Nicotiana glauca whole-genome investigation for cT-DNA study

BMC Research Notes

Volumn 11, Issue 1, 2018, Pages

  Khafizova, Galina ^a   Dobrynin, Pavel ^a,b   Polev, Dmitrii ^a   Matveeva, Tatiana ^a  

^a ST PETERSBURG STATE UNIVERSITY   (Russian Federation)

^b SMITHSONIAN CONSERVATION BIOLOGY INSTITUTE   (United States)

Author keywords

Cellular T DNA; Genome assembly; Nicotiana glauca; Whole genome sequencing

Indexed keywords

BACTERIAL DNA; T-DNA;

DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; HORIZONTAL GENE TRANSFER; PLANT GENOME; PROCEDURES; TOBACCO;

DNA, BACTERIAL; GENE TRANSFER, HORIZONTAL; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA; TOBACCO;

EID: 85040446726     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/s13104-018-3127-x     Document Type: Article

References (13)

1. Long N, Ren X, Xiang Z, Wan W, Dong Y. Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species. J Biol Res (Thessalon). 2016;23:6.
2. White FF, Garfinkel DJ, Huffman GA, Gordon MP, Nester EW. Sequence homologous to Agrobacterium rhizogenes TDNA in the genomes of uninfected plants. Nature. 1983;301:348.
3. Suzuki K, Ichiro Y, Nobukazu T. Tobacco plants were transformed by Agrobacterium rhizogenes infection during their evolution. Plant J. 2002;32:5.
4. Chen K, Dorlhac de Borne F, Szegedi E, Otten L. Deep sequencing of the ancestral tobacco species Nicotiana tomentosiformis reveals multiple T-DNA inserts and a complex evolutionary history of natural transformation in the genus Nicotiana. Plant J. 2014;80:4.
5. Saitoh F, Kawasima N. The alkaloid contents of sixty Nicotiana species. Phytochemistry. 1985;24:477.
6. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 1987;19:11.
7. FastQC program. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 12 Jan 2017.
8. Krueger F. Trim Galore!: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. 2015. http://www.bioinformatics.babraham.ac.uk/projects/trim-galore/. Accessed 12 Jan 2017.
9. Leggett RM, Clavijo BJ, Clissold L, Clark MD, Caccamo M. NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries. Bioinformatics. 2013;30:4.
10. Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marçais G, Yorke JA, Dvořák J, Salzberg SL. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm. Genome Res. 2017;27:5.
11. Sol Genomic Network. https://solgenomics.net. Accessed 25 Feb 2017.
12. Tarailo-Graovac M, Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinform. 2009;25:4-10.
13. Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011;21:3.