The complete mitochondrial genome of the Honduran white bat Ectophylla alba (Allen 1982) (Chiroptera: Phyllostomidae)

Vivas-Toro, Isabela; Ortega, Jorge; Baeza, Juán Antonio

doi:10.1016/j.gene.2021.145868

Cited by 10 publications

(6 citation statements)

References 38 publications

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“…This sample was transported to the Laboratorio de Bioconservación y Manejo, Instituto Politécnico Nacional, Cuidad de Mexico, Mexico, for its posterior laboratory treatment. The Qiagen Blood and Tissue Kit (Qiagen, Hilden, Germany) was used in extraction of total genomic DNA from the tissue sample according to manufacturer’s instructions ( Vivas-Toro, Ortega & Baeza, 2021 ). Following extraction, the Savannah River Ecology Laboratory at the University of Georgia, Aiken, performed next generation sequencing from the extracted DNA sample ( Vivas-Toro, Ortega & Baeza, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

“…An Illumina HiSeq sequencer (Illumina, San Diego, CA, USA) that used 2 × 200 cycle sequenced Illumina paired-end (PE) shotgun library ( Vivas-Toro, Ortega & Baeza, 2021 ). The PE reads were prepared using standard protocol of the Nextera™ DNA Sample Prep Kit (Epicentre ® ).…”

Section: Methodsmentioning

confidence: 99%

“…The PE reads were prepared using standard protocol of the Nextera™ DNA Sample Prep Kit (Epicentre ® ). The pairs generated totaled 5,507,122 and were provided in FASTQ format by the facility ( Vivas-Toro, Ortega & Baeza, 2021 ). DNA-seq data have been deposited in the NCBI Sequence Read Archive (SRA) under Bioproject ID: PRJNA785336 , Biosample accession: SAMN23553527 , and SRA accession: SRR17086167 .…”

Section: Methodsmentioning

confidence: 99%

“…DNA-seq data have been deposited in the NCBI Sequence Read Archive (SRA) under Bioproject ID: PRJNA785336 , Biosample accession: SAMN23553527 , and SRA accession: SRR17086167 . Methods of extraction and sequencing the mitochondrial DNA followed standard protocol and has been utilized previously for other organisms ( López-Cuamatzi, Ortega & Baeza, 2022 ; Vivas-Toro, Ortega & Baeza, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

“…MitoPhAST first extracted all 13 PCG nucleotide sequences from the species available in GenBank as well as from T. bairdii . Clustal Omega aligned the PCG nucleotide sequences after translation into amino acid sequences ( Sievers & Higgins, 2014 ; Vivas-Toro, Ortega & Baeza, 2021 ). Poorly aligned regions were removed with trimAl ( Capella-Gutiérrez, Silla-Martínez & Gabaldón, 2009 ) before the dataset was partitioned and the best fitting models of sequence evolution were selected with ProtTest ( Abascal, Zardoya & Posada, 2005 ).…”

Section: Methodsmentioning

confidence: 99%

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First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird’s) tapir (Tapirus bairdii)

Ennis

Ortega

Baeza

2022

PeerJ

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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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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%