Corrigendum: The genome sequence of the orchid Phalaenopsis equestris (original) (raw)
Related papers
The genome sequence of the orchid Phalaenopsis equestris
Nature genetics, 2015
Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute ...
Orchid Genomics and Developmental Biology, Volume II
Frontiers Research Topics
Editorial on the Research Topic Orchid genomics and developmental biology, volume II Orchidaceae constitute the second-largest flowering plant family worldwide with over 27,000 species found on all continents except Antarctica. Orchids are frequently celebrated for their exceptional morphological and ecological diversity and are highly valued in the horticultural trade. Orchids exhibit distinct floral and physiological features, such as fused male and female flower parts forming the gynostemium, a floral lip often adorned with calli, glands, spurs, and distinctive color patterns, and the crassulacean acid metabolism (CAM), a water-saving physiological pathway which has evolved multiple times independently within the family. Orchids possess highly specialized ecological relationships, such as often speciesspecific plant-pollinator interactions including food-and sexual deception and dependence on mycorrhizal fungi for germination of their minute seed. The broad range of traits renders orchids prime non-model plants for elucidating the genomic underpinnings and regulatory networks responsible for the generation of this exceptional diversity. To keep exploring such an interesting research field, this volume continues our previous Research Topic entitled "Orchid Genomics and Developmental Biology" (Chen and Nargar) to showcase recent findings and providing novel insights into regulatory mechanisms underpinning orchid biologies, such as reproductive development, responses to biotic and abiotic stresses, visual mimicry of orchid flowers, and bioactive metabolic pathways.
Advanced Applications of Next-Generation Sequencing Technologies to Orchid Biology
Current Issues in Molecular Biology, 2018
Next-generation sequencing (NGS) technologies are revolutionizing biology by permitting transcriptome sequencing, whole-genome sequencing and resequencing, and genome-wide single nucleotide polymorphism profiling. Orchid research has benefited from this breakthrough, and a few orchid genomes are now available; new biological questions can be approached and new breeding strategies can be designed. The first part of this review describes the unique features of orchid biology. The second part provides an overview of the current NGS platforms, many of which are already used in plant laboratories. The third part summarizes the state of orchid transcriptome and genome sequencing and illustrates current achievements. The genetic sequences currently obtained will not only provide a broad scope for the study of orchid biology, but also serves as a starting point for uncovering the mystery of orchid evolution.
Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy
Nature Plants
To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterot...
Nusantara bioscience, 2023
Jewel orchid is the common name of several orchid species which can be alike in morphological characteristics but variable in medicinal properties. As these plants are utilized to treat several diseases, their natural existence in the wild habitat is rapidly diminished. Therefore, a better understanding of the genetic information of this plant for better genetic conservation and development of these plants is necessary. In this study, a total of 18 published chloroplast genomes of 18 jewel orchid species determined by the next-generation sequencing method were retrieved from NCBI GenBank and targeted for genomic characterization and phylogenetic analyses. Different bioinformatics tools were utilized to characterize these genomes' genomic structure, repetitive sequences, interspecific variation, divergence, and phylogenetic relationships. The obtained data revealed that the chloroplast genomes of different jewel orchid species varied in length between 151,414 (Anoectochilus formosanus MN880624.1) and 154,375 (Goodyera biflora OM314910.1). Each species contains 34-87 SSR loci which could be useful as molecular markers for further genetic diversity study of this plant. Structural variations in the expansion and contraction of inverted repeat regions were also considered. Phylogenetic analysis identified a close relationship among species belonging to the Goodyera genus, and this genus is distinctive from other genera such as Anoectochilus, Cystorchis, Dossinia, Ludisia, and Macodes. The obtained results show a high potential of deeper characterizing the chloroplast genome of jewel orchids for species classification, identification, molecular breeding, and evolutionary exploration of these important herbal plants.
Mitochondrial DNA, 2015
A partial genome dataset was sequenced for the orchid Cattleya crispata using both Illumina and 454 technologies. The chloroplast genome was assembled using iterative runs of MIRA software that yielded a circular molecule with 148,343 bp in length and deposited in GenBank database (Accession Number KP168671). The plastid genome conserved the quadripartite structure present in most Orchidaceae chloroplasts and was composed by 79 protein-coding genes, 39 tRNAs and 8 rRNAs. Genome structure, gene order and orientation were similar to previously described chloroplasts for Cymbidium orchids, differing in gene order for petN and psbM genes. Data described here contain the first report of a complete chloroplast for the Neotropical subtribe Laeliinae and may contribute to improve the phylogenetic resolution and allow the development of new molecular markers for population genetic studies of orchids.
Botanical Bulletin of Academia Sinica, 2005
All Phalaenopsis species have the same chromosome number (2n=2χ=38), but the sizes of their genomes vary markedly. In this study, we investigated genome organization and relationships of Phalaenopsis species by genomic in situ hybridization (GISH) of seven interspecific hybrids derived from crosses between species with similar or dissimilar sizes of genomes. In the hybrid P. aphrodite × P. sanderiana, in which both parents possess small genomes, the two parental chromosome sets could not be distinguished by the strength and distribution of hybridization signals. Similar results were obtained from the hybrid P. mannii × P. violacea, in which both parents have large genomes. These results suggest that the two parents of these hybrids have similar genomes. In hybrids in which one parent possesses a large and the other parent a small genome, such as P amboinensis × P. stuartiana, the two parental chromosome sets could readily be distinguished by GISH with or without the application of b...
The complete chloroplast genome of a rare orchid species Liparis loeselii (L.)
Conservation Genetics Resources
The fen orchid, Liparis loeselii (L.) Rich. is a species within the family Orchidaceae, distributed in temperate parts of Europe, Asia and North America (Moore 1980). This small perennial plant occurs usually in fens and other wet habitats (Jones 1998; Wheeler 1998). Currently, the range of L. loeselii is declining, mainly due to habitat loss (Grootjans et al. 2016; Žalneravičius and Gudžinskas 2016). The fen orchid is protected in Europe (Pillon et al. 2006), in some parts of North America (Rolfsmeier 2007) and worldwide in scope of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Molecular studies of L. loeselii revealed that there is no diversity in the species within Europe (UK,
The Apostasia genome and the evolution of orchids
Nature, 2017
Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth 1–3. Here we report the draft genome sequence of Apostasia shenzhenica 4 , a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.