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The complete chloroplast genome sequence of Phalaenopsis wilsonii Rolfe, a vulnerable wild moth orchid species (Orchidaceae).

ABSTRACT: Phalaenopsis wilsonii Rolfe is a vulnerable wild moth orchid species with important horticultural value. The complete chloroplast genome sequence of P. wilsonii was generated by de novo assembly using whole genome next-generation sequencing to provide genomic data for further conservation genetics, phylogeny and molecular breeding in Phalaenopsis. The complete plastome of P. wilsonii is 145,096 bp in length, containing two inverted repeats (IR) regions (24,787 bp), a large single-copy (LSC) region (84,688 bp), and a small single-copy (SSC) region (10,834 bp). The chloroplast genome encoded 119 unique genes, including 73 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the whole genome is 36.9%. Phylogenetic analysis indicated P. wilsonii was closely related to P. lowii.

SUBMITTER: Fan ZF

PROVIDER: S-EPMC8439240 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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The complete chloroplast genome sequence of Phalaenopsis wilsonii Rolfe, a vulnerable wild moth orchid species (Orchidaceae).

Fan Zhi-Feng ZF Yu Da-Yong DY Ma Chang-Le CL

Mitochondrial DNA. Part B, Resources 20210913 10

Phalaenopsis wilsonii Rolfe is a vulnerable wild moth orchid species with important horticultural value. The complete chloroplast genome sequence of P. wilsonii was generated by de novo assembly using whole genome next-generation sequencing to provide genomic data for further conservation genetics, phylogeny and molecular breeding in Phalaenopsis. The complete plastome of P. wilsonii is 145,096 bp in length, containing two inverted repeats (IR) regions (24,787 bp), a ...[more]

PMID: 34532582

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Project description:BackgroundThe moth orchid (Phalaenopsis species) is an ornamental crop that is highly commercialized worldwide. Over 30,000 cultivars of moth orchids have been registered at the Royal Horticultural Society (RHS). These cultivars were obtained by artificial pollination of interspecific hybridization. Therefore, the identification of different cultivars is highly important in the worldwide market.Methods/resultsWe used Illumina sequencing technology to analyze an important species for breeding, Phalaenopsis aphrodite subsp. formosana and develop the expressed sequence tag (EST)-simple sequence repeat (SSR) markers. After de novo assembly, the obtained sequence covered 29.1 Mb, approximately 2.2% of the P. aphrodite subsp. formosana genome (1,300 Mb), and a total of 1,439 EST-SSR loci were detected. SSR occurs in the exon region, including the 5' untranslated region (UTR), coding region (CDS), and 3'UTR, on average every 20.22 kb. The di- and tri-nucleotide motifs (51.49% and 35.23%, respectively) were the two most frequent motifs in the P. aphrodite subsp. formosana. To validate the developed EST-SSR loci and to evaluate the transferability to the genus Phalaenopsis, thirty tri-nucleotide motifs of the EST-SSR loci were randomly selected to design EST-SSR primers and to evaluate the polymorphism and transferability across 22 native Phalaenopsis species that are usually used as parents for moth orchid breeding. Of the 30 EST-SSR loci, ten polymorphic and transferable SSR loci across the 22 native taxa can be obtained. The validated EST-SSR markers were further proven to discriminate 12 closely related Phalaenopsis cultivars. The results show that it is not difficult to obtain universal SSR markers by transcriptome deep sequencing in Phalaenopsis species.ConclusionsThis study supported that transcriptome analysis based on deep sequencing is a powerful tool to develop SSR loci in non-model species. A large number of EST-SSR loci can be isolated, and about 33.33% EST-SSR loci are universal markers across the Phalaenopsis breeding germplasm after preliminary validation. The potential universal EST-SSR markers are highly valuable for identifying all of Phalaenopsis cultivars.

Project description:BackgroundThe taxonomy and infrageneric delimitation of Phalaenopsis Blume has been significantly disputed due to some overlapping morphological features between species related, which needed further evidence for clarification. The structural characterization of complete chloroplast genomes of P. storbatiana and P. wilsonii were analyzed and compared with those of related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny.ResultsIt was shown that chloroplast genomes of Phalaenopsis storbatiana and P. wilsonii had a typical quadripartite structure with conserved genome arrangements and moderate divergence. The chloroplast genomes of P. storbatiana and P. wilsonii were 145,885 bp and 145,445 bp in length, respectively, and shared a similar GC content of 36.8%. Gene annotations of two species revealed 109 single-copy genes consistently. In addition, 20 genes duplicated in the inverted regions, 16 genes each possessed one or more introns, and five ndh (NA (D)H dehydrogenase) genes were observed in both. Comparative analysis of the total cp genomes of P. storbatiana and P. wilsonii with those of other six related Phalaenopsis species confirmed the stable sequence identity for coding and non-coding regions and higher sequence variation in SC regions than IR regions. Most of their protein-coding genes had a high degree of codon preference. Moreover, 45 genes were discovered with significantly positive selection. However, different amplifications in IR regions were observed in these eight species. Phylogenetic analysis based on CDS from 60 species representing main clades in Orchidaceae indicated that Phalaenopsis species including P. stobartiana and P. wilsonii formed a monophyletic clade with high bootstrap nested in tribe Vandeae of Epidendroideae, which was consistent with those from previous studies.ConclusionsThe results could provide insight into understanding the plastome evolution and phylogenetic relationships of Phalaenopsis.

Dataset Information

The complete chloroplast genome sequence of Phalaenopsis wilsonii Rolfe, a vulnerable wild moth orchid species (Orchidaceae).

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The complete chloroplast genome sequence of <i>Phalaenopsis wilsonii</i> Rolfe, a vulnerable wild moth orchid species (Orchidaceae).

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