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Population size histories of seven orchid species, including P. aphrodite (yellow), D. catenatum (green), P. equestris (purple), D. officinale (dark blue), V. planifolia (pink), A. shenzhenica (light blue) and A. ramifera (red), between 10 000 and 10 million years ago. Generation times of orchids were assumed to be four years, and mutation rate per generation was 0.5 × 10 − 8
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Background
The Orchidaceae family is one of the most diverse among flowering plants and serves as an important research model for plant evolution, especially “evo-devo” study on floral organs. Recently, sequencing of several orchid genomes has greatly improved our understanding of the genetic basis of orchid biology. To date, however, most sequence...
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... changes [13], was applied to infer population size history based on the genome sequences of seven orchid species, i.e., A. ramifera, A. shenzhenica, P. equestris, P. aphrodite, D. officinale, D. catenatum, and V. planifolia. For the Apostasia species, population size changed between 10 000 and 250 000 years ago, with similar population dynamics (Fig. 2). Earlier history could not be recovered because the lowlevel heterozygosity of the genome sequences of A. ramifera and A. shenzhenica provided limited information on ancient changes in population size. For the other orchids, population size histories showed similar patterns, especially D. catenatum, D. officinale, and P. equestris ...
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... (Fig. 2). Earlier history could not be recovered because the lowlevel heterozygosity of the genome sequences of A. ramifera and A. shenzhenica provided limited information on ancient changes in population size. For the other orchids, population size histories showed similar patterns, especially D. catenatum, D. officinale, and P. equestris (Fig. 2). First, a period of population growth was observed for each of these orchid species. Then, all orchid populations experienced a severe contraction (bottleneck) over the last 100 000 years, from which they have not recovered (Fig. 2). During the reporting period (10 000 to 250 000 years ago), the Apostasia species had the smallest ...
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... population size histories showed similar patterns, especially D. catenatum, D. officinale, and P. equestris (Fig. 2). First, a period of population growth was observed for each of these orchid species. Then, all orchid populations experienced a severe contraction (bottleneck) over the last 100 000 years, from which they have not recovered (Fig. 2). During the reporting period (10 000 to 250 000 years ago), the Apostasia species had the smallest population size compared to other orchid species. The population size of Vanilla was slightly higher than that of Apostasia, but lower than that of all Epidendroideae ...
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... genome, fewer than that detected in the other sequenced orchids (Additional file 1, Table S19). Phylogenetic analysis of the putative MADS-box genes revealed that 23 belonged to the type II MADS-box clade ( Fig. 3 A), fewer again than that found in other orchids, e.g., A. shenzhenica (27 members) [3], V. planifolia (30 members, Additional file 1, Fig. S2A), P. equestris (29) [2], and D. catenatum (35) [5]. Compared to P. equestris, there were fewer members in the A-class, B-class, Eclass, and AGL6-class in A. ramifera and V. planifolia (Additional file 1, Table S19). In contrast, there were more SVP-class, ANR1-class, and AGL12-class members in A. ramifera and V. planifolia than in P. ...
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... AGL12-class members in A. ramifera and V. planifolia than in P. equestris (Additional file 1, Table S19). Type I MADS-box transcription factors are involved in plant reproduction and endosperm development [16]. Here, we identified seven and six type I MADS-box genes in A. ramifera and V. planifolia, respectively ( Fig. 3B and Additional file 1, Fig. S2B and Table S19). Phylogenetic analysis showed that genes in the Mβ-class were absent in A. ramifera and V. planifolia, (Fig. 3B and Additional file 1, Fig. ...
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... in plant reproduction and endosperm development [16]. Here, we identified seven and six type I MADS-box genes in A. ramifera and V. planifolia, respectively ( Fig. 3B and Additional file 1, Fig. S2B and Table S19). Phylogenetic analysis showed that genes in the Mβ-class were absent in A. ramifera and V. planifolia, (Fig. 3B and Additional file 1, Fig. ...
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Genome sequences and gene expression provide important insights into the evolution and function of gene families. A database of complete genome sequences for many plant species, including orchids, is now available. Additionally, transcriptomics via next-generation sequencing can be used to analyze the regulatory mechanisms of various biological processes at the molecular level in many plant species, even nonmodel and wild plants. Recently, whole-genome sequencing and transcriptomic studies have been conducted on some orchids, unveiling the mechanisms underlying orchid mycorrhizal (OM) symbiosis, one of the most important features of Orchidaceae. Because orchids obtain nutrients from their symbiotic fungi during seed germination or even throughout their whole life cycle (mycoheterotrophy), OM symbiosis differs from mutualism, such as arbuscular mycorrhizal (AM) symbiosis. The genetic information of orchids provides a better understanding of how OM symbiosis has evolved, how orchids maintain a delicate balance of immune control during symbiosis, and how OM and AM symbioses differ. This knowledge will help establish a method for maintaining OM symbiosis, which is essential for orchids, and for conserving threatened orchids. The objectives of this chapter are (i) to review genetic study methodologies because practical guidelines of orchid species’ genome sequence and transcriptome analysis are unavailable and (ii) to summarize studies on OM symbiosis.KeywordsGenomicsOrchid mycorrhizal symbiosisTranscriptomics
