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Martínez-Cárdenas A, Becerril V, Ortega J, López-Cuamatzi IL, Arroyo-Cabrales J, Díaz-Pacheco I, Antonio Baeza J. Comparative mitochondrial genomics of endemic Mexican vesper yellow bats genus Rhogeessa (Chiroptera: Vespertilionidae) and insights into internal relationships in the family Vespertilionidae. Gene 2024; 918:148492. [PMID: 38649060 DOI: 10.1016/j.gene.2024.148492] [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: 01/31/2024] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
In the species-rich family Vespertilionidae, vesper yellow bats in the genus Rhogeessa include eleven species, three of them endemic to Mexico. These insectivorous bats provide important ecosystem services, including pest control. Even though some aspects of their biology are well- known, only a few genomic resources are available for these species, which limits our understanding of their biology. In this study, we assembled and annotated the mitochondrial genome of four species: R. aenea, R. genowaysi, R. mira, and R. parvula. We generated a phylomitogenomic hypothesis based on translated protein-coding genes for a total of 52 species in the family Vespertilionidae and examined the phylogenetic position of the genus Rhogeessa and species within the family. The AT-rich mitogenomes of R. aenea, R. genowaysi, R. mira, and R. parvula are 16,763, 16,781, 16,807, and 16,794 pb in length, respectively. Each studied mitogenome encodes 13 Protein Coding Genes (PCGs), 22 transfer RNA genes, and 2 rRNA genes, and contains a putative control region (CR). All tRNAs exhibit a 'cloverleaf' secondary structure, except tRNA-Serine-1 that lacked the DHU arm in all studied mitogenomes. Selective pressure analyses indicated that all protein-coding genes are exposed to purifying selection. The phylomitogenomic analysis supported the monophyletic status of the family Vespertilionidae, confirmed the placement of Rhogeessa within the tribe Antrozoini, and clarified phylogenetic relationships within and among subfamilies and tribes in this family. Our results indicate that phylomitogenomics are useful to explore the evolutionary history of vesper bats. The assembly and comprehensive analysis of mitochondrial genomes offer the potential to generate molecular references and resources beneficial for genetic analyses aimed at understanding the ecology and evolution of these remarkable bats.
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Affiliation(s)
- Anahí Martínez-Cárdenas
- Laboratorio de Biocoservación y Manejo, Posgrado en Ciencias Químico-Biológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala s/n, Col. Santo Tomás, C.P. 11340, Ciudad de México, México; Laboratorio Ecología Evolutiva y Conservación. Departamento de Conservación de la Biodiversidad, ECOSUR-Villahermosa, Carretera Reforma Km 15.5, Ra. Guineo 2da. Sección, Villahermosa, México
| | - Valeria Becerril
- Laboratorio de Biocoservación y Manejo, Posgrado en Ciencias Químico-Biológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala s/n, Col. Santo Tomás, C.P. 11340, Ciudad de México, México
| | - Jorge Ortega
- Laboratorio de Biocoservación y Manejo, Posgrado en Ciencias Químico-Biológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala s/n, Col. Santo Tomás, C.P. 11340, Ciudad de México, México.
| | - Issachar L López-Cuamatzi
- Centro de Investigaciones Tropicales, Universidad Veracruzana, José María Morelos No. 44, Zona Centro, 91000, Xalapa, Veracruz, México
| | - Joaquín Arroyo-Cabrales
- Laboratorio de Arqueozoología, "M. en C. Ticul Álvarez Solórzano". Subdirección de Laboratorios y Apoyo Académico, Instituto Nacional de Antropología e Historia. Moneda No. 16, Centro Histórico, 06060 Ciudad de México, México
| | - Iván Díaz-Pacheco
- Laboratorio de Vertebrados Prioritarios. Facultad de Biología. Universidad Michoacana de San Nicolás de Hidalgo. Avenida Francisco J. Múgica s/n, Ciudad Universitaria, 58030 Morelia Michoacán, 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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Yao Y, Shi Y, Feng K, Du J, Chang Y, Xue Y, Li W. The mitochondrial genome of Homoneura picta (Diptera: Lauxaniidae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:828-831. [PMID: 38919812 PMCID: PMC11198121 DOI: 10.1080/23802359.2024.2333560] [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: 09/15/2023] [Accepted: 03/15/2024] [Indexed: 06/27/2024] Open
Abstract
Homoneura picta belongs to the Homoneurinae subfamily of Lauxaniidae, and it is widely distributed and common in China. This study reports the newly sequenced mitochondrial genome of H. picta. The sequence is 15,469 bp long and contains 37 genes (13 protein-coding, 22 tRNA, and 2 rRNA genes) and a control region. The overall base composition is 38.4% for A, 37.7% for T, 14.1% for C, and 9.8% for G, with a bias toward A + T (76.1%). Phylogenetic analysis show that Homoneura is a sister genus of Cestrotus. We have successfully sequenced the mitochondrial genome of H. picta, which can be useful in investigating the phylogenetic status of Homoneurinae. Our results provide data for further studies of phylogeny in Diptera.
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Affiliation(s)
- Yao Yao
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Yedi Shi
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Keli Feng
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Jiaoyi Du
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Yiming Chang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Yaoyao Xue
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Wenliang Li
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
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de Almeida ELM, da Silveira WB, Fietto LG, Silva MS, Santana WC, Eller MR. Genome assembly and variant analysis of two Saccharomyces cerevisiae strains isolated from stingless bee pollen. Gene 2024; 927:148722. [PMID: 38914244 DOI: 10.1016/j.gene.2024.148722] [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: 10/31/2023] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
Products from stingless bees are rich reservoirs of microbial diversity, including yeasts with fermentative potential. Previously, two Saccharomyces cerevisiae strains, JP14 and IP9, were isolated from Jataí (Tetragonisca angustula) and Iraí (Nannotrigona testaceicornis) bees, respectively, aiming at mead production. Both strains presented great osmotic and sulfite tolerance, and ethanol production, although they have a high free amino nitrogen demand. Herein, their genomes were sequenced, assembled, and annotated, and the variants were compared to the S. cerevisiae S288c reference strain. The final assembly of IP9 and JP14 presented high N50 and BUSCO scores, and more than 6430 protein-coding genes. Additionally, nQuire predicted the ploidy of IP9 as diploid, but the results were not enough to determine the ploidy of JP14. The mitochondrial genomes of IP9 and JP14 presented the same gene content as S288c but the genes were rearranged and fragmented in different patterns. Meanwhile, the genes with mutations of high impact (e.g., indels, gain of stop codon) for both yeasts were enriched for transmembrane transport, electron transfer, oxidoreductase, heme binding, fructose, mannose, and glucose transport, activities related to the respiratory chain and sugar metabolism. The IP9 strain presented copy number gains in genes related to sugar transport and cell morphogenesis; in JP14, genes were enriched for disaccharide metabolism and transport, response to reactive oxygen species, and polyamine transport. On the other hand, IP9 presented copy number losses related to disaccharide, thiamine, and aldehyde metabolism, while JP14 presented depletions related to disaccharide, oligosaccharide, asparagine, and aspartate metabolism. Notably, both strains presented a killer toxin gene, annotated from the assembling of unmapped reads, representing a potential mechanism for the control of other microorganisms population in the environment. Therefore, the annotated genomes of JP14 and IP9 presented a high selective pressure for sugar and nitrogen metabolism and stress response, consistent with their isolation source and fermentative properties.
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Affiliation(s)
- Eduardo Luís Menezes de Almeida
- Laboratory of Microbial Physiology, Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Wendel Batista da Silveira
- Laboratory of Microbial Physiology, Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Luciano Gomes Fietto
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Mayara Salgado Silva
- Department of Food Technology, Federal Institute of Education, Science and Technology of Ceará, Limoeiro Do Norte, Brazil
| | | | - Monique Renon Eller
- Department of Food Technology - Universidade Federal de Viçosa, Viçosa, Brazil.
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Galià-Camps C, Araujo AK, Carmona L, Martín-Hervás MDR, Pola M, Palero F, Cervera JL. New mitogenomes of Runcinidae and Facelinidae: two understudied heterobranch families (Mollusca: Gastropoda). Mitochondrial DNA B Resour 2024; 9:771-776. [PMID: 38919811 PMCID: PMC11198154 DOI: 10.1080/23802359.2024.2363365] [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: 10/05/2023] [Accepted: 05/29/2024] [Indexed: 06/27/2024] Open
Abstract
Here, we present the mitochondrial sequences of two sea slugs (Heterobranchia): Runcina aurata and Facelina auriculata, the latter being the type species of the family. The mitochondrial genomes are 14,282 and 14,171bp in length, respectively, with a complete set of 13 PCGs, 2 rRNAs, and 22 tRNAs. None of the mitogenomes show gene reorganization, keeping the standard mitogenomic structure of Heterobranchia. Nucleotide composition differs significantly between them, with R. aurata showing the most AT-rich mitogenome (25.7% GC content) reported to date in Heterobranchia, and F. auriculata showing a rich GC content (35%) compared with other heterobranch mitochondrial genomes.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Ana Karla Araujo
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
| | - Leila Carmona
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
| | - María del Rosario Martín-Hervás
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
| | - Marta Pola
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, CSIC, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), CSIC, Madrid, Spain
| | - Ferran Palero
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Spain
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Juan Lucas Cervera
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
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Valencia M P, Baeza JA, López-Cuamatzi IL, Ortega J. Characterization of the mitochondrial genomes of the Mexican endemic bats Corynorhinus mexicanus and Corynorhinus leonpaniaguae (Chiroptera: Vespertilionidae). Mol Biol Rep 2024; 51:760. [PMID: 38874795 DOI: 10.1007/s11033-024-09700-5] [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: 03/19/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND The genus Corynorhinus is composed of four recognized species: C. rafinesquii, C. townsendii, C. mexicanus, and C. leonpaniaguae, the latter two being endemic to Mexico. According to the IUCN, C. mexicanus is considered "Near Threatened", as its populations are dwindling and habitats are affected by anthropogenic disturbance. Corynorhinus leonpaniaguae has not been assigned to an IUCN Red List risk category due to its recent description. METHODS AND RESULTS In this study, the mitochondrial genomes of C. mexicanus and C. leonpaniaguae were assembled and characterized in detail. The mitochondrial genomes (mtDNA) of C. mexicanus and C. leonpaniaguae have lengths of 16,470 and 16,581 bp respectively, with a predominant nucleotide usage of adenine (31.670% and 31.729%, respectively) and thymine (26.15% and 26.18%, respectively). The mtDNA of C. mexicanus and C. leonpaniaguae is composed of 37 coding and non-coding elements: 22 transfer RNAs (tRNA), 13 protein-coding genes (PCGs), two ribosomal RNAs and a non-coding region, the control region, which has a length of 933 bp and 1,149 bp, respectively. All tRNAs exhibited a cloverleaf secondary structure, with the exception of trn-Ser1 which showed a deletion of the dihydrouridine arm in the two species. All PCGs are subjected to purifying selection, with atp8 being the gene showing the highest Ka/Ks value. CONCLUSIONS These are the first whole mitogenomic resources developed for C. mexicanus and C. leonpaniaguae and enhance our knowledge of the ecology of these species and aid in their conservation.
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Affiliation(s)
- Pablo Valencia M
- Laboratorio de Bioconservación y Manejo, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Manuel Carpio y Plan de Ayala s/n, Col. Santo Tomás C.P. 11340 Alcaldía Miguel Hidalgo, 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
| | - Issachar L López-Cuamatzi
- Centro de Investigaciones Tropicales, Universidad Veracruzana, José María Morelos 44, Zona Centro, Centro, Xalapa-Enríquez, 91000, México
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Manuel Carpio y Plan de Ayala s/n, Col. Santo Tomás C.P. 11340 Alcaldía Miguel Hidalgo, Ciudad de México, México.
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Davison A, Chowdhury M, Johansen M, Uliano-Silva M, Blaxter M. High heteroplasmy is associated with low mitochondrial copy number and selection against non-synonymous mutations in the snail Cepaea nemoralis. BMC Genomics 2024; 25:596. [PMID: 38872121 DOI: 10.1186/s12864-024-10505-w] [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: 03/01/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
Molluscan mitochondrial genomes are unusual because they show wide variation in size, radical genome rearrangements and frequently show high variation (> 10%) within species. As progress in understanding this variation has been limited, we used whole genome sequencing of a six-generation matriline of the terrestrial snail Cepaea nemoralis, as well as whole genome sequences from wild-collected C. nemoralis, the sister species C. hortensis, and multiple other snail species to explore the origins of mitochondrial DNA (mtDNA) variation. The main finding is that a high rate of SNP heteroplasmy in somatic tissue was negatively correlated with mtDNA copy number in both Cepaea species. In individuals with under ten mtDNA copies per nuclear genome, more than 10% of all positions were heteroplasmic, with evidence for transmission of this heteroplasmy through the germline. Further analyses showed evidence for purifying selection acting on non-synonymous mutations, even at low frequency of the rare allele, especially in cytochrome oxidase subunit 1 and cytochrome b. The mtDNA of some individuals of Cepaea nemoralis contained a length heteroplasmy, including up to 12 direct repeat copies of tRNA-Val, with 24 copies in another snail, Candidula rugosiuscula, and repeats of tRNA-Thr in C. hortensis. These repeats likely arise due to error prone replication but are not correlated with mitochondrial copy number in C. nemoralis. Overall, the findings provide key insights into mechanisms of replication, mutation and evolution in molluscan mtDNA, and so will inform wider studies on the biology and evolution of mtDNA across animal phyla.
