Whole-genome sequencing and analysis of two azaleas, Rhododendron ripense and Rhododendron kiyosumense

Abstract

To enhance the genomics and genetics of azalea, the whole-genome sequences of two species of Rhododendron were determined and analyzed in this study: Rhododendron ripense, the cytoplasmic donor and ancestral species of large-flowered and evergreen azalea cultivars, respectively; and Rhododendron kiyosumense, a native of Chiba prefecture (Japan) seldomly bred and cultivated. A chromosome-level genome sequence assembly of R. ripense was constructed by single-molecule real-time (SMRT) sequencing and genetic mapping, while the genome sequence of R. kiyosumense was assembled using the single-tube long fragment read (stLFR) sequencing technology. The R. ripense genome assembly contained 319 contigs (506.7 Mb; N50 length: 2.5 Mb) and was assigned to the genetic map to establish 13 pseudomolecule sequences. On the other hand, the genome of R. kiyosumense was assembled into 32,308 contigs (601.9 Mb; N50 length: 245.7 kb). A total of 34,606 genes were predicted in the R. ripense genome, while 35,785 flower and 48,041 leaf transcript isoforms were identified in R. kiyosumense through Iso-Seq analysis. Overall, the genome sequence information generated in this study enhances our understanding of genome evolution in the Ericales and reveals the phylogenetic relationship of closely-related species. This information will also facilitate the development of phenotypically attractive azalea cultivars.

Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum

“…The phylogenetic trees in this study showed that R. ripense was a sister to R. × pulchrum (Figures 2, 6). Previous studies indicated R. × pulchrum cultivar owned cpDNA of R. ripense (Shirasawa et al, 2021), and R. ripense is considered as one of the putative ancestral species of R. × pulchrum (Scariot et al, 2007;Meanchaipiboon et al, 2021), These findings are consistent with our study. The R. × pulchrum mitochondrial genome was used as a reference; a whole-genome collinear alignment compared among five species from the Ericaceae family found a high degree of homology with R. × pulchrum in the gene regions compared with interval regions.…”

“…In addition, the chloroplast (cpDNA) origin of "Omurasaki" and Hirado azalea cultivar groups were reported in Kobayashi et al (2021). "Omurasaki" and the most of Hirado azalea cultivar owned cpDNA of R. ripense, Japanese wild azalea (Shirasawa et al, 2021). So far, there has been no report on the mitochondrial genome of R. × pulchrum.…”