Genome Sequences of Both Organelles of the Grapevine Rootstock Cultivar 'Börner'

Overview

Journal Microbiol Resour Announc

Publisher American Society for Microbiology

Specialty Microbiology

Date 2020 Apr 11

PMID 32273371

Citations 3

Authors

Bianca Frommer

Daniela Holtgrawe

Ludger Hausmann

Prisca Viehover

Bruno Huettel

Reinhard Topfer

Bernd Weisshaar

Affiliations

Soon will be listed here.

Abstract

Genomic long reads of the interspecific grapevine rootstock cultivar 'Börner' ( GM183 × Arnold) were used to assemble its chloroplast and mitochondrion genome sequences. We annotated 133 chloroplast and 172 mitochondrial genes, including the RNA editing sites. The organelle genomes in 'Börner' were maternally inherited from .

Citing Articles

Chromosome-level phased genome assembly of "Antonovka" identified candidate apple scab-resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1.

Svara A, Sun H, Fei Z, Khan A G3 (Bethesda). 2023; 14(1).

PMID: 37936323 PMC: 10755186. DOI: 10.1093/g3journal/jkad253.

Long-read assemblies reveal structural diversity in genomes of organelles - an example with .

Syme A, McLay T, Udovicic F, Cantrill D, Murphy D GigaByte. 2023; 2021:gigabyte36.

PMID: 36824345 PMC: 9650277. DOI: 10.46471/gigabyte.36.

Mitochondrial Genome of L. as a Source for Taxonomic Marker Development in the Fagales.

Mader M, Schroeder H, Schott T, Schoning-Stierand K, Leite Montalvao A, Liesebach H Plants (Basel). 2020; 9(10).

PMID: 32992588 PMC: 7650814. DOI: 10.3390/plants9101274.

References

Goremykin V, Salamini F, Velasco R, Viola R . Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Mol Biol Evol. 2008; 26(1):99-110. DOI: 10.1093/molbev/msn226. View

Wheeler T, Eddy S . nhmmer: DNA homology search with profile HMMs. Bioinformatics. 2013; 29(19):2487-9. PMC: 3777106. DOI: 10.1093/bioinformatics/btt403. View

Stadermann K, Weisshaar B, Holtgrawe D . SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome. BMC Bioinformatics. 2015; 16:295. PMC: 4573686. DOI: 10.1186/s12859-015-0726-6. View

Koren S, Walenz B, Berlin K, Miller J, Bergman N, Phillippy A . Canu: scalable and accurate long-read assembly via adaptive -mer weighting and repeat separation. Genome Res. 2017; 27(5):722-736. PMC: 5411767. DOI: 10.1101/gr.215087.116. View

Pucker B, Holtgrawe D, Stadermann K, Frey K, Huettel B, Reinhardt R . A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PLoS One. 2019; 14(5):e0216233. PMC: 6529160. DOI: 10.1371/journal.pone.0216233. View

Lohse M, Drechsel O, Bock R . OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet. 2007; 52(5-6):267-74. DOI: 10.1007/s00294-007-0161-y. View

Laslett D, Canback B . ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 2004; 32(1):11-6. PMC: 373265. DOI: 10.1093/nar/gkh152. View

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

Brenner W, Mader M, Muller N, Hoenicka H, Schroeder H, Zorn I . High Level of Conservation of Mitochondrial RNA Editing Sites Among Four Species. G3 (Bethesda). 2019; 9(3):709-717. PMC: 6404595. DOI: 10.1534/g3.118.200763. View

10.

Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones E, Fischer A, Bock R . GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45(W1):W6-W11. PMC: 5570176. DOI: 10.1093/nar/gkx391. View

11.

Wick R, Schultz M, Zobel J, Holt K . Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 2015; 31(20):3350-2. PMC: 4595904. DOI: 10.1093/bioinformatics/btv383. View

12.

Jansen R, Kaittanis C, Saski C, Lee S, Tomkins J, Alverson A . Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol. 2006; 6:32. PMC: 1479384. DOI: 10.1186/1471-2148-6-32. View

13.

Chan P, Lowe T . tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 2019; 1962:1-14. PMC: 6768409. DOI: 10.1007/978-1-4939-9173-0_1. View

14.

Lohse M, Drechsel O, Kahlau S, Bock R . OrganellarGenomeDRAW--a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 2013; 41(Web Server issue):W575-81. PMC: 3692101. DOI: 10.1093/nar/gkt289. View

15.

Ferrarini M, Moretto M, Ward J, Surbanovski N, Stevanovic V, Giongo L . An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome. BMC Genomics. 2013; 14:670. PMC: 3853357. DOI: 10.1186/1471-2164-14-670. View

16.

Lowe T, Eddy S . tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5):955-64. PMC: 146525. DOI: 10.1093/nar/25.5.955. View