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Affiliation(s)
- Angus Davison
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Mehrab Chowdhury
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Margrethe Johansen
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Marcela Uliano-Silva
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
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Ferrari RR, Ricardo PC, Dias FC, de Souza Araujo N, Soares DO, Zhou QS, Zhu CD, Coutinho LL, Arias MC, Batista TM. The nuclear and mitochondrial genome assemblies of Tetragonisca angustula (Apidae: Meliponini), a tiny yet remarkable pollinator in the Neotropics. BMC Genomics 2024; 25:587. [PMID: 38862915 PMCID: PMC11167848 DOI: 10.1186/s12864-024-10502-z] [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: 01/04/2024] [Accepted: 06/05/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND The field of bee genomics has considerably advanced in recent years, however, the most diverse group of honey producers on the planet, the stingless bees, are still largely neglected. In fact, only eleven of the ~ 600 described stingless bee species have been sequenced, and only three using a long-read (LR) sequencing technology. Here, we sequenced the nuclear and mitochondrial genomes of the most common, widespread and broadly reared stingless bee in Brazil and other neotropical countries-Tetragonisca angustula (popularly known in Brazil as jataí). RESULTS A total of 48.01 Gb of DNA data were generated, including 2.31 Gb of Pacific Bioscience HiFi reads and 45.70 Gb of Illumina short reads (SRs). Our preferred assembly comprised 683 contigs encompassing 284.49 Mb, 62.84 Mb of which (22.09%) corresponded to 445,793 repetitive elements. N50, L50 and complete BUSCOs reached 1.02 Mb, 91 contigs and 97.1%, respectively. We predicted that the genome of T. angustula comprises 17,459 protein-coding genes and 4,108 non-coding RNAs. The mitogenome consisted of 17,410 bp, and all 37 genes were found to be on the positive strand, an unusual feature among bees. A phylogenomic analysis of 26 hymenopteran species revealed that six odorant receptor orthogroups of T. angustula were found to be experiencing rapid evolution, four of them undergoing significant contractions. CONCLUSIONS Here, we provided the first nuclear and mitochondrial genome assemblies for the ecologically and economically important T. angustula, the fourth stingless bee species to be sequenced with LR technology thus far. We demonstrated that even relatively small amounts of LR data in combination with sufficient SR data can yield high-quality genome assemblies for bees.
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Affiliation(s)
- Rafael Rodrigues Ferrari
- Centro de Formação em Ciências Ambientais, Universidade Federal do Sul da Bahia, Porto Seguro, Brazil
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Paulo Cseri Ricardo
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Felipe Cordeiro Dias
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Dalliane Oliveira Soares
- Centro de Formação em Ciências Ambientais, Universidade Federal do Sul da Bahia, Porto Seguro, Brazil
| | - Qing-Song Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Sate Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Luiz Lehmann Coutinho
- Departamento de Ciências Animais, Universidade de São Paulo/ESALQ, Piracicaba, Brazil
| | - Maria Cristina Arias
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - Thiago Mafra Batista
- Centro de Formação em Ciências Ambientais, Universidade Federal do Sul da Bahia, Porto Seguro, Brazil.
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Matos A, Gomes-Dos-Santos A, Teixeira A, Varandas S, Sousa R, Karaouzas I, Zogaris S, Froufe E, Lopes-Lima M. The complete mitochondrial genome of Potomida acarnanica (Kobelt, 1879). Mitochondrial DNA B Resour 2024; 9:696-700. [PMID: 38835640 PMCID: PMC11149565 DOI: 10.1080/23802359.2024.2353271] [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: 01/24/2024] [Accepted: 05/05/2024] [Indexed: 06/06/2024] Open
Abstract
Freshwater mussels (Bivalvia, Unionida) play essential roles in the well-functioning of ecosystems, even providing essential services to humans. However, these bivalves face numerous threats (e.g. habitat loss and fragmentation, pollution, introduction of invasive species, and climate change) which have already led to the extinction of many populations. This underscores the need to fully characterize the biology of these species, particularly those, such as Potomida acarnanica, that are still poorly studied. This study presents the first mitogenome of P. acarnanica (Kobelt, 1879), an endemic species of Greece with a distribution limited to only two river basins. The mitochondrial genome of a P. acarnanica specimen, collected at Pamisos River (Peloponnese, Greece), was sequenced by Illumina high-throughput sequencing. This mitogenome (16,101 bp) is characterized by 13 protein-coding genes, 22 transfer RNA and 2 ribosomal RNA genes. The size of this mitogenome is within the range of another Potomida mitogenome already published for the species Potomida littoralis. In the phylogenetic inference, P. acarnanica was recovered as monophyletic with P. littoralis mitogenome in the Lamprotulini tribe, as expected. This genomic resource will assist in genetically characterizing the species, potentially benefiting future evolutionary studies and conservation efforts.
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Affiliation(s)
- Ana Matos
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - André Gomes-Dos-Santos
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Amílcar Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
- Mountain Research Centre, School of Agriculture, Polytechnic Institute of Bragança, Bragança, Portugal
| | - Simone Varandas
- Forestry Department, Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Ronaldo Sousa
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Ioannis Karaouzas
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavyssos, Greece
| | - Stamatis Zogaris
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavyssos, Greece
| | - Elsa Froufe
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Manuel Lopes-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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Ueda H, Ito M, Yonezawa R, Hayashi K, Tomonou T, Kashitani M, Oyama H, Shirai K, Suo R, Yoshitake K, Kinoshita S, Asakawa S, Itoi S. Japanese Planocerid Flatworms: Difference in Composition of Tetrodotoxin and Its Analogs and the Effects of Ingestion by Toxin-Bearing Fishes in the Ryukyu Islands, Japan. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:500-510. [PMID: 38630353 PMCID: PMC11178581 DOI: 10.1007/s10126-024-10312-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/09/2024] [Indexed: 06/15/2024]
Abstract
Tetrodotoxin (TTX), known as pufferfish toxin, is a potent neurotoxin blocking sodium channels in muscle and nerve tissues. TTX has been detected in various taxa other than pufferfish, including marine polyclad flatworms, suggesting that pufferfish toxin accumulates in fish bodies via food webs. The composition of TTX and its analogs in the flatworm Planocera multitentaculata was identical to those in wild grass puffer Takifugu alboplumbeus. Previously, Planocera sp. from Okinawa Island, Japan, were reported to possess high level of TTX, but no information was available on TTX analogs in this species. Here we identified TTX and analogs in the planocerid flatworm using high-resolution liquid chromatography-mass spectrometry, and compared the composition of TTX and analogs with those of another toxic and non-toxic planocerid species. We show that the composition of TTX and several analogs, such as 5,6,11-trideoxyTTX, dideoxyTTXs, deoxyTTXs, and 11-norTTX-6(S)-ol, of Planocera sp. was identical to those of toxic species, but not to its non-toxic counterpart. The difference in the toxin composition was reflected in the phylogenetic relationship based on the mitochondrial genome sequence. A toxification experiment using predatory fish and egg plates of P. multitentaculata demonstrated that the composition of TTX and analogs in wild T. alboplumbeus juveniles was reproduced in artificially toxified pufferfish. Additionally, feeding on the flatworm egg plates enhanced the signal intensities of all TTX compounds in Chelonodon patoca and that of deoxyTTXs in Yongeichthys criniger.
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Affiliation(s)
- Hiroyuki Ueda
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
| | - Masaaki Ito
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
| | - Ryo Yonezawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Kentaro Hayashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Taiga Tomonou
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
| | - Maho Kashitani
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
| | - Hikaru Oyama
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Kyoko Shirai
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
| | - Rei Suo
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Shiro Itoi
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan.
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10
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McDiarmid CS, Hooper DM, Stier A, Griffith SC. Mitonuclear interactions impact aerobic metabolism in hybrids and may explain mitonuclear discordance in young, naturally hybridizing bird lineages. Mol Ecol 2024; 33:e17374. [PMID: 38727686 DOI: 10.1111/mec.17374] [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: 12/22/2023] [Revised: 02/26/2024] [Accepted: 03/20/2024] [Indexed: 06/07/2024]
Abstract
Understanding genetic incompatibilities and genetic introgression between incipient species are major goals in evolutionary biology. Mitochondrial genes evolve rapidly and exist in dense gene networks with coevolved nuclear genes, suggesting that mitochondrial respiration may be particularly susceptible to disruption in hybrid organisms. Mitonuclear interactions have been demonstrated to contribute to hybrid dysfunction between deeply divergent taxa crossed in the laboratory, but there are few empirical examples of mitonuclear interactions between younger lineages that naturally hybridize. Here, we use controlled hybrid crosses and high-resolution respirometry to provide the first experimental evidence in a bird that inter-lineage mitonuclear interactions impact mitochondrial aerobic metabolism. Specifically, respiration capacity of the two mitodiscordant backcrosses (with mismatched mitonuclear combinations) differs from one another, although they do not differ significantly from the parental groups or mitoconcordant backcrosses as we would expect of mitonuclear disruptions. In the wild hybrid zone between these subspecies, the mitochondrial cline centre is shifted west of the nuclear cline centre, which is consistent with the direction of our experimental results. Our results therefore demonstrate asymmetric mitonuclear interactions that impact the capacity of cellular mitochondrial respiration and may help to explain the geographic discordance between mitochondrial and nuclear genomes observed in the wild.
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Affiliation(s)
- Callum S McDiarmid
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Daniel M Hooper
- Institute for Comparative Genomics and Richard Gilder Graduate School, American Museum of Natural History, New York, New York, USA
| | - Antoine Stier
- Department of Biology, University of Turku, Turku, Finland
- Institut Pluridisciplinaire Hubert Curien, UMR7178, Université de Strasbourg, CNRS, Strasbourg, France
| | - Simon C Griffith
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
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11
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Zhang X, Li C, Jiang L, Qiao G, Chen J. Characteristics and Comparative Analysis of Mitochondrial Genomes of the Aphid Genus Hyalopterus Koch (Hemiptera: Aphididae: Aphidinae). INSECTS 2024; 15:389. [PMID: 38921104 PMCID: PMC11204073 DOI: 10.3390/insects15060389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/18/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
Using Illumina sequencing technology, we generated complete mitochondrial genomes (mitogenomes) of three constituent species of the aphid genus Hyalopterus Koch, Hyalopterus amygdali (Blanchard), Hyalopterus arundiniformis Ghulamullah, and Hyalopterus pruni (Geoffroy). The sizes of the Hyalopterus mitogenomes range from 15,306 to 15,410 bp, primarily due to variations in the length of non-coding regions. The Hyalopterus mitogenomes consist of 37 coding genes arranged in the order of the ancestral insect mitogenome, a control region, and a repeat region between trnE and trnF. According to the COI-based analysis, one previously reported mitogenome of H. pruni should be assigned to H. arundiniformis. The gene order, nucleotide composition, and codon usage in the Hyalopterus mitogenomes are highly conserved and similar to those of other species of Aphidinae. The tandem repeat units differ in nucleotide composition, length, and copy number across three Hyalopterus species. Within the widespread Eurasian species H. arundiniformis, variation in repeat units among different geographic populations is observed, indicating that the repeat region may provide valuable insights for studying the intraspecific diversification of aphids. Phylogenetic analyses based on 28 complete mitogenomes of Aphidinae supported the monophyly of Aphidinae, Aphidini, Macrosiphini, and two subtribes of Aphidini. Hyalopterus was monophyletic. H. amygdali and H. pruni formed a sister group, while H. arundiniformis was placed basally. Characterization of the mitogenomes of Hyalopterus provides valuable resources for further comparative studies and for advancing our understanding of the aphid mitogenome architecture.
