Nicotiana glauca whole-genome investigation for cT-DNA study

被引：4
|
作者：
Khafizova G. [1 ]
Dobrynin P. [3 ,4 ]
Polev D. [2 ]
Matveeva T. [1 ]
机构：
[1] Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb. 7/9, Saint Petersburg
[2] Research Park, Saint Petersburg State University, 17 Botanicheskaya St, Peterhof, Saint Petersburg
[3] Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Ave, Saint Petersburg
[4] National Zoological Park, Smithsonian Conservation Biology Institute, 3001 Connecticut Ave NW, Washington, 20008, DC
来源：
BMC Research Notes | / 11卷 / 1期
基金：
俄罗斯科学基金会;
关键词：
Cellular T-DNA; Genome assembly; Nicotiana glauca; Whole genome sequencing;
D O I：
10.1186/s13104-018-3127-x
中图分类号：
学科分类号：
摘要：
Objective: Nicotiana glauca (tree tobacco) is a naturally transgenic plant, containing sequences acquired from Agrobacterium rhizogenes by horizontal gene transfer. Besides, N. glauca contains a wide profile of alkaloids of medical interest. Data description: We report a high-depth sequencing and de novo assembly of N. glauca full genome and analysis of genome elements with bacterial origin. The draft genome assembly is 3.2 Gb, with N50 size of 31.1 kbp. Comparative analysis confirmed the presence of single, previously described gT insertion. No evidence was acquired to support idea of multiple T-DNA insertions in the N. glauca genome. Our data is the first comprehensive de novo assembly of tree tobacco and provide valuable information for researches in pharmacological and in phylogenetic fields. © 2018 The Author(s).
引用
收藏
相关论文
共 50 条
  • [1] Whole-genome DNA sequencing
    Myers, G
    COMPUTING IN SCIENCE & ENGINEERING, 1999, 1 (03) : 33 - 43
  • [2] Intersection of DNA Privacy and Whole-Genome Sequencing
    Hong, Changjin
    Wang, Jason
    Xing, Chao
    Hwang, Tae Hyun
    Park, Jason Y.
    CLINICAL CHEMISTRY, 2015, 61 (07) : 900 - 902
  • [3] Spectral and Electrochemical Investigation of Intercalations of Adrenaline and CT-DNA
    郑赛晶
    林祥钦
    ChineseJournalofChemistry, 2003, (07) : 767 - 771
  • [4] Spectral and electrochemical investigation of intercalations of adrenaline and CT-DNA
    Zheng, SJ
    Lin, XQ
    CHINESE JOURNAL OF CHEMISTRY, 2003, 21 (07) : 767 - 771
  • [5] A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak
    Reuter, Sandra
    Harrison, Timothy G.
    Koeser, Claudio U.
    Ellington, Matthew J.
    Smith, Geoffrey P.
    Parkhill, Julian
    Peacock, Sharon J.
    Bentley, Stephen D.
    Toeroek, M. Estee
    BMJ OPEN, 2013, 3 (01):
  • [6] An investigation of whole-genome genotyping and whole-genome sequencing in metabolic syndrome, a circadian rhythm-related disease
    Tsai, S. Y.
    Chou, Y. T.
    Tsai, M. H.
    BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY, 2018, 124 : 10 - 10
  • [7] Applications of DNA tiling arrays for whole-genome analysis
    Mockler, TC
    Ecker, JR
    GENOMICS, 2005, 85 (01) : 1 - 15
  • [8] The Emerging Role of Whole-Genome Investigation to Identify Undetected Nephropathies: The HIDDEN Study
    Mallett, Andrew J.
    Mallawaarachchi, Amali
    Stark, Zornitza
    Simons, Cas
    Quinlan, Catherine
    Patel, Chirag
    JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY, 2021, 32 (10): : 415 - 415
  • [9] Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data
    Birol, Inanc
    Raymond, Anthony
    Jackman, Shaun D.
    Pleasance, Stephen
    Coope, Robin
    Taylor, Greg A.
    Saint Yuen, Macaire Man
    Keeling, Christopher I.
    Brand, Dana
    Vandervalk, Benjamin P.
    Kirk, Heather
    Pandoh, Pawan
    Moore, Richard A.
    Zhao, Yongjun
    Mungall, Andrew J.
    Jaquish, Barry
    Yanchuk, Alvin
    Ritland, Carol
    Boyle, Brian
    Bousquet, Jean
    Ritland, Kermit
    MacKay, John
    Bohlmann, Joerg
    Jones, Steven J. M.
    BIOINFORMATICS, 2013, 29 (12) : 1492 - 1497
  • [10] Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing
    Thurlow, Charles M.
    Joseph, Sandeep J.
    Ganova-Raeva, Lilia
    Katz, Samantha S.
    Pereira, Lara
    Chen, Cheng
    Debra, Alyssa
    Vilfort, Kendra
    Workowski, Kimberly
    Cohen, Stephanie E.
    Reno, Hilary
    Sun, Yongcheng
    Burroughs, Mark
    Sheth, Mili
    Chi, Kai-Hua
    Danavall, Damien
    Philip, Susan S.
    Cao, Weiping
    Kersh, Ellen N.
    Pillay, Allan
    MSPHERE, 2022, 7 (03)
12345