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      The complete chloroplast genome of Rhus punjabensis var. sinica

      research-article
      a , a , a , a , b
      Mitochondrial DNA. Part B, Resources
      Taylor & Francis
      Rhus punjabensis var. sinica, chloroplast, genome sequence

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          Abstract

          Rhus punjabensis var. sinica belongs to the family Anacardiaceae in the order Sapindales. In this study, we first reported the complete chloroplast genome sequence of R. punjabensis var. sinica. The cp genome was sequenced on Illumina Hiseq 2000 platform. The sequence was found to be 159,617 bp in length with 37.9% GC contents, including a large single-copy region of 87,694 bp, a small single-copy region of 18,971 bp, and a pair of inverted repeats of 26,476 bp. The chloroplast genome of R. punjabensis var. sinica contains 133 genes, including 86 protein-coding genes, 8 rRNA genes, and 2 pseudogenes identified by CPGAVAS2 and BLAST search, and 37 tRNA genes annotated by tRNAscan-SE. Maximum-likelihood (ML) phylogenetic analysis showed that R. punjabensis var. sinica was sister to Rhus potaninii.

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          SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

          Background There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. Findings To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. Conclusions Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.
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            CPGAVAS2, an integrated plastome sequence annotator and analyzer

            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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              The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

              Transfer RNAs (tRNAs) and small nucleolar RNAs (snoRNAs) are two of the largest classes of non-protein-coding RNAs. Conventional gene finders that detect protein-coding genes do not find tRNA and snoRNA genes because they lack the codon structure and statistical signatures of protein-coding genes. Previously, we developed tRNAscan-SE, snoscan and snoGPS for the detection of tRNAs, methylation-guide snoRNAs and pseudouridylation-guide snoRNAs, respectively. tRNAscan-SE is routinely applied to completed genomes, resulting in the identification of thousands of tRNA genes. Snoscan has successfully detected methylation-guide snoRNAs in a variety of eukaryotes and archaea, and snoGPS has identified novel pseudouridylation-guide snoRNAs in yeast and mammals. Although these programs have been quite successful at RNA gene detection, their use has been limited by the need to install and configure the software packages on UNIX workstations. Here, we describe online implementations of these RNA detection tools that make these programs accessible to a wider range of research biologists. The tRNAscan-SE, snoscan and snoGPS servers are available at , and , respectively.
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                Author and article information

                Journal
                Mitochondrial DNA B Resour
                Mitochondrial DNA B Resour
                Mitochondrial DNA. Part B, Resources
                Taylor & Francis
                2380-2359
                24 January 2022
                2022
                24 January 2022
                : 7
                : 1
                : 243-244
                Affiliations
                [a ]Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College , Beijing, PR China
                [b ]Engineering Research Center of Chinese Medicine Resource, Ministry of Education , Beijing, PR China
                Author notes
                Yulin Lin linyulin@ 123456hotmail.com Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College , Beijing, PR China
                Article
                1925983
                10.1080/23802359.2021.1925983
                8788377
                35087942
                d8e5f85c-f5b1-4441-bd2e-c74cbf2bb30d
                © 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                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.

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                Page count
                Figures: 1, Tables: 0, Pages: 2, Words: 1177
                Categories
                Research Article
                Mitogenome Announcement

                rhus punjabensis var. sinica,chloroplast,genome sequence

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