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Affiliation(s)
- Xiaolu Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cailing Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
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12
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Pfingstl T, Hiruta SF, Shimano S. Mitochondrial metagenomics reveal the independent colonization of the world's coasts by intertidal oribatid mites (Acari, Oribatida, Ameronothroidea). Sci Rep 2024; 14:11634. [PMID: 38773202 PMCID: PMC11109099 DOI: 10.1038/s41598-024-59423-7] [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: 02/12/2024] [Accepted: 04/10/2024] [Indexed: 05/23/2024] Open
Abstract
Oribatid mites are an ancient group that already roamed terrestrial ecosystems in the early and middle Devonian. The superfamily of Ameronothroidea, a supposedly monophyletic lineage, represents the only group of oribatid mites that has successfully invaded the marine coastal environment. By using mitogenome data and nucleic ribosomal RNA genes (18S, 5.8S, 28S), we show that Ameronothroidea are a paraphyletic assemblage and that the land-to-sea transition happened three times independently. Common ancestors of the tropical Fortuyniidae and Selenoribatidae were the first to colonize the coasts and molecular calibration of our phylogeny dates this event to a period in the Triassic and Jurassic era (225-146 mya), whereas present-day distribution indicates that this event might have happened early in this period during the Triassic, when the supercontinent Pangaea still existed. The cold temperate northern hemispheric Ameronothridae colonized the marine littoral later in the late Jurassic-Early Cretaceous and had an ancient distribution on Laurasian coasts. The third and final land-to-sea transition happened in the same geological period, but approx. 30 my later when ancestors of Podacaridae invaded coastal marine environments of the Gondwanan landmasses.
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Affiliation(s)
- Tobias Pfingstl
- Department of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.
| | - Shimpei F Hiruta
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki, 305-0005, Japan
| | - Satoshi Shimano
- Science Research Center, Hosei University, Fujimi 2-17-1 Chiyoda-ku, Tokyo, 102-8160, Japan.
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13
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Zhou S, Wang X, Wang L, Gao X, Lyu T, Xia T, Shi L, Dong Y, Mei X, Zhang Z, Zhang H. Different Evolutionary Trends of Galloanseres: Mitogenomics Analysis. Animals (Basel) 2024; 14:1437. [PMID: 38791655 PMCID: PMC11117303 DOI: 10.3390/ani14101437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/27/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The two existing clades of Galloanseres, orders Galliformes (landfowl) and Anseriformes (waterfowl), exhibit dramatically different evolutionary trends. Mitochondria serve as primary sites for energy production in organisms, and numerous studies have revealed their role in biological evolution and ecological adaptation. We assembled the complete mitogenome sequences of two species of the genus Aythya within Anseriformes: Aythya baeri and Aythya marila. A phylogenetic tree was constructed for 142 species within Galloanseres, and their divergence times were inferred. The divergence between Galliformes and Anseriformes occurred ~79.62 million years ago (Mya), followed by rapid evolution and diversification after the Middle Miocene (~13.82 Mya). The analysis of selective pressure indicated that the mitochondrial protein-coding genes (PCGs) of Galloanseres species have predominantly undergone purifying selection. The free-ratio model revealed that the evolutionary rates of COX1 and COX3 were lower than those of the other PCGs, whereas ND2 and ND6 had faster evolutionary rates. The CmC model also indicated that most PCGs in Anseriformes exhibited stronger selective constraints. Our study suggests that the distinct evolutionary trends and energy requirements of Galliformes and Anseriformes drive different evolutionary patterns in the mitogenome.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Jingxuan West Street No. 57, Qufu 273165, China; (S.Z.); (X.W.); (L.W.); (X.G.); (T.L.); (T.X.); (L.S.); (Y.D.); (X.M.); (Z.Z.)
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14
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Leite DJ, Schönauer A, Blakeley G, Harper A, Garcia-Castro H, Baudouin-Gonzalez L, Wang R, Sarkis N, Nikola AG, Koka VSP, Kenny NJ, Turetzek N, Pechmann M, Solana J, McGregor AP. An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis. EvoDevo 2024; 15:5. [PMID: 38730509 PMCID: PMC11083766 DOI: 10.1186/s13227-024-00224-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/15/2024] [Indexed: 05/13/2024] Open
Abstract
Spiders are a diverse order of chelicerates that diverged from other arthropods over 500 million years ago. Research on spider embryogenesis, particularly studies using the common house spider Parasteatoda tepidariorum, has made important contributions to understanding the evolution of animal development, including axis formation, segmentation, and patterning. However, we lack knowledge about the cells that build spider embryos, their gene expression profiles and fate. Single-cell transcriptomic analyses have been revolutionary in describing these complex landscapes of cellular genetics in a range of animals. Therefore, we carried out single-cell RNA sequencing of P. tepidariorum embryos at stages 7, 8 and 9, which encompass the establishment and patterning of the body plan, and initial differentiation of many tissues and organs. We identified 20 cell clusters, from 18.5 k cells, which were marked by many developmental toolkit genes, as well as a plethora of genes not previously investigated. We found differences in the cell cycle transcriptional signatures, suggestive of different proliferation dynamics, which related to distinctions between endodermal and some mesodermal clusters, compared with ectodermal clusters. We identified many Hox genes as markers of cell clusters, and Hox gene ohnologs were often present in different clusters. This provided additional evidence of sub- and/or neo-functionalisation of these important developmental genes after the whole genome duplication in an arachnopulmonate ancestor (spiders, scorpions, and related orders). We also examined the spatial expression of marker genes for each cluster to generate a comprehensive cell atlas of these embryonic stages. This revealed new insights into the cellular basis and genetic regulation of head patterning, hematopoiesis, limb development, gut development, and posterior segmentation. This atlas will serve as a platform for future analysis of spider cell specification and fate, and studying the evolution of these processes among animals at cellular resolution.
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Affiliation(s)
- Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Grace Blakeley
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Amber Harper
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Helena Garcia-Castro
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | | | - Ruixun Wang
- Institute for Zoology, Biocenter, University of Cologne, Zuelpicher Str. 47B, 50674, Cologne, Germany
| | - Naïra Sarkis
- Institute for Zoology, Biocenter, University of Cologne, Zuelpicher Str. 47B, 50674, Cologne, Germany
| | - Alexander Günther Nikola
- Evolutionary Ecology, Faculty of Biology, Biocenter, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Venkata Sai Poojitha Koka
- Evolutionary Ecology, Faculty of Biology, Biocenter, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Nathan J Kenny
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
- Department of Biochemistry Te Tari Matū Koiora, University of Otago, Dunedin, New Zealand
| | - Natascha Turetzek
- Evolutionary Ecology, Faculty of Biology, Biocenter, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Matthias Pechmann
- Institute for Zoology, Biocenter, University of Cologne, Zuelpicher Str. 47B, 50674, Cologne, Germany
| | - Jordi Solana
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.
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15
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Broggini C, Cavallini M, Vanetti I, Abell J, Binelli G, Lombardo G. From Caves to the Savannah, the Mitogenome History of Modern Lions ( Panthera leo) and Their Ancestors. Int J Mol Sci 2024; 25:5193. [PMID: 38791233 PMCID: PMC11121052 DOI: 10.3390/ijms25105193] [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: 04/16/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Lions (Panthera leo) play a crucial ecological role in shaping and maintaining fragile ecosystems within Africa. Conservation efforts should focus on genetic variability within wild populations when considering reintroduction attempts. We studied two groups of lions from two conservation sites located in Zambia and Zimbabwe to determine their genetic make-up, information that is usually unknown to the sites. In this study, we analysed 17 specimens for cytb and seven microsatellite markers to ascertain family relationships and genetic diversity previously obtained by observational studies. We then produced a standardised haplogroup phylogeny using all available entire mitogenomes, as well as calculating a revised molecular clock. The modern lion lineage diverged ~151 kya and was divided into two subspecies, both containing three distinct haplogroups. We confirm that Panthera leo persica is not a subspecies, but rather a haplogroup of the northern P.l. leo that exited Africa at least ~31 kya. The progenitor to all lions existed ~1.2 Mya, possibly in SE Africa, and later exited Africa and split into the two cave lion lineages ~175 kya. Species demography is correlated to major climactic events. We now have a detailed phylogeny of lion evolution and an idea of their conservation status given the threat of climate change.
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Affiliation(s)
- Camilla Broggini
- Wildlife Research Unit (UIRCP-UCO), University of Cordoba, 14071 Córdoba, Spain;
| | - Marta Cavallini
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (I.V.); (G.B.)
| | - Isabella Vanetti
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (I.V.); (G.B.)
| | - Jackie Abell
- Centre for Agroecology, Water and Resilience, Coventry University, Coventry CV8 3LG, UK;
| | - Giorgio Binelli
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (I.V.); (G.B.)
| | - Gianluca Lombardo
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (I.V.); (G.B.)
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16
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Al-Yazeedi T, Adams S, Tandonnet S, Turner A, Kim J, Lee J, Pires-daSilva A. The contribution of an X chromosome QTL to non-Mendelian inheritance and unequal chromosomal segregation in Auanema freiburgense. Genetics 2024; 227:iyae032. [PMID: 38431281 DOI: 10.1093/genetics/iyae032] [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: 12/24/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
Auanema freiburgense is a nematode with males, females, and selfing hermaphrodites. When XO males mate with XX females, they typically produce a low proportion of XO offspring because they eliminate nullo-X spermatids. This process ensures that most sperm carry an X chromosome, increasing the likelihood of X chromosome transmission compared to random segregation. This occurs because of an unequal distribution of essential cellular organelles during sperm formation, likely dependent on the X chromosome. Some sperm components are selectively segregated into the X chromosome's daughter cell, while others are discarded with the nullo-X daughter cell. Intriguingly, the interbreeding of 2 A. freiburgense strains results in hybrid males capable of producing viable nullo-X sperm. Consequently, when these hybrid males mate with females, they yield a high percentage of male offspring. To uncover the genetic basis of nullo-spermatid elimination and X chromosome drive, we generated a genome assembly for A. freiburgense and genotyped the intercrossed lines. This analysis identified a quantitative trait locus spanning several X chromosome genes linked to the non-Mendelian inheritance patterns observed in A. freiburgense. This finding provides valuable clues to the underlying factors involved in asymmetric organelle partitioning during male meiotic division and thus non-Mendelian transmission of the X chromosome and sex ratios.
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Affiliation(s)
- Talal Al-Yazeedi
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Sally Adams
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Sophie Tandonnet
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Anisa Turner
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Jun Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Junho Lee
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
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17
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Fields PD, Jalinsky JR, Bankers L, McElroy KE, Sharbrough J, Higgins C, Morgan-Richards M, Boore JL, Neiman M, Logsdon JM. Genome Evolution and Introgression in the New Zealand mud Snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa. Genome Biol Evol 2024; 16:evae091. [PMID: 38776329 PMCID: PMC11110935 DOI: 10.1093/gbe/evae091] [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] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
We have sequenced, assembled, and analyzed the nuclear and mitochondrial genomes and transcriptomes of Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa, two prosobranch snail species native to New Zealand that together span the continuum from estuary to freshwater. These two species are the closest known relatives of the freshwater species Potamopyrgus antipodarum-a model for studying the evolution of sex, host-parasite coevolution, and biological invasiveness-and thus provide key evolutionary context for understanding its unusual biology. The P. estuarinus and P. kaitunuparaoa genomes are very similar in size and overall gene content. Comparative analyses of genome content indicate that these two species harbor a near-identical set of genes involved in meiosis and sperm functions, including seven genes with meiosis-specific functions. These results are consistent with obligate sexual reproduction in these two species and provide a framework for future analyses of P. antipodarum-a species comprising both obligately sexual and obligately asexual lineages, each separately derived from a sexual ancestor. Genome-wide multigene phylogenetic analyses indicate that P. kaitunuparaoa is likely the closest relative to P. antipodarum. We nevertheless show that there has been considerable introgression between P. estuarinus and P. kaitunuparaoa. That introgression does not extend to the mitochondrial genome, which appears to serve as a barrier to hybridization between P. estuarinus and P. kaitunuparaoa. Nuclear-encoded genes whose products function in joint mitochondrial-nuclear enzyme complexes exhibit similar patterns of nonintrogression, indicating that incompatibilities between the mitochondrial and the nuclear genome may have prevented more extensive gene flow between these two species.
