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Clc sequence viewer ncbi12/31/2022 ![]() ![]() This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: All sequence files are available from the NCBI-Genbank database (accession numbers MN597437, MN597436, MN597435, MN597434, MN597433, MN597432).įunding: ECS would like to thank Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for grant Bolsa de Produtividade em Pesquisa CNPq-Nível 2 (proc. Received: NovemAccepted: JanuPublished: January 28, 2020Ĭopyright: © 2020 Smidt et al. PLoS ONE 15(1):Įditor: Zhong-Jian Liu, The National Orchid Conservation Center of China The Orchid Conservation & Research Center of Shenzhen, CHINA (2020) Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae). The use of whole plastomes or exclusive no-gap matrices also positioned with high support the holomycotrophic Rhizanthella among Orchidoideae plastomes in model-based analyses, showing the utility of plastomes for phylogenetic placement of this unusual genus.Ĭitation: Smidt EdC, Páez MZ, Vieira LdN, Viruel J, de Baura VA, Balsanelli E, et al. These regions have much more variation than all those used previously in phylogenetics of the group and offer useful plastid markers for phylogenetic, barcoding and population genetic studies. Three of them ( rps16-trnQ, trnT-trnL, rpl32-trnL) seem to be universal hotspots in the family, and the other five ( trnG-trnR, trnR-atpA, trnP-psaJ, rpl32-infA, and rps15-ycf1) are described for the first time as orchid molecular hotspots. Eight mutation hotspots were identified based on nucleotide diversity, sequence variability and parsimony-informative sites. For the two genera of epiphytic clade in Spiranthinae, almost whole sets of the ndh-gene family were missing. Variation detected in the LSC/IR and SSC/IR junctions is explained by the loss of ndhF and ycf1 length variation. These structure of these six plastomes is relatively conserved, exhibiting lengths ranging between 142,599 to 154,562 bp with 36.7% GC on average and exhibiting typical quadripartite arrangement (LSC, SSC and two IRs). PMID: 33239395.This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification of the most variable regions (hotspots) in this group of orchids. Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV). Rangwala SH, Kuznetsov A, Ananiev V, Asztalos A, Borodin E, Evgeniev V, Joukov V, Lotov V, Pannu R, Rudnev D, Shkeda A, Weitz EM, Schneider VA. NCBI Sequence Viewer uses third party tools and libraries. The link will open with three panels (an overview graphical panel a zoomed in graphical panel and a sequence panel) additionally, a marker is set at position 800. This link provides an example of how a viral genome can be shown. Viral genome: AC_000020, sequence viewport and marker This link will open with two views by default: a graphical panel showing the feature annotation on the sequence and a sequence panel providing the bases of the sequence itself. This link shows a sample mRNA sequence from the Mammalian Genome Collection. Two panels are shown by default: an overview panel showing the density of annotated genes along with a select number of genes for reference and a zoomed in graphical view showing individual features on the record. This particular record shows the beta globin locus on chromosome 11. This link shows a reference genomic region, that is, a genomic region that has undergone substantial curation by staff at NCBI. Human reference genomic region: NG_000007 There are two panels shown by default: an overview panel showing the density of annotated genes along with a select number of genes for reference and a zoomed in graphical view showing a region of the chromosome itself. This link provides a look at human chromosome 1. Embedding the NCBI Sequence View in Web Content ![]()
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