1
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      The first complete mitochondrial genome sequence of Cynopterusbrachyotis (Chiroptera, Pteropodidae) from the Philippines

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The technical limitations of capillary sequencing in providing insights on phylogeny have been greatly aided in recent years by the implementation of next generation sequencing platforms which can generate whole mitochondrial genome (mitogenome) sequences. In this study, enriched mitochondrial DNA of Cynopterus brachyotis from Mindanao, Philippines was sequenced using the Illumina MiSeq platform. A total of 653,967 clean paired-end reads was assembled using a MIRA-MITObim pipeline, resulting in a consensus mitogenome sequence length of 17,382 bases and a GC content of 41.48%, which is consistent with other published mitogenomes in fruit bats. The assembled C. brachyotis mitogenome was annotated using the MITOS online server and was able to resolve all mitochondrial genes, except for one transfer RNA gene (trnT) which may be further resolved by additional capillary sequencing of the region. Sequence analysis showed that the Philippine C. brachyotis is only 90%-91% homologous with other Cynopterus spp., based on its full mitogenome sequence. Phylogenetic analysis of fruit bat mitogenomes, deposited in online repositories, revealed that the Philippine C. brachyotis in this study has diverged from Asian Cynopterus , namely Cynopterus brachyotis and Cynopterus sphinx from other parts of Asia (100% bootstrap support) with the latter two forming a separate clade. This divergence at the species level was consistent with phylogentic inference using cytochrome oxidase 1 (CO1) and cytochrome B (cytb) gene markers. Our results strengthen the previously reported hypothesis that the Cynopterus cf. brachyotis in the Philippines is distinct from its Asian counterparts and should be, therefore, treated as a new species.

          Related collections

          Most cited references29

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

            We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Circos: an information aesthetic for comparative genomics.

              We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.
                Bookmark

                Author and article information

                Contributors
                Journal
                Biodivers Data J
                Biodivers Data J
                1
                urn:lsid:arphahub.com:pub:F9B2E808-C883-5F47-B276-6D62129E4FF4
                urn:lsid:zoobank.org:pub:245B00E9-BFE5-4B4F-B76E-15C30BA74C02
                Biodiversity Data Journal
                Pensoft Publishers
                1314-2836
                1314-2828
                2022
                14 February 2022
                : 10
                : e72768
                Affiliations
                [1 ] Philippine Genome Center Mindanao, University of the Philippines Mindanao, Davao City, Philippines Philippine Genome Center Mindanao, University of the Philippines Mindanao Davao City Philippines
                [2 ] Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Davao City, Philippines Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao Davao City Philippines
                [3 ] Wildlife-Human Interaction Studies, Ecological Research and Biodiversity Conservation Laboratory, University of the Philippines Mindanao, Davao City, Philippines Wildlife-Human Interaction Studies, Ecological Research and Biodiversity Conservation Laboratory, University of the Philippines Mindanao Davao City Philippines
                Author notes
                Corresponding author: Lyre Anni E. Murao ( lemurao@ 123456up.edu.ph ).

                Academic editor: Ricardo Moratelli

                Author information
                https://orcid.org/0000-0003-4981-8332
                https://orcid.org/0000-0003-4557-1109
                Article
                72768 17494
                10.3897/BDJ.10.e72768
                8860972
                d0a39fde-18ab-4932-8902-12452d95c37f
                Paul Lorenzo A. Gaite, Wilson F. Aala, Jr., Michael G. Bacus, Christian C. Labrador, April Mae M. Numeron, Lief Erikson D. Gamalo, Lyre Anni E. Murao

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 09 August 2021
                : 28 September 2021
                Page count
                Figures: 3, Tables: 3, References: 29
                Funding
                Department of Science and Technology (DOST) - Philippines, University of the Philippines Mindanao
                Categories
                Research Article

                ngs,mitogenome,bats,taxonomy,phylogenetic analysis
                ngs, mitogenome, bats, taxonomy, phylogenetic analysis

                Comments

                Comment on this article