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Affiliation(s)
- Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | | | - Laura Bankers
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Kyle E McElroy
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Joel Sharbrough
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Chelsea Higgins
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Mary Morgan-Richards
- School of Natural Sciences, Massey University Manawatū, Palmerston North, New Zealand
| | - Jeffrey L Boore
- Phenome Health, Seattle, WA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA, USA
- Department of Gender, Women's, and Sexuality Studies, University of Iowa, Iowa City, IA, USA
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, USA
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18
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Rivera D, Henderson JB, Lam AW, Hostetter NJ, Collazo JA, Bell RC. High-Quality, Chromosome-Level Reference Genomes of the Viviparous Caribbean Skinks Spondylurus nitidus and S. culebrae. Genome Biol Evol 2024; 16:evae079. [PMID: 38619022 PMCID: PMC11065358 DOI: 10.1093/gbe/evae079] [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: 03/01/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/16/2024] Open
Abstract
New World mabuyine skinks are a diverse radiation of morphologically cryptic lizards with unique reproductive biologies. Recent studies examining population-level data (morphological, ecological, and genomic) have uncovered novel biodiversity and phenotypes, including the description of dozens of new species and insights into the evolution of their highly complex placental structures. Beyond the potential for this diverse group to serve as a model for the evolution of viviparity in lizards, much of the taxonomic diversity is concentrated in regions experiencing increasing environmental instability from climate and anthropogenic change. Consequently, a better understanding of genome structure and diversity will be an important tool in the adaptive management and conservation of this group. Skinks endemic to Caribbean islands are particularly vulnerable to global change with several species already considered likely extinct and several remaining species either endangered or threatened. Combining PacBio long-read sequencing, Hi-C, and RNAseq data, here we present the first genomic resources for this group by describing new chromosome-level reference genomes for the Puerto Rican Skink Spondylurus nitidus and the Culebra Skink S. culebrae. Results indicate two high quality genomes, both ∼1.4 Gb, assembled nearly telomere to telomere with complete mitochondrion assembly and annotation.
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Affiliation(s)
- Danielle Rivera
- North Carolina Cooperative Fish and Wildlife Research Unit, Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - James B Henderson
- Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Athena W Lam
- Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Nathan J Hostetter
- U.S. Geological Survey, North Carolina Cooperative Fish and Wildlife Research Unit, Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Jaime A Collazo
- U.S. Geological Survey, North Carolina Cooperative Fish and Wildlife Research Unit, Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Rayna C Bell
- Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118, USA
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19
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Najer T, Doña J, Buček A, Sweet AD, Sychra O, Johnson KP. Mitochondrial genome fragmentation is correlated with increased rates of molecular evolution. PLoS Genet 2024; 20:e1011266. [PMID: 38701107 PMCID: PMC11095710 DOI: 10.1371/journal.pgen.1011266] [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: 12/20/2023] [Revised: 05/15/2024] [Accepted: 04/20/2024] [Indexed: 05/05/2024] Open
Abstract
While mitochondrial genome content and organization is quite diverse across all Eukaryotes, most bilaterian animal mitochondrial genomes (mitogenomes) exhibit highly conserved gene content and organisation, with genes typically encoded on a single circular chromosome. However, many species of parasitic lice (Insecta: Phthiraptera) are among the notable exceptions, having mitogenomes fragmented into multiple circular chromosomes. To better understand the process of mitogenome fragmentation, we conducted a large-scale genomic study of a major group of lice, Amblycera, with extensive taxon sampling. Analyses of the evolution of mitogenome structure across a phylogenomic tree of 90 samples from 53 genera revealed evidence for multiple independent origins of mitogenome fragmentation, some inferred to have occurred less than five million years ago. We leveraged these many independent origins of fragmentation to compare the rates of DNA substitution and gene rearrangement, specifically contrasting branches with fragmented and non-fragmented mitogenomes. We found that lineages with fragmented mitochondrial genomes had significantly higher rates of mitochondrial sequence evolution. In addition, lineages with fragmented mitochondrial genomes were more likely to have mitogenome gene rearrangements than those with single-chromosome mitochondrial genomes. By combining phylogenomics and mitochondrial genomics we provide a detailed portrait of mitogenome evolution across this group of insects with a remarkably unstable mitogenome structure, identifying processes of molecular evolution that are correlated with mitogenome fragmentation.
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Affiliation(s)
- Tomáš Najer
- Department of Veterinary Sciences, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
| | - Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
- Departamento de Biología Animal, Universidad de Granada, Granada, Spain
| | - Aleš Buček
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Okinawa Institute of Science & Technology Graduate University, Onna-son, Okinawa, Japan
| | - Andrew D. Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Oldřich Sychra
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
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20
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Kraberger S, Serieys LEK, Leighton GRM, De Koch MD, Munday JS, Bishop JM, Varsani A. Two Lineages of Papillomaviruses Identified from Caracals ( Caracal caracal) in South Africa. Viruses 2024; 16:701. [PMID: 38793583 PMCID: PMC11125996 DOI: 10.3390/v16050701] [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: 04/03/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Papillomaviruses (PV) infect epithelial cells and can cause hyperplastic or neoplastic lesions. In felids, most described PVs are from domestic cats (Felis catus; n = 7 types), with one type identified in each of the five wild felid species studied to date (Panthera uncia, Puma concolor, Leopardus wiedii, Panthera leo persica and Lynx rufus). PVs from domestic cats are highly diverse and are currently classified into three genera (Lambdapapillomavirus, Dyothetapapillomavirus, and Taupapillomavirus), whereas those from wild felids, although diverse, are all classified into the Lambdapapillomavirus genus. In this study, we used a metagenomic approach to identify ten novel PV genomes from rectal swabs of five deceased caracals (Caracal caracal) living in the greater Cape Town area, South Africa. These are the first PVs to be described from caracals, and represent six new PV types, i.e., Caracal caracal papillomavirus (CcarPV) 1-6. These CcarPV fall into two phylogenetically distinct genera: Lambdapapillomavirus, and Treisetapapillomavirus. Two or more PV types were identified in a single individual for three of the five caracals, and four caracals shared at least one of the same PV types with another caracal. This study broadens our understanding of wild felid PVs and provides evidence that there may be several wild felid PV lineages.
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Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | | | - Gabriella R M Leighton
- Institute for Communities and Wildlife in Africa (iCWild), Department of Biological Sciences, University of Cape Town, Cape Town 7701, South Africa
| | - Matthew D De Koch
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - John S Munday
- School of Veterinary Science, Massey University, Tennant Drive, Palmerston North 4442, New Zealand
| | - Jacqueline M Bishop
- Institute for Communities and Wildlife in Africa (iCWild), Department of Biological Sciences, University of Cape Town, Cape Town 7701, South Africa
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
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21
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Kapoor S, Yang YT, Hall RN, Gasser RB, Bowles VM, Perry T, Anstead CA. Complete Mitochondrial Genome for Lucilia cuprina dorsalis (Diptera: Calliphoridae) from the Northern Territory, Australia. Genes (Basel) 2024; 15:506. [PMID: 38674440 PMCID: PMC11050061 DOI: 10.3390/genes15040506] [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: 03/20/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The Australian sheep blowfly, Lucilia cuprina dorsalis, is a major sheep ectoparasite causing subcutaneous myiasis (flystrike), which can lead to reduced livestock productivity and, in severe instances, death of the affected animals. It is also a primary colonizer of carrion, an efficient pollinator, and used in maggot debridement therapy and forensic investigations. In this study, we report the complete mitochondrial (mt) genome of L. c. dorsalis from the Northern Territory (NT), Australia, where sheep are prohibited animals, unlike the rest of Australia. The mt genome is 15,943 bp in length, comprising 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region. The gene order of the current mt genome is consistent with the previously published L. cuprina mt genomes. Nucleotide composition revealed an AT bias, accounting for 77.5% of total mt genome nucleotides. Phylogenetic analyses of 56 species/taxa of dipterans indicated that L. c. dorsalis and L. sericata are the closest among all sibling species of the genus Lucilia, which helps to explain species evolution within the family Luciliinae. This study provides the first complete mt genome sequence for L. c. dorsalis derived from the NT, Australia to facilitate species identification and the examination of the evolutionary history of these blowflies.
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Affiliation(s)
- Shilpa Kapoor
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Ying Ting Yang
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
| | - Robyn N. Hall
- CSIRO Health & Biosecurity, Acton, ACT 2601, Australia;
- Ausvet Pty Ltd., Fremantle, WA 6160, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Vernon M. Bowles
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Trent Perry
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
| | - Clare A. Anstead
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
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22
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Alkathiry HA, Alghamdi SQ, Sinha A, Margos G, Stekolnikov AA, Alagaili AN, Darby AC, Makepeace BL, Khoo JJ. Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia. BMC Genomics 2024; 25:380. [PMID: 38632506 PMCID: PMC11025265 DOI: 10.1186/s12864-024-10301-6] [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: 01/05/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear. RESULTS Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin. CONCLUSIONS P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.
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Affiliation(s)
- Hadil A Alkathiry
- Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Samia Q Alghamdi
- Department of Biology, Faculty of Science, Al-Baha University, P.O.Box1988, Al-Baha, 65799, Saudi Arabia
| | - Amit Sinha
- New England Biolabs, Ipswich, Massachusetts, 01938, USA
| | - Gabriele Margos
- National Reference Centre for Borrelia, Bavarian Health and Food Safety Authority, Veterinärstr. 2, Oberschleissheim, 85764, Germany
| | - Alexandr A Stekolnikov
- Laboratory of Parasitic Arthropods, Zoological Institute of the Russian Academy of Sciences, Universitetskaya embankment 1, St. Petersburg, 199034, Russia
| | | | - Alistair C Darby
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Benjamin L Makepeace
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Jing Jing Khoo
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK.
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23
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Chang H, Liu X, Xie Z. The complete mitochondrial genome of Phymateus saxosus (Coquerel, 1861) (Orthoptera: Pyrgomorphidae) and phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:457-460. [PMID: 38591051 PMCID: PMC11000610 DOI: 10.1080/23802359.2024.2316064] [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: 12/20/2023] [Accepted: 02/03/2024] [Indexed: 04/10/2024] Open
Abstract
Phymateus saxosus is a member of the family Pyrgomorphidae, Orthoptera. In this study, the complete mitochondrial genome (mitogenome) of P. saxosus was determined and analyzed. Assembled mitogenome sequence of P. saxosus is 15,672 bp in size, containing 37 genes and a control region. The gene orientation and arrangement of P. saxosus are identical to other species in the Pyrgomorphoidea family. The overall nucleotide composition is as follows: A (43.6%) > T (30.2%) > C (16.1%) > G (10.1%). Phylogenetic analysis suggested that P. saxosus forms sister groups with P. morbillosus, and the monophyly of Pyrgomorphidae is supported. In general, this study provided valuable genetic information for P. saxosus and explored the phylogenetic relationships in the family Pyrgomorphidae.
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Affiliation(s)
- Huihui Chang
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, Henan, China
| | - Xinhu Liu
- School of Energy and Building Environment Engineering, Henan University of Urban Construction, Pingdingshan, Henan, China
| | - Zhaohui Xie
- CONTACT Zhaohui Xie College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, Henan467036, China
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24
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Sosale MS, Roelke-Parker M, Machange GA, Edwards CW, Figueiró HV, Koepfli KP. The complete mitochondrial genome of Meller's mongoose ( Rhynchogale melleri). Mitochondrial DNA B Resour 2024; 9:432-436. [PMID: 38586507 PMCID: PMC10993741 DOI: 10.1080/23802359.2024.2333567] [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: 08/08/2023] [Accepted: 03/15/2024] [Indexed: 04/09/2024] Open
Abstract
Meller's mongoose (Rhynchogale melleri) is a member of the family Herpestidae (Mammalia: Carnivora) and the sole species in the genus Rhynchogale. It is primarily found in savannas and open woodlands of eastern sub-Saharan Africa. Here, we report the first complete mitochondrial genome for a female Meller's mongoose collected in Tanzania, generated using a genome-skimming approach. The mitogenome had a final length of 16,644 bp and a total of 37 annotated genes. Phylogenetic analysis validated the placement of this species in the herpestid subfamily Herpestinae. Ultimately, the outcomes of this research offer a genetic foundation for future studies of Meller's mongoose.
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Affiliation(s)
- Medhini S. Sosale
- Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, Virginia, USA
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
| | - Melody Roelke-Parker
- Laboratory Animal Science Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Cody W. Edwards
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
- Department of Biology, George Mason University, Fairfax, Virginia, USA
| | - Henrique V. Figueiró
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, Virginia, USA
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25
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Halstead-Nussloch G, Signorini SG, Giulio M, Crocetta F, Munari M, Della Torre C, Weber AAT. The genome of the rayed Mediterranean limpet Patella caerulea (Linnaeus, 1758). Genome Biol Evol 2024; 16:evae070. [PMID: 38546725 PMCID: PMC11003540 DOI: 10.1093/gbe/evae070] [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] [Accepted: 03/23/2024] [Indexed: 04/11/2024] Open
Abstract
Patella caerulea (Linnaeus, 1758) is a mollusc limpet species of the class Gastropoda. Endemic to the Mediterranean Sea, it is considered a keystone species due to its primary role in structuring and regulating the ecological balance of tidal and subtidal habitats. It is currently being used as a bioindicator to assess the environmental quality of coastal marine waters and as a model species to understand adaptation to ocean acidification. Here, we provide a high-quality reference genome assembly and annotation for P. caerulea. We generated ∼30 Gb of Pacific Biosciences high-fidelity data from a single individual and provide a final 749.8 Mb assembly containing 62 contigs, including the mitochondrial genome (14,938 bp). With an N50 of 48.8 Mb and 98% of the assembly contained in the 18 largest contigs, this assembly is near chromosome-scale. Benchmarking Universal Single-Copy Orthologs scores were high (Mollusca, 87.8% complete; Metazoa, 97.2% complete) and similar to metrics observed for other chromosome-level Patella genomes, highlighting a possible bias in the Mollusca database for Patellids. We generated transcriptomic Illumina data from a second individual collected at the same locality and used it together with protein evidence to annotate the genome. A total of 23,938 protein-coding gene models were found. By comparing this annotation with other published Patella annotations, we found that the distribution and median values of exon and gene lengths was comparable with other Patella species despite different annotation approaches. The present high-quality P. caerulea reference genome, available on GenBank (BioProject: PRJNA1045377; assembly: GCA_036850965.1), is an important resource for future ecological and evolutionary studies.
