Sequence analysis of the genome of carnation (Dianthus caryophyllus L.)

DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes
Masafumi YagiSatoshi Tabata

Abstract

The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. 'Francesco' was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568,887,315 bp, consisting of 45,088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16,644 bp and 60,737 bp, respectively, and the longest scaffold was 1,287,144 bp. The average GC content of the contig sequences was 36%. A total of 1050, 13, 92 and 143 genes for tRNAs, rRNAs, snoRNA and miRNA, respectively, were identified in the assembled genomic sequences. For protein-encoding genes, 43 266 complete and partial gene structures excluding those in transposable elements were deduced. Gene coverage was ∼ 98%, as deduced from the coverage of the core eukaryotic genes. Intensive characterization of the assigned carnation genes and comparison with those of other plant species revealed characteristic features of the carnation genome. The results of this study will serve as a valuable resource for fundamental and applied research of carnation, especially for breeding new carnation varieties. Further information on the genom...Continue Reading

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Citations

Mar 16, 2016·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hidenori TanakaShusei Sato
Oct 16, 2015·BMC Genomics·Carlos Villacorta-MartínJosé Manuel Pérez-Pérez
May 15, 2015·The New Phytologist·Samuel F BrockingtonStephen A Smith
Mar 31, 2015·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Huaan YangShancen Zhao
Nov 25, 2014·Plant & Cell Physiology·Satoshi NatsumeEiichiro Ono
Oct 30, 2016·Journal of Experimental Botany·Kenichi ShibuyaKazuo Ichimura
Jul 17, 2019·Antimicrobial Agents and Chemotherapy·Hassan TarabaiMonika Dolejska
Nov 9, 2018·Applied Microbiology and Biotechnology·Hien T T PhamSander S van Leeuwen
Jan 29, 2019·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hideki HirakawaSachiko N Isobe
Aug 1, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Weilong KongXiaopeng Fu
May 15, 2018·Frontiers in Plant Science·Antonio CanoJosé Manuel Pérez-Pérez
Apr 2, 2021·Horticulture Research·Tangchun ZhengQixiang Zhang
Aug 8, 2021·International Journal of Molecular Sciences·Manjulatha MekapoguSeonghoe Jang
Sep 30, 2021·The Plant Journal : for Cell and Molecular Biology·Han XuFan Zhang

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Datasets Mentioned

BETA
DRX012627
DRX012629
DF340864-DF357213

Methods Mentioned

BETA
transgenic
RNA-seq

Software Mentioned

BLAST
CROSS
PASA
map2slim
TransposonPSI
CD
Augustus
HIT
BLASTX
Piler

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