Characterisation of the Complete Chloroplast Genomes of Seven Hyacinthus orientalis L. Cultivars: Insights into Cultivar Phylogeny

Abstract

To improve agricultural performance and obtain potential economic benefits, an understanding of phylogenetic relationships of Hyacinthus cultivars is needed. This study aims to revisit the phylogenetic relationships of Hyacinthus cultivars using complete chloroplast genomes. Nine chloroplast genomes were de novo sequenced, assembled and annotated from seven cultivars of Hyacinthus orientalis and two Scilloideae species including Bellevalia paradoxa and Scilla siberica. The chloroplast genomes of Hyacinthus cultivars ranged from 154,458 bp to 154,641 bp, while those of Bellevalia paradoxa and Scilla siberica were 154,020 bp and 154,943 bp, respectively. Each chloroplast genome was annotated with 133 genes, including 88 protein-coding genes, 38 transfer RNA genes and 8 ribosomal RNA genes. Simple sequence repeats AAGC/CTTG and ACTAT/AGTAT were identified only in ‘Eros’, while AAATC/ATTTG were identified in all cultivars except ‘Eros’. Five haplotypes were identified based on 460 variable sites. Combined with six other previously published chloroplast genomes of Scilloideae, a sliding window analysis and a phylogenetic analysis were performed. Divergence hotspots ndhA and trnG-UGC were identified with a nucleotide diversity threshold at 0.04. The phylogenetic positions of Hyacinthus cultivars were different from the previous study using ISSR. Complete chloroplast genomes serve as new evidence in Hyacinthus cultivar phylogeny, contributing to cultivar identification, preservation and breeding.

Comparative chloroplast genomes and phylogenetic relationships of Aglaonema modestum and five variegated cultivars of Aglaonema

“…Similar phenomena were also found in Hyacinthus and Utricularia cultivars [36,37]. In Hyacinthus cultivars, 'Woodstock', 'Delft Blue' and 'Aiolos' displayed the same chloroplast genome size of 154,640 bp [36].…”

“…Similar phenomena were also found in Hyacinthus and Utricularia cultivars [36,37]. In Hyacinthus cultivars, 'Woodstock', 'Delft Blue' and 'Aiolos' displayed the same chloroplast genome size of 154,640 bp [36]. In the case of two Utricularia amethystina cultivars, Purple and Yellow, only a 95 bp difference was found [37].…”

“…Chloroplast genomes are rich in SSRs, long repeats, highly divergent regions, SNPs and indels [39][40][41]. They have been extensively used to identify species and cultivars [36] and for phylogenetic analyses [37,41]. In the present study, SSR detection results were the same as most other Araceae plants; for example, most SSRs were mononucleotide repeats and usually comprised short repeats of A/T [31,41,42].…”

“…In the case of two Utricularia amethystina cultivars, Purple and Yellow, only a 95 bp difference was found [37]. These chloroplast genome sizes were not changed substantially, possibly because the chloroplast genomes did not undergo recombination among the tested cultivars [36].…”