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Affiliation(s)
| | - Silvia Giorgia Signorini
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
- Department of Biosciences, University of Milan, Milan, Italy
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Marco Giulio
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Fabio Crocetta
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Marco Munari
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Biology, Stazione Idrobiologica ‘Umberto d’Ancona’, University of Padova, Chioggia, Italy
| | - Camilla Della Torre
- Department of Biosciences, University of Milan, Milan, Italy
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Alexandra Anh-Thu Weber
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
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26
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Decker SH, Saadi AJ, Baranyi C, Hirose M, Lemer S, Sombke A, Aguilera F, Vieira LM, Smith AM, Waeschenbach A, Schwaha T. Boring systematics: A genome skimmed phylogeny of ctenostome bryozoans and their endolithic family Penetrantiidae with the description of one new species. Ecol Evol 2024; 14:e11276. [PMID: 38638369 PMCID: PMC11024686 DOI: 10.1002/ece3.11276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/19/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024] Open
Abstract
Ctenostomes are a group of gymnolaemate bryozoans with an uncalcified chitinous body wall having few external, skeletal characters. Hence, species identification is challenging and their systematics remain poorly understood, even more so when they exhibit an endolithic (boring) lifestyle. Currently, there are four Recent families of endolithic bryozoans that live inside mineralized substrates like mollusk shells. In particular, Penetrantiidae Silén, 1946 has received considerable attention and its systematic affinity to either cheilostomes or ctenostomes has been debated. Species delimitation of penetrantiids remains difficult, owing to a high degree of colonial and zooidal plasticity. Consequently, an additional molecular approach is essential to unravel the systematics of penetrantiids, their phylogenetic placement and their species diversity. We therefore sequenced the mitochondrial (mt) genomes and two nuclear markers of 27 ctenostome species including nine penetrantiids. Our phylogeny supports the Penetrantiidae as a monophyletic group placed as sister taxon to the remaining ctenostomes alongside paludicellids, arachnidioids and terebriporids. The boring family Terebriporidae d'Orbigny, 1847 were previously considered to be among vesicularioids, but our results suggest an arachnidioid affinity instead. Ctenostome paraphyly is supported by our data, as the cheilostomes nest within them. A Multiporata clade is also well supported, including the former victorelloid genus Sundanella. Altogether, this study provides new insights into ctenostome systematics, assists with species delimitation and contributes to our understanding of the bryozoan tree of life.
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Affiliation(s)
| | - Ahmed J. Saadi
- Department of Evolutionary BiologyUniversity of ViennaViennaAustria
| | | | - Masato Hirose
- School of Marine BiosciencesKitasato UniversityMinato‐kuJapan
| | | | - Andy Sombke
- Center for Anatomy and Cell Biology, Cell and Developmental BiologyMedical University of ViennaViennaAustria
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias BiológicasUniversidad de ConcepciónConcepciónChile
| | - Leandro M. Vieira
- Laboratório de Estudos de Bryozoa—LAEBry, Departamento de Zoologia, Centro de BiociênciasUniversidade Federal de PernambucoRecifePEBrazil
- Department of Life ScienceNatural History MuseumLondonUK
| | - Abigail M. Smith
- Department of Marine ScienceUniversity of OtagoDunedinNew Zealand
| | | | - Thomas Schwaha
- Department of Evolutionary BiologyUniversity of ViennaViennaAustria
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27
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Saha A, Baca M, Popović D, Mohammadi Z, Olsson U, Roycroft E, Fostowicz-Frelik Ł. The first complete mitochondrial genome data of the Afghan pika Ochotona rufescens (Lagomorpha, Ochotonidae), near the type locality. Data Brief 2024; 53:110246. [PMID: 38533117 PMCID: PMC10964060 DOI: 10.1016/j.dib.2024.110246] [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: 10/09/2023] [Revised: 02/03/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024] Open
Abstract
The Afghan pika Ochotona rufescens (Gray, 1842) is widely distributed across the mountains of Afghanistan, Iran, Pakistan, and southwestern Turkmenistan, most often at elevations between 2,000 and 3,000 m. Here we present, for the first time, the complete mitochondrial genomes of two specimens of the nominotypical subspecies Ochotona rufescens rufescens, de novo assembled from Illumina short reads of fragmented probe-enriched DNA. The lengths of the circular mitogenomes are 16,408 bp and 16,407 bp, respectively. Both mitogenomes contain 13 protein-coding genes (PCGs), two ribosomal RNAs (16S rRNA and 12S rRNA), 22 transfer RNA genes, and a control region. The gene NAD6 and the tRNA (Gln), tRNA (Ala), tRNA (Asn), tRNA (Cys), tRNA (Tyr), tRNA (Ser), tRNA (Glu), and tRNA (Pro) are encoded on the light strand while the rest are encoded on the heavy strand. The overall nucleotide composition was ∼30% for A, 25% for T, 15% for G, and 29% for C. The mitogenome data are available in the GenBank under the accession numbers ON859136 and ON859137.
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Affiliation(s)
- Anwesha Saha
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00–818 Warsaw, Poland
- Centre of New Technologies (CeNT), University of Warsaw, S. Banacha 2c, 02–097 Warsaw, Poland
| | - Mateusz Baca
- Centre of New Technologies (CeNT), University of Warsaw, S. Banacha 2c, 02–097 Warsaw, Poland
| | - Danijela Popović
- Centre of New Technologies (CeNT), University of Warsaw, S. Banacha 2c, 02–097 Warsaw, Poland
| | | | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Emily Roycroft
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Acton, ACT 2601, Australia
| | - Łucja Fostowicz-Frelik
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00–818 Warsaw, Poland
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28
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Lan X, Wang J, Zhang M, Zhou Q, Xiang H, Jiang W. Molecular Identification of Acrossocheilus jishouensis (Teleostei: Cyprinidae) and Its Complete Mitochondrial Genome. Biochem Genet 2024; 62:1396-1412. [PMID: 37620638 DOI: 10.1007/s10528-023-10501-x] [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: 01/11/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Molecular identification, such as DNA barcoding, is a useful tool that is widely applied in distinguishing species. To identify the cyprinid Acrossocheilus jishouensis, which was previously known to be restricted to only its type locality, we conducted molecular identification of this species based on 23 samples in five localities. Molecular identification based on the mitochondrial COI gene sequence showed that the morphologically similar samples from the five populations were all A. jishouensis, as the mean genetic distances between populations were very small (0.1-1.6%); thus, the distribution of this species was substantially expanded. The whole mitochondrial genome of one sample was also assembled, which was 16,594 bp in length and consisted of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. All PCGs began with ATG except the COI gene, which started with GTG; seven PCGs used the complete stop codon TAA, while four terminated in T(AA) and two ended with TAG. The overall base composition reflected a higher proportion of A+T than G+C and a positive AT-skew and negative GC-skew pattern except for the opposite in ND6. Phylogenetic relationships inferred using BI and ML methods revealed that both Acrossocheilus and Onychostoma were nonmonophyletic, which indicated that the traditional diagnoses between these two genera need to be assessed further. The results of this study not only expanded the known distribution ranges of A. jishouensis, but also provided a valuable data resource for future molecular and evolutionary studies of Acrossocheilus and other cyprinids in Barbinae.
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Affiliation(s)
- Xiangying Lan
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Jinxiu Wang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Mingyao Zhang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Qiang Zhou
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Hongmei Xiang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
| | - Wansheng Jiang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China.
- College of Biology and Environmental Sciences, Jishou University, Jishou, China.
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Nagy NA, Tóth GE, Kurucz K, Kemenesi G, Laczkó L. The updated genome of the Hungarian population of Aedes koreicus. Sci Rep 2024; 14:7545. [PMID: 38555322 PMCID: PMC10981705 DOI: 10.1038/s41598-024-58096-6] [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: 12/11/2023] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
Vector-borne diseases pose a potential risk to human and animal welfare, and understanding their spread requires genomic resources. The mosquito Aedes koreicus is an emerging vector that has been introduced into Europe more than 15 years ago but only a low quality, fragmented genome was available. In this study, we carried out additional sequencing and assembled and characterized the genome of the species to provide a background for understanding its evolution and biology. The updated genome was 1.1 Gbp long and consisted of 6099 contigs with an N50 value of 329,610 bp and a BUSCO score of 84%. We identified 22,580 genes that could be functionally annotated and paid particular attention to the identification of potential insecticide resistance genes. The assessment of the orthology of the genes indicates a high turnover at the terminal branches of the species tree of mosquitoes with complete genomes, which could contribute to the adaptation and evolutionary success of the species. These results could form the basis for numerous downstream analyzes to develop targets for the control of mosquito populations.
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Affiliation(s)
- Nikoletta Andrea Nagy
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, Hungary.
- HUN-REN-UD Behavioural Ecology Research Group, University of Debrecen, Debrecen, Hungary.
- Institute of Metagenomics, University of Debrecen, Debrecen, Hungary.
| | - Gábor Endre Tóth
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pecs, Hungary
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Kornélia Kurucz
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pecs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pecs, Hungary
| | - Gábor Kemenesi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pecs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pecs, Hungary
| | - Levente Laczkó
- HUN-REN-UD Conservation Biology Research Group, University of Debrecen, Debrecen, Hungary
- One Health Institute, University of Debrecen, Debrecen, Hungary
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30
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Despabiladeras JB, Bautista MAM. Complete Mitochondrial Genome of the Eggplant Fruit and Shoot Borer, Leucinodes orbonalis Guenée (Lepidoptera: Crambidae), and Comparison with Other Pyraloid Moths. INSECTS 2024; 15:220. [PMID: 38667350 PMCID: PMC11050083 DOI: 10.3390/insects15040220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024]
Abstract
The eggplant fruit and shoot borer (EFSB) (Leucinodes orbonalis Guenée) is a devastating lepidopteran pest of eggplant (Solanum melongena L.) in the Philippines. Management of an insect pest like the EFSB requires an understanding of its biology, evolution, and adaptations. Genomic resources provide a starting point for understanding EFSB biology, as the resources can be used for phylogenetics and population structure studies. To date, genomic resources are scarce for EFSB; thus, this study generated its complete mitochondrial genome (mitogenome). The circular mitogenome is 15,244 bp-long. It contains 37 genes, namely 13 protein-coding, 22 tRNA, and 2 rRNA genes, and has conserved noncoding regions, motifs, and gene syntenies characteristic of lepidopteran mitogenomes. Some protein-coding genes start and end with non-canonical codons. The tRNA genes exhibit a conserved cloverleaf structure, with the exception in trnS1. Partitioned phylogenetic analysis using 72 pyraloids generated highly supported maximum likelihood and Bayesian inference trees revealing expected basal splits between Crambidae and Pyralidae, and Spilomelinae and Pyraustinae. Spilomelinae was recovered to be paraphyletic, with the EFSB robustly placed before the split of Spilomelinae and Pyraustinae. Overall, the EFSB mitogenome resource will be useful for delineations within Spilomelinae and population structure analysis.
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Affiliation(s)
| | - Ma. Anita M. Bautista
- Functional Genomics Laboratory, National Institute of Molecular Biology and Biotechnology, College of Science, University of the Philippines-Diliman, Quezon City 1101, Philippines;
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Luo J, Zhang R, Deng W. First mitogenomic characterization of Macromotettixoides (Orthoptera, Tetrigidae), with the descriptions of two new species. Zookeys 2024; 1195:95-120. [PMID: 38525351 PMCID: PMC10958162 DOI: 10.3897/zookeys.1195.112623] [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: 09/12/2023] [Accepted: 01/05/2024] [Indexed: 03/26/2024] Open
Abstract
Classification of species is commonly based on morphological, molecular, and distribution depending on the taxa. Macromotettixoides Zheng, Wei & Jiang, 2005 and Formosatettix Tinkham, 1937 are both wingless types of Tetrigidae with extremely similar morphological characteristics, and in the current taxonomic system they are placed in two different subfamilies, Metrodorinae and Tetriginae, respectively. It is difficult to clearly identify the species of these two genera by morphological characteristics, and molecular data is often needed to assist identification. Here, the complete mitogenomes of two new species were sequenced and assembled, with that of Macromotettixoidesorthomargina. Molecular data of species of Formosatettix were used to test the monophyly of Macromotettixoides and to re-assess the generic characters, and also to test whether Macromotettixoides belongs to the Asian Metrodorinae or Tetriginae. Furthermore, mitochondrial characteristics were analyzed and the phylogeny of the Tetrigidae reconstructed based on mitochondrial protein-coding genes (PCGs). The results indicated that the two new species were clustered with Macromotettixoides rather than Formosatettix, and the anterior margin of the fastigium and pronotum of the two new species usually had the humeral angle different from that of Formosatettix. Therefore, after integrating morphological and molecular data, the two new species were placed in the genus Macromotettixoides, M.maoershanensissp. nov. and M.brachycornasp. nov. Finally, a phylogenetic reconstruction supported Macromotettixoides being assigned to Tetriginae rather than Metrodorinae, in contrast to the previous classification of this genus.
