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      The complete chloroplast genome sequence of Lycoris radiata

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      Author(s): , , , ,
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Lycoris radiata, chloroplast genome, phylogenetic analysis

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          Abstract

          Lycoris radiata, widely known as red spider lily. It belongs to the Amaryllidaceae family and has highly ornamental and medical value. Here, we assembled the complete chloroplast genome sequence by high-throughput sequencing and bioinformatics, which will provide more genomic information to the analysis of genetic diversity and phylogenetic relationship. The full length of chloroplast genome is 158,335 bp, composed of a large single-copy region (LSC) of 86,612 bp, a small single-copy region (SSC) of 18,261 bp, and a pair of inverted repeats (IR) of 26,731 bp. A total of 137 genes were annotated, including 87 protein-coding genes, 42 tRNA, and 8 rRNA genes. Phylogenetic tree analysis revealed that the close relationship between L. radiata and L. squamigera in the Amaryllidaceae family.

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          CPGAVAS2, an integrated plastome sequence annotator and analyzer

          Linchun Shi, Haimei Chen, Mei Jiang … (2019)
          Abstract We previously developed a web server CPGAVAS for annotation, visualization and GenBank submission of plastome sequences. Here, we upgrade the server into CPGAVAS2 to address the following challenges: (i) inaccurate annotation in the reference sequence likely causing the propagation of errors; (ii) difficulty in the annotation of small exons of genes petB, petD and rps16 and trans-splicing gene rps12; (iii) lack of annotation for other genome features and their visualization, such as repeat elements; and (iv) lack of modules for diversity analysis of plastomes. In particular, CPGAVAS2 provides two reference datasets for plastome annotation. The first dataset contains 43 plastomes whose annotation have been validated or corrected by RNA-seq data. The second one contains 2544 plastomes curated with sequence alignment. Two new algorithms are also implemented to correctly annotate small exons and trans-splicing genes. Tandem and dispersed repeats are identified, whose results are displayed on a circular map together with the annotated genes. DNA-seq and RNA-seq data can be uploaded for identification of single-nucleotide polymorphism sites and RNA-editing sites. The results of two case studies show that CPGAVAS2 annotates better than several other servers. CPGAVAS2 will likely become an indispensible tool for plastome research and can be accessed from http://www.herbalgenomics.org/cpgavas2.
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            MAFFT-DASH: integrated protein sequence and structural alignment

            John Rozewicki, Songling Li, Karlou Mar Amada … (2019)
            Abstract Here, we describe a web server that integrates structural alignments with the MAFFT multiple sequence alignment (MSA) tool. For this purpose, we have prepared a web-based Database of Aligned Structural Homologs (DASH), which provides structural alignments at the domain and chain levels for all proteins in the Protein Data Bank (PDB), and can be queried interactively or by a simple REST-like API. MAFFT-DASH integration can be invoked with a single flag on either the web (https://mafft.cbrc.jp/alignment/server/) or command-line versions of MAFFT. In our benchmarks using 878 cases from the BAliBase, HomFam, OXFam, Mattbench and SISYPHUS datasets, MAFFT-DASH showed 10–20% improvement over standard MAFFT for MSA problems with weak similarity, in terms of Sum-of-Pairs (SP), a measure of how well a program succeeds at aligning input sequences in comparison to a reference alignment. When MAFFT alignments were supplemented with homologous sequences, further improvement was observed. Potential applications of DASH beyond MSA enrichment include functional annotation through detection of remote homology and assembly of template libraries for homology modeling.
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              Phylogenetic Relationships and Possible Hybrid Origin of Lycoris Species (Amaryllidaceae) Revealed by ITS Sequences

              Shude Shi, Yingxiong Qiu, Enxiang Li … (2006)
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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): 10 September 2019
                Publication date (Electronic, collection): 2019
                Volume: 4
                Issue: 2
                Pages: 2886-2887
                Affiliations
                Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen) , Nanjing, China
                Author notes
                CONTACT Zhong Wang wangzhong19@ 123456163.com Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen) , Nanjing, 210014, China
                Author information
                https://orcid.org/0000-0002-7933-4075
                Article
                Publisher ID: 1660265
                DOI: 10.1080/23802359.2019.1660265
                PMC ID: 7706845
                PubMed ID: 33365775
                SO-VID: e509b435-17dc-41d8-8204-834bbd8b7b5f
                Copyright © © 2019 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: 1166
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: lycoris radiata,chloroplast genome,phylogenetic analysis
                Data availability:
                Keywords: lycoris radiata, chloroplast genome, phylogenetic analysis

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