovice; Zátiší 728/II Vodňany Czech Republic
| | - Angela J. Roles
- Biology Department; Oberlin College, Oberlin; Ohio 44074 USA
| | - Christopher M. Austin
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
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Tan MH, Gan HM, Lee YP, Poore GC, Austin CM. Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda). PeerJ 2017; 5:e2982. [PMID: 28265498 PMCID: PMC5335691 DOI: 10.7717/peerj.2982] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/12/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information. METHODS Sequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements. RESULTS We present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps, Callianassa ceramica and Trypaea australiensis, along with three caridean shrimps, Macrobrachium bullatum, Alpheus lobidens, and Caridina cf. nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders. DISCUSSION Our findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.
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Affiliation(s)
- Mun Hua Tan
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Yin Peng Lee
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | | | - Christopher M. Austin
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
- School of Life and Environmental Sciences, Deakin University, Burwood, VIC, Australia
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Liu QN, Zhang HB, Jiang SH, Xuan FJ, Li CF, Zhang DZ, Zhou CL, Tang BP. The complete mitochondrial genome of Eriocheir japonica sinensis (Decapoda: Varunidae) and its phylogenetic analysis. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Shen H, Braband A, Scholtz G. The complete mitogenomes of lobsters and crayfish (Crustacea: Decapoda: Astacidea) reveal surprising differences in closely related taxa and convergences to Priapulida. J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Hong Shen
- Institut für Biologie/Vergleichende Zoologie; Humboldt-Universität zu Berlin; Berlin Germany
| | - Anke Braband
- Institut für Biologie/Vergleichende Zoologie; Humboldt-Universität zu Berlin; Berlin Germany
| | - Gerhard Scholtz
- Institut für Biologie/Vergleichende Zoologie; Humboldt-Universität zu Berlin; Berlin Germany
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Krzeminska U, Wilson R, Rahman S, Song BK, Seneviratne S, Gan HM, Austin CM. Mitochondrial genomes of the jungle crow Corvus macrorhynchos (Passeriformes: Corvidae) from shed feathers and a phylogenetic analysis of genus Corvus using mitochondrial protein-coding genes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2668-70. [DOI: 10.3109/19401736.2015.1043540] [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]
Affiliation(s)
- Urszula Krzeminska
- School of Science, Monash University Malaysia, Selangor, Malaysia,
- Genomics Facility Monash University Malaysia, Selangor, Malaysia, and
| | - Robyn Wilson
- School of Science, Monash University Malaysia, Selangor, Malaysia,
- Genomics Facility Monash University Malaysia, Selangor, Malaysia, and
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Selangor, Malaysia,
- Genomics Facility Monash University Malaysia, Selangor, Malaysia, and
| | - Beng Kah Song
- School of Science, Monash University Malaysia, Selangor, Malaysia,
- Genomics Facility Monash University Malaysia, Selangor, Malaysia, and
| | - Sampath Seneviratne
- Avian Evolution Node, Department of Zoology, University of Colombo, Colombo, Sri Lanka
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Selangor, Malaysia,
- Genomics Facility Monash University Malaysia, Selangor, Malaysia, and
| | - Christopher M. Austin
- School of Science, Monash University Malaysia, Selangor, Malaysia,
- Genomics Facility Monash University Malaysia, Selangor, Malaysia, and
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