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Affiliation(s)
- Jieling Luo
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, Guangxi 541006, China Guangxi Normal University Guilin China
| | - Rongjiao Zhang
- School of Chemistry and Bioengineering, Hechi University, 546300, Yizhou, Guangxi China Hechi University Yizhou China
| | - Weian Deng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, Guangxi 541006, China Guangxi Normal University Guilin China
- School of Chemistry and Bioengineering, Hechi University, 546300, Yizhou, Guangxi China Hechi University Yizhou China
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Wang H, Zeng S, Zhang Z, Yang D. The complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994 (Decapoda: Rhynchocinetidae). Mitochondrial DNA B Resour 2024; 9:347-351. [PMID: 38476839 PMCID: PMC10930117 DOI: 10.1080/23802359.2023.2261636] [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: 07/10/2023] [Accepted: 09/17/2023] [Indexed: 03/14/2024] Open
Abstract
We report the complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994. The mitogenome was found to contain 16158 bp with 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs), and 1 putative control region. Phylogenetic analysis indicated that R. brucei was sister to Rhynchocinetes durbanensis (PP= 1), of the same family Rhynchocinetidae. These results are helpful for research on the phylogenetic and evolutionary studies of this group.
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Affiliation(s)
- Hangjun Wang
- Wenzhou Marine Center, Ministry of Natural Resources of the People’s Republic of China, Beijing, China
- Marine Ecosystem Observation and Research Station on the Yangtze River Estuary, Wenzhou, China
| | - Sheng Zeng
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhao Zhang
- Wenzhou Marine Center, Ministry of Natural Resources of the People’s Republic of China, Beijing, China
- Marine Ecosystem Observation and Research Station on the Yangtze River Estuary, Wenzhou, China
| | - Deyuan Yang
- College of the Environment and Ecology, Xiamen University, Xiamen, China
- National Taiwan Ocean University, Keelung, Taiwan, China
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Chandra S, Abhilash R, Sidharthan A, Raghavan R, Dahanukar N. Complete mitogenome of Lepidopygopsis typus, an evolutionarily-distinct, endangered cyprinid fish from the Western Ghats Biodiversity Hotspot: Phylogenetic relationships and implications for conservation. Gene 2024; 898:148098. [PMID: 38128794 DOI: 10.1016/j.gene.2023.148098] [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: 10/29/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
The mitogenome of Lepidopygopsis typus, an evolutionarily distinct, endangered, cyprinid fish from the Western Ghats Biodiversity Hotspot, was characterized. Total length of the mitogenome was 16,729 bp, and comprised of 13 protein coding, 22 tRNA and two rRNA genes. Thirteen protein coding genes contributed a total nucleotide length of 11,408 bp, which coded for a total of 3794 amino acids and accounting for 68.2 % of the mitogenome. A maximum likelihood phylogenetic tree based on mitogenomes of members of cyprinid subfamilies Torinae, Schizothoracinae and Schizopygopsinae, recovered L. typus in a well-resolved clade of Torinae with members of the Western Ghats endemic genus Hypselobarbus as sister taxa. Selection analysis suggested that the branch of L. typus and Hypselobarbus spp. was under intensified selection with reference to other members of Torinae. There were 19 codons under diversifying selection in L. typus, which could be the result of positive selection for adapting to high-altitude, upstream tributaries of Periyar River, where the species has a restricted distribution. With respect to Hypselobarbus spp., L. typus was under relaxed selection with about 68 % of codons experiencing neutral evolution. Restricted distribution, low population size and relaxation in selection can likely trigger extinction in L. typus, and therefore urgent conservation and monitoring plans are required to secure the future of this evolutionary distinct, and globally endangered species.
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Affiliation(s)
- Swetha Chandra
- Zoology Research Group, St. Stephen's College, Pathanapuram, University of Kerala, India
| | - Ravimohanan Abhilash
- Department of Zoology, Christian College, Chengannur, University of Kerala, Kerala, India
| | - Arya Sidharthan
- Faculty of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi, India
| | - Neelesh Dahanukar
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, India.
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Schwaha T, Decker SH, Baranyi C, Saadi AJ. Rediscovering the unusual, solitary bryozoan Monobryozoon ambulans Remane, 1936: first molecular and new morphological data clarify its phylogenetic position. Front Zool 2024; 21:5. [PMID: 38443908 PMCID: PMC10913646 DOI: 10.1186/s12983-024-00527-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND One of the most peculiar groups of the mostly colonial phylum Bryozoa is the taxon Monobryozoon, whose name already implies non-colonial members of the phylum. Its peculiarity and highly unusual lifestyle as a meiobenthic clade living on sand grains has fascinated many biologists. In particular its systematic relationship to other bryozoans remains a mystery. Despite numerous searches for M. ambulans in its type locality Helgoland, a locality with a long-lasting marine station and tradition of numerous courses and workshops, it has never been reencountered until today. Here we report the first observations of this almost mythical species, Monobryozoon ambulans. RESULTS For the first time since 1938, we present new modern, morphological analyses of this species as well as the first ever molecular data. Our detailed morphological analysis confirms most previous descriptions, but also ascertains the presence of special ambulatory polymorphic zooids. We consider these as bud anlagen that ultimately consecutively separate from the animal rendering it pseudo-colonial. The remaining morphological data show strong ties to alcyonidioidean ctenostome bryozoans. Our morphological data is in accordance with the phylogenomic analysis, which clusters it with species of Alcyonidium as a sister group to multiporate ctenostomes. Divergence time estimation and ancestral state reconstruction recover the solitary state of M. ambulans as a derived character that probably evolved in the Late Cretaceous. In this study, we also provide the entire mitogenome of M. ambulans, which-despite the momentary lack of comparable data-provides important data of a unique and rare species for comparative aspects in the future. CONCLUSIONS We were able to provide first sequence data and modern morphological data for the unique bryozoan, M. ambulans, which are both supporting an alcyonidioidean relationship within ctenostome bryozoans.
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Affiliation(s)
- Thomas Schwaha
- Department of Evolutionary Biology, University of Vienna, Schlachthausgasse 43, 1030, Vienna, Austria.
| | - Sebastian H Decker
- Department of Evolutionary Biology, University of Vienna, Schlachthausgasse 43, 1030, Vienna, Austria
| | - Christian Baranyi
- Department of Evolutionary Biology, University of Vienna, Schlachthausgasse 43, 1030, Vienna, Austria
| | - Ahmed J Saadi
- Department of Evolutionary Biology, University of Vienna, Schlachthausgasse 43, 1030, Vienna, Austria
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Ryder D, Stone D, Minardi D, Riley A, Avant J, Cross L, Soeffker M, Davidson D, Newman A, Thomson P, Darby C, van Aerle R. De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome. BMC Genomics 2024; 25:233. [PMID: 38438840 PMCID: PMC10910785 DOI: 10.1186/s12864-024-10141-4] [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: 11/13/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited. RESULTS A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. CONCLUSIONS We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.
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Affiliation(s)
- David Ryder
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK.
| | - David Stone
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Diana Minardi
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Ainsley Riley
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Justin Avant
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Lisa Cross
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Marta Soeffker
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
- Collaborative Centre for Sustainable Use of the Seas, University of East Anglia, Norwich, UK
| | | | | | | | - Chris Darby
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Ronny van Aerle
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
- Centre for Sustainable Aquaculture Futures , University of Exeter, Exeter, UK
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Liu J, Chen J, Cai X, Yang D, Li X, Liu X. Comparative Analysis of the Mitochondrial Genomes of Chloropidae and Their Implications for the Phylogeny of the Family. Int J Mol Sci 2024; 25:2920. [PMID: 38474171 DOI: 10.3390/ijms25052920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Chloropidae, commonly known as grass flies, represent the most taxonomically diverse family of Diptera Carnoidea, comprising over 3000 described species worldwide. Previous phylogenetic studies of this family have predominantly relied on morphological characters, with mitochondrial genomes being reported in a few species. This study presents 11 newly sequenced mitochondrial genomes (10 Chloropidae and 1 Milichiidae) and provides the first comprehensive comparative analysis of mitochondrial genomes for Chloropidae. Apart from 37 standard genes and the control region, three conserved intergenic sequences across Diptera Cyclorrhapha were identified in all available chloropid mitochondrial genomes. Evolutionary rates within Chloropidae exhibit significant variation across subfamilies, with Chloropinae displaying higher rates than the other three subfamilies. Phylogenetic relationships based on mitochondrial genomes were inferred using maximum likelihood and Bayesian methods. The monophyly of Chloropidae and all four subfamilies is consistently strongly supported, while subfamily relationships within Chloropidae remain poorly resolved, possibly due to rapid evolution.
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Affiliation(s)
- Jiuzhou Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jiajia Chen
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaodong Cai
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xuankun Li
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xiaoyan Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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37
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Ahuja N, Cao X, Schultz DT, Picciani N, Lord A, Shao S, Jia K, Burdick DR, Haddock SHD, Li Y, Dunn CW. Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores. Genome Biol Evol 2024; 16:evae048. [PMID: 38502059 PMCID: PMC10980510 DOI: 10.1093/gbe/evae048] [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: 05/24/2023] [Revised: 02/20/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024] Open
Abstract
Siphonophores (Cnidaria: Hydrozoa) are abundant predators found throughout the ocean and are important constituents of the global zooplankton community. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these roughly 200 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing of 32 species sampled broadly across the phylogeny. Sequencing depth was sufficient to estimate nuclear genome size from k-mer spectra in six specimens, ranging from 0.7 to 2.3 Gb, with heterozygosity estimates between 0.69% and 2.32%. Incremental k-mer counting indicates k-mer peaks can be absent with nearly 20× read coverage, suggesting minimum genome sizes range from 1.4 to 5.6 Gb in the 25 samples without peaks in the k-mer spectra. This work confirms most siphonophore nuclear genomes are large relative to the genomes of other cnidarians, but also identifies several with reduced size that are tractable targets for future siphonophore nuclear genome assembly projects. We also assembled complete mitochondrial genomes for 33 specimens from these new data, indicating a conserved gene order shared among nonsiphonophore hydrozoans, Cystonectae, and some Physonectae, revealing the ancestral mitochondrial gene order of siphonophores. Our results also suggest extensive rearrangement of mitochondrial genomes within other Physonectae and in Calycophorae. Though siphonophores comprise a small fraction of cnidarian species, this survey greatly expands our understanding of cnidarian genome diversity. This study further illustrates both the importance of deep phylogenetic sampling and the utility of k-mer-based genome skimming in understanding the genomic diversity of a clade.
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Affiliation(s)
- Namrata Ahuja
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Xuwen Cao
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Darrin T Schultz
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Natasha Picciani
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Arianna Lord
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Shengyuan Shao
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Kejue Jia
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | | | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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38
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Benson CW, Sheltra MR, Huff DR. The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss. G3 (BETHESDA, MD.) 2024; 14:jkad238. [PMID: 37847611 PMCID: PMC10849329 DOI: 10.1093/g3journal/jkad238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
To complete its parasitic lifecycle, Salmacisia buchloëana, a biotrophic fungus, manipulates reproductive organ development, meristem determinacy, and resource allocation in its dioecious plant host, buffalograss (Bouteloua dactyloides; Poaceae). To gain insight into S. buchloëana's ability to manipulate its host, we sequenced and assembled the 20.1 Mb genome of S. buchloëana into 22 chromosome-level pseudomolecules. Phylogenetic analysis suggests that S. buchloëana is nested within the genus Tilletia and diverged from Tilletia caries and Tilletia walkeri ∼40 MYA. We find that S. buchloëana contains a novel chromosome arm with no syntenic relationship to other publicly available Tilletia genomes, and that genes on the novel arm are upregulated upon infection, suggesting that this unique chromosomal segment may have played a critical role in S. buchloëana's evolution and host specificity. Salmacisia buchloëana has one of the largest fractions of serine peptidases (1.53% of the proteome) and one of the highest GC contents (62.3%) in all classified fungi. Analysis of codon base composition indicated that GC content is controlled more by selective constraints than directional mutation, and that S. buchloëana has a unique bias for the serine codon UCG. Finally, we identify 3 inteins within the S. buchloëana genome, 2 of which are located in a gene often used in fungal taxonomy. The genomic and transcriptomic resources generated here will aid plant pathologists and breeders by providing insight into the extracellular components contributing to sex determination in dioecious grasses.
