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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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Barrera CA, Ortega J, Gutierrez-Guerrero YT, Baeza JA. Comparative mitochondrial genomics of American nectar-feeding long-nosed bats Leptonycteris spp. with insights into the phylogeny of the family Phyllostomidae. Gene 2023:147588. [PMID: 37364695 DOI: 10.1016/j.gene.2023.147588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/05/2023] [Accepted: 06/21/2023] [Indexed: 06/28/2023]
Abstract
Among leaf-nosed bats (family Phyllostomidae), the genus Leptonycteris (subfamily Glossophaginae), contains three migratory and obligate nectar-dwelling species of great ecological and economic importance; the greater long-nosed bat L. nivalis, the lesser long-nosed bat L. yerbabuenae, and the southern long-nosed bat L. curasoae. According to the IUCN, the three species are categorized as 'vulnerable', 'endangered', and 'near threatened', respectively. In this study, we assembled and characterized in detail the mitochondrial genome of Leptonycteris spp. and examined the phylogenetic position of this genus in the family Phyllostomidae based on protein coding genes (PCGs). The mitogenomes of L. nivalis, L. curasoae, and L. yerbabuenae are 16,708, 16,758, and 16,729 bp in length and each encode 13 PCGs, 22 transfer RNA genes, 2 rRNA genes, and a putative control region (CR). Mitochondrial gene order is identical to that reported before for the family Phyllostomidae. All tRNAs exhibit a 'cloverleaf' secondary structure, except tRNA-Serine-1 that is missing the DHU arm in the three species. All PCGs are exposed to purifying selection with atp8 experiencing the most relaxed purifying selection as the ω ratio was higher for this gene compared to the other PCGs in each species. The CR of each species contains three functional domains: extended termination associated sequence (ETAS), Central, and conserved sequence block domain (CSB). A phylomitogenomic analysis revealed that Leptonycteris is monophyletic and most closely related to the genus Glossophaga. The analysis also supported the monophyly of the family Glossophaginae in the speciose family Phyllostomidae. The mitochondria characterization of these species provides relevant information to develop molecular markers for conservation purposes.
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Affiliation(s)
- Carlos A Barrera
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico City, Mexico.
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico City, Mexico.
| | - Yocelyn T Gutierrez-Guerrero
- Museum of Vertebrate Zoology, Department of Integrative Biology, University of California Berkeley, Berkeley, CA, US.
| | - J A Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634, USA; Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL 34949, USA; Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, Coquimbo 1281, Chile.
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The mitochondrial genomes of big-eared bats, Macrotus waterhousii and Macrotus californicus (Chiroptera: Phyllostomidae: Macrotinae). Gene 2023; 863:147295. [PMID: 36804001 DOI: 10.1016/j.gene.2023.147295] [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: 10/06/2022] [Revised: 01/25/2023] [Accepted: 02/15/2023] [Indexed: 02/21/2023]
Abstract
In the species-rich family Phyllostomidae, the genus Macrotus ('big eared' bats) contains only two species; Macrotus waterhousii, distributed in western, central, and southern Mexico, Guatemala and some Caribbean Islands, and Macrotus californicus, distributed in the southwestern USA, and in the Baja California peninsula and the state of Sonora in Mexico. In this study, we sequenced and assembled the mitochondrial genome of Macrotus waterhousii and characterized in detail this genome and that of the congeneric M. californicus. Then, we examined the phylogenetic position of Macrotus in the family Phyllostomidae based on protein coding genes (PCGs). The AT-rich mitochondrial genomes of M. waterhousii and M. californicus are 16,792 and 16,691 bp long, respectively, and each encode 13 PCGs, 22 tRNA genes, 2 rRNA genes, and a putative non-coding control region 1,336 and 1,232 bp long, respectively. Mitochondrial synteny in Macrotus is identical to that reported before for all other cofamilial species. In the two studied species, all tRNAs exhibit a 'typical' cloverleaf secondary structure with the exception of trnS1, which lacks the D arm. A selective pressure analysis demonstrated that all PCGs are under purifying selection. The CR of the two species feature three domains previously reported in other mammals, including bats: extended terminal associated sequences (ETAS), central (CD), and conserved sequence block (CSB). A phylogenetic analysis based on the 13 mitochondrial PCGs demonstrated that Macrotus is monophyletic and the subfamily Macrotinae is a sister group of all remaining phyllostomids in our analysis, except Micronycterinae. The assembly and detailed analysis of these mitochondrial genomes represents a step further to continue improving the understanding of phylogenetic relationships within the species-rich family Phyllostomidae.
