Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae

Abstract

The species in the genus Cypripedium (Orchidaceae) are considered endangered, mainly distributed in the temperate regions of the Northern Hemisphere, with high ornamental and economic value. Despite previous extensive studies based on both morphology and molecular data, species and sections relationships within Cypripedium remain controversial. Here, we employed two newly generated Cypripedium chloroplast genomes with five other published genomes to elucidate their genomic characteristics. The two genomes were 162,773–207,142 bp in length and contained 128–130 genes, including 82–84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. We identified 2,192 simple sequence repeats, 786 large repeat sequences, and 7,929 variable loci. The increase of repeat sequences (simple sequence repeats and large repeat sequences) causes a significant amplification in the chloroplast genome size of Cypripedium. The expansion of the IR region led to the pseudogenization or loss of genes in the SSC region. In addition, we identified 12 highly polymorphic loci (Pi > 0.09) suitable for inferring the phylogeny of Cypripedium species. Based on data sets of whole chloroplast genomes (IRa excluded) and protein-coding sequences, a well-supported phylogenetic tree was reconstructed, strongly supporting the five subfamilies of Orchidaceae and the genus Cypripedium as monophyletic taxa. Our findings also supported that C. palangshanense belonged to sect. Palangshanensia rather than sect. Retinervia. This study also enriched the genomic resources of Cypripedium, which may help to promote the conservation efforts of these endangered species.

Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae

“…We observed that the GC content of the LSC region was also significantly higher than other Annonaceae species, which may influence the increase in GC content of the plastome. In addition, consistent with observations in other taxa ( Hishamuddin et al., 2020 ; Zhang et al., 2022 ), the GC content of the LSC and SSC regions of Annonaceae plastomes was significantly lower than that of the IR region, which is associated with a decrease in A/T bases in the four rRNA genes within the IR region.…”

“…Repetitive sequences also play a significant role in genome enlargement. Zhang et al. (2022) observed that the enlarged plastomes in Cypripedium have more long sequence repeats and SSRs, suggesting that the increase in repetitive sequences contributes to the obvious enlargement of the genome.…”

Complete chloroplast genome of the Jewel Orchid, Anoectochilus formosanus (Orchidaceae) and its relatives

“…Early studies have reported the abundance of repeated motifs in cp genomes, which are associated with various types of genome rearrangements, recombination, and large inversions, making them valuable for phylogenetic studies (Ho et al 2023;Lei et al 2016;Zhang et al, 2022). In our study, we observed variable numbers of repeats among the cp genomes, consistent with findings in a study on 13 Aroideae species where repeat numbers were found to be unrelated to genome size and phylogenetic position of the species (Henriquez et al 2022).…”

Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid GenusCypripediumL

“…Unlike other slipper orchids, Cypripedium species are traditionally recognized by their (usually) plicate leaves and unilocular ovaries with parietal placentation (Cox et al ., 1997; Cribb, 1997). Although the reliability of these distinctive characters has been questioned (Atwood, 1984), phylogenetic studies consistently support the monophyly of the genus (Fatihah et al ., 2011; J Li et al ., 2011; Guo et al ., 2012; H Liu et al ., 2021 a ; Szlachetko et al ., 2021; J-Y Zhang et al ., 2022). On the other hand, its infrageneric classification has constantly changed during the last two centuries.…”

“…After the publication of J Li et al . (2011), several studies included molecular phylogenies with Cypripedium species, four of which specifically focused on the relationships of the infrageneric taxa of Cypripedium (Fatihah et al ., 2011; Guo et al ., 2012; H Liu et al ., 2021 a ; Szlachetko et al ., 2021; J-Y Zhang et al ., 2022). These studies used a multilocus approach with up to eight Sanger-sequenced nuclear and chloroplast DNA markers in different combinations and with different phylogenetic reconstruction methodologies (i.e., Parsimony, Maximum Likelihood, and Bayesian Inference).…”