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      Complete chloroplast genome sequence and annotation of Actinodaphne lecomtei C.K.Allen, 1938 (Lauraceae)

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          Abstract

          Actinodaphne lecomtei C.K.Allen, 1938 is an evergreen tree of the Lauraceae family and grows at the mountainous areas of southwestern China. In this study, we presented the first complete chloroplast genome sequence of A. lecomtei. We analyzed the chloroplast genome structure of A. lecomtei and performed a phylogenetic analysis. The complete chloroplast genome of A. lecomtei was 152,863 bp in length which contains a large single-copy (LSC) region of 93,763 bp, a small single-copy (SSC) region of 18,814 bp, and two inverted repeat (IR) regions of 20,143 bp. The analysis identified 128 genes, comprised of 84 protein-coding genes, 36 tRNAs, and eight rRNAs. The GC content of A. lecomtei complete chloroplast genome was 39.1%. The phylogenetic analysis result demonstrated that A. lecomtei was closely related to A. obovate.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          Kazutaka Katoh, Daron Standley (2013)
          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

            Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)
            The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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              GeSeq – versatile and accurate annotation of organelle genomes

              Michael Tillich, Pascal Lehwark, Tommaso Pellizzer … (2017)
              Abstract We have developed the web application GeSeq (https://chlorobox.mpimp-golm.mpg.de/geseq.html) for the rapid and accurate annotation of organellar genome sequences, in particular chloroplast genomes. In contrast to existing tools, GeSeq combines batch processing with a fully customizable reference sequence selection of organellar genome records from NCBI and/or references uploaded by the user. For the annotation of chloroplast genomes, the application additionally provides an integrated database of manually curated reference sequences. GeSeq identifies genes or other feature-encoding regions by BLAT-based homology searches and additionally, by profile HMM searches for protein and rRNA coding genes and two de novo predictors for tRNA genes. These unique features enable the user to conveniently compare the annotations of different state-of-the-art methods, thus supporting high-quality annotations. The main output of GeSeq is a GenBank file that usually requires only little curation and is instantly visualized by OGDRAW. GeSeq also offers a variety of optional additional outputs that facilitate downstream analyzes, for example comparative genomic or phylogenetic studies.
              Article 0 comments Cited 1261 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mitochondrial DNA B Resour
                Journal ID (iso-abbrev): Mitochondrial DNA B Resour
                Title: Mitochondrial DNA. Part B, Resources
                Publisher: Taylor & Francis
                ISSN (Electronic): 2380-2359
                Publication date (Electronic, pub): 28 March 2022
                Publication date (Electronic, collection): 2022
                Publication date PMC-release: 28 March 2022
                Volume: 7
                Issue: 3
                Pages: 548-549
                Affiliations
                [a ]College of Marine Science and Biological Engineering, Qingdao University of Science and Technology , Qingdao, China
                [b ]College of Art, Qingdao University of Science and Technology , Qingdao, China
                [c ]Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences , Kunming, China
                Author notes
                [*]

                Both authors contributed equally to this work.

                CONTACT Chao Shi chsh1111@ 123456aliyun.com College of Marine Science and Biological Engineering, Qingdao University of Science and Technology , Qingdao, China
                Article
                Publisher ID: 2054382
                DOI: 10.1080/23802359.2022.2054382
                PMC ID: 8967194
                SO-VID: 2f0cdf5a-e12f-49b8-864f-d33626b16def
                Copyright © © 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Page count
                Figures: 1, Tables: 0, Pages: 2, Words: 1453
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: actinodaphne lecomtei,lauraceae,chloroplast genome,phylogenetic relationships
                Data availability:
                Keywords: actinodaphne lecomtei, lauraceae, chloroplast genome, phylogenetic relationships

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