Sequence Analysis of the Genome of Carnation (Dianthus caryophyllus L.)

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 genomic sequences is available at .

Identification and Characterization of Plasma Membrane Intrinsic Protein (PIP) Aquaporin Genes in Petals of Opening Carnation Flowers

“…The amino acid sequences of XIPs from tobacco (XIP1;1α and XIP1;1β; Bienert et al, 2011), soybeans (GmXIP1;1 and GmXIP1;2; Zhang et al, 2013), and tomatoes (SlXIP1;1-SlXIP1;6; Reuscher et al, 2013) were also retrieved from the Ensembl Genomes. These sequences were used as queries for a BLAST (Altschul et al, 1997) search to identify open reading frames (ORFs) encoding AQP in the carnation genome sequence database (Carnation DB; Yagi et al, 2014; http://carnation.kazusa.or.jp/index.html). ORFs with an E-value less than 1e-30 were retrieved as candidates for carnation AQPs.…”

“…The carnation genome sequence was determined in the cultivar 'Francesco' (Yagi et al, 2014). We first characterized AQP genes encoded in the 'Francesco' genome by an in silico search.…”

“…The carnation genome sequence was recently determined in the cultivar 'Francesco' (Yagi et al, 2014), which enabled us to perform comprehensive analysis of the carnation AQP family. In the present study, we aimed to characterize AQP genes expressed in carnation flowers in silico using the carnation genome sequence in order to better understand the flower opening process at the molecular level.…”

Gibberellin is not Associated with the Enhancing Effect of 2,4-Pyridinedicarboxylic Acid on Flower Opening of ‘Light Pink Barbara’ Carnation

“…arabidopsis.org). Carnation open reading frames (ORFs) homologous to the Arabidopsis DELLAs were searched for by BLAST (Altschul et al, 1997) in the carnation genome sequence database (Carnation DB; Yagi et al, 2014; http://carnation.kazusa.or.jp/index. html).…”

Transcriptional regulators of flavonoid biosynthesis and their application to flower color modification in Japanese gentians

“…Recent nextgeneration sequencing technologies have been applied to several flower species including petunia (Zenoni et al 2011), rose (Kim et al 2012), carnation (Tanase et al 2012), and orchid (Chou et al 2013), yielding data that have provided a foundation for novel research. It is noteworthy that the whole genome sequence of carnation, one of the major cut-flowers sold worldwide, has recently been reported (Yagi et al 2013); the data will be useful for the discovery of novel genes and the elucidation of the complex metabolic networks of flavonoid biosynthesis in flowers. We also aim to deepen our understanding of flavonoid biosynthesis in Japanese gentian and to promote a Japanese gentian breeding program in the near future.…”