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Affiliation(s)
- Christopher W Benson
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - Matthew R Sheltra
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - David R Huff
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
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Baeza JA, Stephens NC, Baker A, Lyons A, Franks B, Pirro S, Feldheim KA. Insights into the nuclear and mitochondrial genome of the Lemon shark Negaprion brevirostris using low-coverage sequencing: Genome size, repetitive elements, mitochondrial genome, and phylogenetic placement. Gene 2024; 894:147939. [PMID: 38572145 PMCID: PMC10990291 DOI: 10.1016/j.gene.2023.147939] [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] [Indexed: 04/05/2024]
Abstract
The Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA operon, and assembled and described in detail the mitochondrial genome. Lastly, the phylogenetic position of N. brevirostris in the family Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ranged between 2.29 and 2.58 Gbp using a k-mer analysis, which is slightly below the genome size estimated for other sharks belonging to the family Carcharhinidae. Using a k-mer analysis, approx. 64-71 % of the genome of N. brevirostris was composed of repetitive elements. A relatively large proportion of the 'repeatome' could not be annotated. Taking into account only annotated repetitive elements, Class I - Long Interspersed Nuclear Element (LINE) were the most abundant repetitive elements followed by Class I - Penelope and Satellite DNA. The nuclear ribosomal operon was fully assembled. The AT-rich complete mitochondrial genome was 16,703 bp long and encoded 13 protein coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Negaprion brevirostris is closely related to the genera Carcharhinus, Glyphis and Lamiopsis in the family Carcharinidae. This new genomic resources will aid with the development of conservation plans for this large coastal shark.
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Affiliation(s)
- J. Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
- Smithsonian Marine Station at Fort Pierce, Smithsonian Institution, Fort Pierce, FL, USA
- Departamento de Biología Marina, Universidad Catolica del Norte, Coquimbo, Chile
| | | | - Alyssa Baker
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Andrew Lyons
- Marine Science Research Institute, Jacksonville University, Florida, USA
| | - Bryan Franks
- Marine Science Research Institute, Jacksonville University, Florida, USA
| | | | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, Chicago, IL, USA
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Yi J, Liu J, Mao Y, Cheng Y, Lin M, Xu H, An Y, Li J, Wu H. The Complete Mitochondrial Genome of Chilo infuscatellus (Lepidoptera: Pyralidae), and Related Phylogenetic Analysis. Biochem Genet 2024:10.1007/s10528-023-10639-8. [PMID: 38306003 DOI: 10.1007/s10528-023-10639-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/12/2023] [Indexed: 02/03/2024]
Abstract
The Chilo infuscatellus (Lepidoptera: Pyralidae) is a significant pest of sugarcane in China. The genome-level characteristics of this pest are important genetic resources for identification, phylogenetic analysis, and even management. In the present study, the complete mitogenome of C. infuscatellus was sequenced and characterized. The assembled mitochondrial genome is 15,252 bp in length and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and an A + T-rich region. Except for the CGA codon for the cox1 gene, the PCGs are initiated with ATN codons (ATG, ATT, and ATA). These PCGs are terminated with TAA or an incomplete termination codon of a single T. Except for the loss of the "DHU" arm for trnS1, the tRNA genes were folded into the typical cloverleaf structure. The A + T-rich region has a high AT content of 96.19% and contains the motifs "ATAGA" and "ATTTA", as well as a 19 bp poly-T stretch and microsatellite regions. The C. infuscatellus mitogenome exhibits a conserved gene order among lepidopteran insects, with a rearrangement of the trnM gene compared to the ancestral insect gene order. Phylogenetic analysis based on the 13 PCGs using Bayesian inference (BI) and maximum likelihood (ML) methods confirmed the monophyly of Pyralidae and Crambidae within Pyraloidea. The relationships between subfamilies in Pyralidae can be described as (Galleriinae + (Phycitinae + (Pyralinae + Epipaschiinae))). The "PS clade" and "non-PS clade" were formed within the family Crambidae. These findings provide valuable genetic resources for the identification, phylogenetic analysis, and management of sugarcane borers, contributing significantly to our understanding of the phylogeny of Pyraloidea insects and their evolution.
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Affiliation(s)
- Jiequn Yi
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Jianbai Liu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yongkai Mao
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yinjie Cheng
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Minjiang Lin
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Hanliang Xu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yuxing An
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Jihu Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China.
| | - Han Wu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China.
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Haugen MN, Gusarov VI, Struck TH. The complete mitochondrial genome of Aegialites californicus (Motchoulsky, 1845) (insecta: coleoptera: salpingidae). Mitochondrial DNA B Resour 2024; 9:214-218. [PMID: 38298223 PMCID: PMC10829811 DOI: 10.1080/23802359.2024.2309255] [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: 08/08/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
The flightless intertidal beetle genus Aegialites (family Salpingidae) is distributed along the Northern Pacific coasts, from California to Alaska and from Northern Japan to Kamchatka. Systematics of Aegialites and its phylogenetic relationships to other members of Salpingidae are unclear, and little genetic information is available. We here present the first complete mitochondrial genome of this genus, represented by Aegialites californicus (Motchoulsky, 1845) from Sonoma County, California, U.S.A. The complete mitochondrial genome of A. californicus is 15,899 bp long and comprises 13 protein-coding (PCG), two ribosomal RNA (rRNA) and 22 transfer RNA (tRNA) genes. The phylogenetic analysis places A.californicus as sister to other members of family Salpingidae. The mitochondrial genome sequence of A. californicus will contribute to future phylogenetic and taxonomic studies of genus Aegialites, family Salpingidae and superfamily Tenebrionoidea.
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Zhang TT, Yan CL, Qiao JX, Yang AS, Liu ML, Kou YX, Li ZH. Demographic dynamics and molecular evolution of the rare and endangered subsect. Gerardianae of Pinus: insights from chloroplast genomes and mitochondrial DNA markers. PLANTA 2024; 259:45. [PMID: 38281265 DOI: 10.1007/s00425-023-04316-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024]
Abstract
MAIN CONCLUSION The divergence of subsect. Gerardianae was likely triggered by the uplift of the Qinghai-Tibetan Plateau and adjacent mountains. Pinus bungeana might have probably experienced expansion since Last Interglacial period. Historical geological and climatic oscillations have profoundly affected patterns of nucleotide variability, evolutionary history, and species divergence in numerous plants of the Northern Hemisphere. However, how long-lived conifers responded to geological and climatic fluctuations in East Asia remain poorly understood. Here, based on paternally inherited chloroplast genomes and maternally inherited mitochondrial DNA markers, we investigated the population demographic history and molecular evolution of subsect. Gerardianae (only including three species, Pinus bungeana, P. gerardiana, and P. squamata) of Pinus. A low level of nucleotide diversity was found in P. bungeana (π was 0.00016 in chloroplast DNA sequences, and 0.00304 in mitochondrial DNAs). The haplotype-based phylogenetic topology and unimodal distributions of demographic analysis suggested that P. bungeana probably originated in the southern Qinling Mountains and experienced rapid population expansion since Last Interglacial period. Phylogenetic analysis revealed that P. gerardiana and P. squamata had closer genetic relationship. The species divergence of subsect. Gerardianae occurred about 27.18 million years ago (Mya) during the middle to late Oligocene, which was significantly associated with the uplift of the Qinghai-Tibetan Plateau and adjacent mountains from the Eocene to the mid-Pliocene. The molecular evolutionary analysis showed that two chloroplast genes (psaI and ycf1) were under positive selection, the genetic lineages of P. bungeana exhibited higher transition and nonsynonymous mutations, which were involved with the strongly environmental adaptation. These findings shed light on the population evolutionary history of white pine species and provide striking insights for comprehension of their species divergence and molecular evolution.
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Affiliation(s)
- Ting-Ting Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Chun-Li Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jin-Xia Qiao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Ao-Shuang Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yi-Xuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China.
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Sterling-Montealegre RA, Prada CF. Variability and evolution of gene order rearrangement in mitochondrial genomes of arthropods (except Hexapoda). Gene 2024; 892:147906. [PMID: 37844850 DOI: 10.1016/j.gene.2023.147906] [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: 06/07/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
In the species-rich Phylum Arthropoda, the mitochondrial genome is relatively well conserved both in terms of number and order of genes. However, specific clades have a 'typical' gene order that differs from the putative arthropod ancestral arrangement. The aim of this work was to compare the rate of mitochondrial gene rearrangements at inter- and intra-taxonomic levels in the Arthropoda and to postulate the most parsimonious ancestral orders representing the four major arthropod lineages. For this purpose, we performed a comparative genomic analysis of arthropod mitochondrial genomes available in the NCBI database. Using a combination of bioinformatics methods that examined mitochondrial gene rearrangements in 464 species of arthropods from three subphyla (Chelicerata, Myriapoda, and Crustacea [except Hexapoda, previously analyzed]), we observed differences in the rate of rearrangement within major lineages. A higher rate of mitochondrial genome rearrangement was observed in Crustacea and Chelicerata compared to Myriapoda. Likewise, early branching clades exhibit less variability in mitochondrial genome order than late branching clades, within each subphylum. We identified 'hot regions' in the mitochondrial genome of each studied subphylum, and postulated the most likely ancestral gene order in each subphylum and taxonomic order. Our work provides new evidence on the evolutionary dynamics of mitochondrial genome gene order in arthropods and new mitochondrial genome architectures in different taxonomic divisions within each major lineage of arthropods.
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Affiliation(s)
| | - Carlos Fernando Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Colombia.
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Baeza JA, González MT, Sigwart JD, Greve C, Pirro S. Insights into the genome of the 'Loco' Concholepas concholepas (Gastropoda: Muricidae) from low-coverage short-read sequencing: genome size, ploidy, transposable elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Muricidae. BMC Genomics 2024; 25:77. [PMID: 38243187 PMCID: PMC10797722 DOI: 10.1186/s12864-023-09953-7] [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: 09/21/2023] [Accepted: 12/28/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND The Peruvian 'chanque' or Chilean 'loco' Concholepas concholepas is an economically, ecologically, and culturally important muricid gastropod heavily exploited by artisanal fisheries in the temperate southeastern Pacific Ocean. In this study, we have profited from a set of bioinformatics tools to recover important biological information of C. concholepas from low-coverage short-read NGS datasets. Specifically, we calculated the size of the nuclear genome, ploidy, and estimated transposable elements content using an in silico k-mer approach, we discovered, annotated, and quantified those transposable elements, we assembled and annotated the 45S rDNA RNA operon and mitochondrial genome, and we confirmed the phylogenetic position of C. concholepas within the muricid subfamily Rapaninae based on translated protein coding genes. RESULTS Using a k-mer approach, the haploid genome size estimated for the predicted diploid genome of C. concholepas varied between 1.83 Gbp (with kmer = 24) and 2.32 Gbp (with kmer = 36). Between half and two thirds of the nuclear genome of C. concholepas was composed of transposable elements. The most common transposable elements were classified as Long Interspersed Nuclear Elements and Short Interspersed Nuclear Elements, which were more abundant than DNA transposons, simple repeats, and Long Terminal Repeats. Less abundant repeat elements included Helitron mobile elements, 45S rRNA DNA, and Satellite DNA, among a few others.The 45S rRNA DNA operon of C. concholepas that encodes for the ssrRNA, 5.8S rRNA, and lsrRNA genes was assembled into a single contig 8,090 bp long. The assembled mitochondrial genome of C. concholepas is 15,449 bp long and encodes 13 protein coding genes, two ribosomal genes, and 22 transfer RNAs. CONCLUSION The information gained by this study will inform the assembly of a high quality nuclear genome for C. concholepas and will support bioprospecting and biomonitoring using environmental DNA to advance development of conservation and management plans in this overexploited marine snail.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.
- Departamento de Biología Marina, Universidad Catolica del Norte, Coquimbo, Chile.