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Mitochondrial Genomes Assembled from Non-Invasive eDNA Metagenomic Scat Samples in Critically Endangered Mammals. Genes (Basel) 2023; 14:genes14030657. [PMID: 36980929 PMCID: PMC10048355 DOI: 10.3390/genes14030657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
The abundance of many large-bodied vertebrates, both in marine and terrestrial environments, has declined substantially due to global and regional climate stressors that define the Anthropocene. The development of genetic tools that can serve to monitor population’s health non-intrusively and inform strategies for the recovery of these species is crucial. In this study, we formally evaluate whether whole mitochondrial genomes can be assembled from environmental DNA (eDNA) metagenomics scat samples. Mitogenomes of four different large vertebrates, the panda bear (Ailuropoda melanoleuca), the moon bear (Ursus thibetanus), the Java pangolin (Manis javanica), and the the North Atlantic right whale (Eubalaena glacialis) were assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 12x to 480x in 14 out of 18 different eDNA samples. Partial mitochondrial genomes were retrieved from three other eDNA samples. The complete mitochondrial genomes of the studied species were AT-rich and comprised 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative D-loop/control region. Synteny observed in all assembled mitogenomes was identical to that reported for specimens of the same and other closely related species. This study demonstrates that it is possible to assemble accurate whole mitochondrial chromosomes from eDNA samples (scats) using forthright bench and bioinformatics workflows. The retrieval of mitochondrial genomes from eDNA samples represents a tool to support bioprospecting, bio-monitoring, and other non-intrusive conservation strategies in species considered ‘vulnerable’, ‘endangered’, and/or ‘critically endangered’ by the IUCN Red List of Threatened Species.
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Baeza JA, Macdonald-Shedd A, Latorre-Cárdenas MC, Griffin E, Gutiérrez-Rodríguez C. The first genomic resource for the ‘near threatened’ Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae. J NAT HIST 2023. [DOI: 10.1080/00222933.2023.2186809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Ennis CC, Ortega J, Baeza JA. First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird's) tapir ( Tapirus bairdii). PeerJ 2022; 10:e13440. [PMID: 35669959 PMCID: PMC9166683 DOI: 10.7717/peerj.13440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/25/2022] [Indexed: 01/14/2023] Open
Abstract
Baird's tapir, or the Central American Tapir Tapirus bairdii (family Tapiridae), is one of the largest mammals native to the forests and wetlands of southern North America and Central America, and is categorized as 'endangered' on the 2014 IUCN Red List of Threatened Species. This study reports, for the first time, the complete mitochondrial genome of T. bairdii and examines the phylogenetic position of T. bairdii amongst closely related species in the same family and order to which it belongs using mitochondrial protein-coding genes (PCG's). The circular, double-stranded, A-T rich mitochondrial genome of T. bairdii is 16,697 bp in length consisting of 13 protein-coding genes (PCG's), two ribosomal RNA genes (rrnS (12s ribosomal RNA and rrnL (16s ribosomal RNA)), and 22 transfer RNA (tRNA) genes. A 33 bp long region was identified to be the origin of replication for the light strand (OL), and a 1,247 bp long control region (CR) contains the origin of replication for the heavy strand (OH). A majority of the PCG's and tRNA genes are encoded on the positive, or heavy, strand. The gene order in T. baiirdi is identical to that of T. indicus and T. terrestris, the only two other species of extant tapirs with assembled mitochondrial genomes. An analysis of Ka/Ks ratios for all the PCG's show values <1, suggesting that all these PCGs experience strong purifying selection. A maximum-likelihood phylogenetic analysis supports the monophyly of the genus Tapirus and the order Perissodactyla. The complete annotation and analysis of the mitochondrial genome of T. bairdii will contribute to a better understanding of the population genomic diversity and structure of this species, and it will assist in the conservation and protection of its dwindling populations.
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Affiliation(s)
- Caroline C. Ennis
- Biological Sciences, Clemson University, Clemson, SC, United States of America
| | - Jorge Ortega
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de Mexico, Mexico DF, Mexico
| | - J. Antonio Baeza
- Biological Sciences, Clemson University, Clemson, SC, United States of America,Departamento de Biologia Marina, Universidad Catolica del Norte, Coquimbo, IV Region, Chile,Smithsonian Marine Station at Fort Pierce, Smithsonian Institute, Fort Pierce, FL, United States of America
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