- Smithsonian Marine Station at Fort Pierce, Smithsonian Institution, Fort Pierce, FL, USA.
| | - M Teresa González
- Facultad de Ciencias del Mar y Recursos Biológicos, Instituto de Ciencias Naturales Alexander Von Humboldt, Universidad de Antofagasta, Angamos 601, Antofagasta, Chile
| | - Julia D Sigwart
- Marine Zoology Department, Senckenberg Research Institute and Museum, Frankfurt, Germany
- Institute of Ecology, Evolution & Diversity, Goethe University, Frankfurt, Germany
| | - Carola Greve
- LOEWE -Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, Frankfurt Am Main, Germany
- Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt am Main, Germany
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Wei ZF, Ta KW, Zhang NN, Liu SS, Meng L, Liu KQ, Cai CY, Peng XT, Shao CW. Molecular phylogenetic relationships based on mitochondrial genomes of novel deep-sea corals (Octocorallia: Alcyonacea): Insights into slow evolution and adaptation to extreme deep-sea environments. Zool Res 2024; 45:215-225. [PMID: 38247179 PMCID: PMC10839654 DOI: 10.24272/j.issn.2095-8137.2023.039] [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: 03/27/2023] [Accepted: 09/11/2023] [Indexed: 01/23/2024] Open
Abstract
A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1 633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea (SCS). Based on mitochondrial genomic characteristics, morphological examination, and sclerite scanning electron microscopy, the samples were categorized into four suborders (Calcaxonia, Holaxonia, Scleraxonia, and Stolonifera), and identified as 9 possible new cold-water coral species. Assessments of GC-skew dissimilarity, phylogenetic distance, and average nucleotide identity (ANI) revealed a slow evolutionary rate for the octocoral mitochondrial sequences. The nonsynonymous ( Ka) to synonymous ( Ks) substitution ratio ( Ka/ Ks) suggested that the 14 protein-coding genes (PCGs) were under purifying selection, likely due to specific deep-sea environmental pressures. Correlation analysis of the median Ka/ Ks values of five gene families and environmental factors indicated that the genes encoding cytochrome b (cyt b) and DNA mismatch repair protein ( mutS) may be influenced by environmental factors in the context of deep-sea species formation. This study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.
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Affiliation(s)
- Zhan-Fei Wei
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Kai-Wen Ta
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
| | - Nan-Nan Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Shan-Shan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Liang Meng
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Kai-Qiang Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Chong-Yang Cai
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xiao-Tong Peng
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China. E-mail:
| | - Chang-Wei Shao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China. E-mail:
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Lan G, Yu J, Liu J, Zhang Y, Ma R, Zhou Y, Zhu B, Wei W, Liu J, Qi G. Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae). Genes (Basel) 2024; 15:90. [PMID: 38254979 PMCID: PMC10815732 DOI: 10.3390/genes15010090] [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: 11/09/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Tarsiger indicus (Vieillot, 1817), the White-browed Bush Robin, is a small passerine bird widely distributed in Asian countries. Here, we successfully sequenced its mitogenome using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) for PE 2 × 150 bp sequencing. Combined with other published mitogenomes, we conducted the first comprehensive comparative mitogenome analysis of Muscicapidae birds and reconstructed the phylogenetic relationships between Muscicapidae and related groups. The T. indicus mitogenome was 16,723 bp in size, and it possessed the typical avian mitogenome structure and organization. Most PCGs of T. indicus were initiated strictly with the typical start codon ATG, while COX1 and ND2 were started with GTG. RSCU statistics showed that CUA, CGA, and GCC were relatively high frequency in the T. indicus mitogenome. T. cyanurus and T. indicus shared very similar mitogenomic features. All 13 PCGs of Muscicapidae mitogenomes had experienced purifying selection. Specifically, ATP8 had the highest rate of evolution (0.13296), whereas COX1 had the lowest (0.01373). The monophylies of Muscicapidae, Turdidae, and Paradoxornithidae were strongly supported. The clade of ((Muscicapidae + Turdidae) + Sturnidae) in Passeriformes was supported by both Bayesian Inference and Maximum likelihood analyses. The latest taxonomic status of many passerine birds with complex taxonomic histories were also supported. For example, Monticola gularis, T. indicus, and T. cyanurus were allocated to Turdidae in other literature; our phylogenetic topologies clearly supported their membership in Muscicapidae; Paradoxornis heudei, Suthora webbiana, S. nipalensis, and S. fulvifrons were formerly classified into Muscicapidae; we supported their membership in Paradoxornithidae; Culicicapa ceylonensis was originally classified as a member of Muscicapidae; our results are consistent with a position in Stenostiridae. Our study enriches the genetic data of T. indicus and provides new insights into the molecular phylogeny and evolution of passerine birds.
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Affiliation(s)
- Guanwei Lan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (G.L.); (W.W.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Jiaojiao Yu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Juan Liu
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Yue Zhang
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Rui Ma
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Yanshan Zhou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Biqing Zhu
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Wei Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (G.L.); (W.W.)
| | - Jiabin Liu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
- Institute of Wildlife Conservation, Central South University of Forestry and Technology, Changsha 410004, China
| | - Guilan Qi
- Animal Husbandry Institute, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
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Ni Y, Wu H, Chen Y, Chen J, Tian W, Chen W, Xu Z, Zhong J. The first record of Egglestonichthys bombylios (Gobiiformes: Gobiidae) from China with its first fresh colouration information. Zootaxa 2024; 5399:37-51. [PMID: 38221177 DOI: 10.11646/zootaxa.5399.1.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Indexed: 01/16/2024]
Abstract
During bottom trawl surveys carried out between 20132021, 52 specimens (33.854.0 mm SL) of Egglestones bumblebee goby Egglestonichthys bombylios were collected at a depth of 1.515 m from Dongshan Bay, Sanmen Bay, and Niushan Island, China. They represent the first records of this species from China. A full description, including fresh colouration of the species is provided as it is poorly known. The individuals collected in China agree with most morphological features of the holotype, except for the pelvic fin fraenum that was not observed or appears to be absent in most specimens. A strong relationship between E. bombylios, Larsonella pumilus, and the genus Priolepis is herein demonstrated by the mitochondrial genome sequences of E. bombylios and twenty closely related species. This study enriches the existing genetic data of the so-called Priolepis lineage and provides useful insights into the phylogenetic relationships across species of the genera Egglestonichthys, Priolepis, and Larsonella.
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Affiliation(s)
- Yong Ni
- East China Sea Fisheries Research Institute; Fisheries Science of Chinese Academy; Shanghai; 200090; China.
| | - Hanlin Wu
- College of Fisheries and Life Science; Shanghai Ocean University; Shanghai; 201306; China.
| | - Yuange Chen
- East China Sea Fisheries Research Institute; Fisheries Science of Chinese Academy; Shanghai; 200090; China; College of Fisheries and Life Science; Shanghai Ocean University; Shanghai; 201306; China.
| | - Jiajie Chen
- East China Sea Fisheries Research Institute; Fisheries Science of Chinese Academy; Shanghai; 200090; China.
| | - Wei Tian
- Zhejiang Institute of Hydraulics & Estuary (Zhejiang Institute of Marine Planning and Design); Hangzhou; 310017; China.
| | - Weifeng Chen
- East China Sea Fisheries Research Institute; Fisheries Science of Chinese Academy; Shanghai; 200090; China.
| | - Zhaoli Xu
- College of Fisheries and Life Science; Shanghai Ocean University; Shanghai; 201306; China.
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Zhang W, Zhao S, Qian L, Ma H, Shi J, Wang Y, Cui P. The complete mitochondrial genome of Slaty-backed Forktail, Enicurus schistaceus (Passeriformes: Muscicapidae) and phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:66-69. [PMID: 38197051 PMCID: PMC10776053 DOI: 10.1080/23802359.2023.2301024] [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: 02/07/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024] Open
Abstract
The complete mitogenome of the Slaty-backed Forktail (Enicurus schistaceus) was first sequenced using next-generation sequencing. It was 17,112 bp long, with a base composition of 14.17% G, 31.77% C, 30.73% A, and 23.33% T and an AT content of 54.06%. Similar to other mitochondrial genomes within the Muscicapidae family, E. schistaceus exhibited a relatively consistent mitogenome arrangement; it consisted of 22 tRNA genes, two rRNA genes, 13 protein-coding genes, and one control region. Notably, ND6 and eight tRNA genes were encoded on the light strand. Phylogenetic analysis of the 12 Muscicapidae mitogenomes substantiated the monophyly of all genera, including E. schistaceus. Furthermore, the analysis demonstrated a close relationship between Enicurus and Myophonus.
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Affiliation(s)
- Wenwen Zhang
- Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, Jiangsu, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing, Jiangsu, China
- Biodiversity Comprehensive Observation Station for Wuyi Mountains, Nanjing, Jiangsu, China
| | - Shengjun Zhao
- Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, Jiangsu, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing, Jiangsu, China
- Biodiversity Comprehensive Observation Station for Wuyi Mountains, Nanjing, Jiangsu, China
| | - Lifu Qian
- School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, China
| | - Haohao Ma
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Jie Shi
- Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, Jiangsu, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing, Jiangsu, China
- Biodiversity Comprehensive Observation Station for Wuyi Mountains, Nanjing, Jiangsu, China
| | - Yifei Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Peng Cui
- Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, Jiangsu, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains, Nanjing, Jiangsu, China
- Biodiversity Comprehensive Observation Station for Wuyi Mountains, Nanjing, Jiangsu, China
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49
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Mu XH, Liang XX, Zheng YT, Zhao K. Complete mitochondrial genome sequence of Aureoboletus raphanaceus (Boletales, Basidiomycota). Mitochondrial DNA B Resour 2024; 9:20-23. [PMID: 38187009 PMCID: PMC10769141 DOI: 10.1080/23802359.2023.2294887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/10/2023] [Indexed: 01/09/2024] Open
Abstract
Aureoboletus raphanaceus is a member of boletoid mushroom, which is named after its distinctive radish smell. The mitochondrial genome and phylogenetic relationships with other boletes need to be investigated to gain a comprehensive understanding of it. In this study, we sequenced the mitochondrial genome of A. raphanaceus using next-generation sequencing technology and found that its mitochondrial genome is a circular DNA molecule measuring 42,157 bp. It consists of 15 core protein-coding genes, 27 transfer RNA genes, and two ribosomal RNA genes. The mitochondrial genome had a base composition of A (39.89%), C (11.06%), G (11.67%), and T (37.38%), with a GC content of 22.73%. A phylogenetic tree based on 22 mitochondrial genomes was constructed, which provided the first insights into the phylogenetic relationships of this species with related boletes.
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Affiliation(s)
- Xin-Hua Mu
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Xin-Xin Liang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yu-Ting Zheng
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Kuan Zhao
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
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50
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Elameen A, Maduna SN, Mageroy MH, van Eerde A, Knudsen G, Hagen SB, Eiken HG. Novel insight into lepidopteran phylogenetics from the mitochondrial genome of the apple fruit moth of the family Argyresthiidae. BMC Genomics 2024; 25:21. [PMID: 38166583 PMCID: PMC10759517 DOI: 10.1186/s12864-023-09905-1] [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: 06/23/2023] [Accepted: 12/14/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND The order Lepidoptera has an abundance of species, including both agriculturally beneficial and detrimental insects. Molecular data has been used to investigate the phylogenetic relationships of major subdivisions in Lepidoptera, which has enhanced our understanding of the evolutionary relationships at the family and superfamily levels. However, the phylogenetic placement of many superfamilies and/or families in this order is still unknown. In this study, we determine the systematic status of the family Argyresthiidae within Lepidoptera and explore its phylogenetic affinities and implications for the evolution of the order. We describe the first mitochondrial (mt) genome from a member of Argyresthiidae, the apple fruit moth Argyresthia conjugella. The insect is an important pest on apples in Fennoscandia, as it switches hosts when the main host fails to produce crops. RESULTS The mt genome of A. conjugella contains 16,044 bp and encodes all 37 genes commonly found in insect mt genomes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and a large control region (1101 bp). The nucleotide composition was extremely AT-rich (82%). All detected PCGs (13) began with an ATN codon and terminated with a TAA stop codon, except the start codon in cox1 is ATT. All 22 tRNAs had cloverleaf secondary structures, except trnS1, where one of the dihydrouridine (DHU) arms is missing, reflecting potential differences in gene expression. When compared to the mt genomes of 507 other Lepidoptera representing 18 superfamilies and 42 families, phylogenomic analyses found that A. conjugella had the closest relationship with the Plutellidae family (Yponomeutoidea-super family). We also detected a sister relationship between Yponomeutoidea and the superfamily Tineidae. CONCLUSIONS Our results underline the potential importance of mt genomes in comparative genomic analyses of Lepidoptera species and provide valuable evolutionary insight across the tree of Lepidoptera species.
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Affiliation(s)
- Abdelhameed Elameen
- Division of Biotechnology and Plant Health, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway.
| | - Simo N Maduna
- Division of Environment and Natural Resources, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway
| | - Melissa H Mageroy
- Division of Biotechnology and Plant Health, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway
| | - André van Eerde
- Division of Biotechnology and Plant Health, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway
| | - Geir Knudsen
- Division of Biotechnology and Plant Health, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway
| | - Snorre B Hagen
- Division of Environment and Natural Resources, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway
| | - Hans Geir Eiken
- Division of Environment and Natural Resources, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway
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