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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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... genomic DNA of A. ramifera was sequenced using the Illumina Hiseq 2000 platform. Sequencing of five libraries with different insert sizes ranging from 250 to 5 000 bp generated more than 57 Gb of clean data, accounting for 156X of the genome sequence (Additional file 1, Table S1). Based on the clean reads, we generated a 365.59-Mb long assembly with a scaffold N50 of 287.45 kb (Table 1 and Additional file 1, Table S2). ...Context 2
... of five libraries with different insert sizes ranging from 250 to 5 000 bp generated more than 57 Gb of clean data, accounting for 156X of the genome sequence (Additional file 1, Table S1). Based on the clean reads, we generated a 365.59-Mb long assembly with a scaffold N50 of 287.45 kb (Table 1 and Additional file 1, Table S2). To assess the quality of the final assembly, clean reads were mapped to the genome sequence, resulting in a mapping ratio of 99.7 %. ...Context 3
... protein-coding gene models were predicted through a combination of de novo and homology-based annotation. In total, 22 841 putative genes were identified in the A. ramifera genome, similar to that in A. shenzhenica (21 831) but less than that in V. planifolia (28 279), P. equestris (29 545), and D. catenatum (29 257) (Add- itional file 1, Table S6). Further functional annotation of the predicted genes was carried out by homology searches against various databases, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), SwissProt, TrEMBL, nr database, and InterPro. ...Context 4
... comparison based on gene annotations of A. ramifera and A. shenzhenica identified 927 synteny blocks with an average block size of 12.89 genes (Add- itional file 1, Table S9). A total of 11 950 gene pairs were covered by these synteny blocks, accounting for 61 and 66 % of the genome sequences of A. ramifera and A. shenzhenica, respectively (Additional file 1, Table S9). ...Context 5
... high co-linearity between their genomes suggested a close relationship between these two species. Table S11 and S12). Furthermore, a total of 1 145 gene families were specifically expanded in Apostasia (see Methods), and were significantly enriched in several pathways, such as 'Ribosome biogenesis in eukaryotes' (ko03008), 'mRNA surveillance pathway' (ko03015) and 'Plant-pathogen interaction' (ko04626) (Additional file 1, Table S13 and S14). ...Context 6
... S11 and S12). Furthermore, a total of 1 145 gene families were specifically expanded in Apostasia (see Methods), and were significantly enriched in several pathways, such as 'Ribosome biogenesis in eukaryotes' (ko03008), 'mRNA surveillance pathway' (ko03015) and 'Plant-pathogen interaction' (ko04626) (Additional file 1, Table S13 and S14). ...Context 7
... family expansions and contractions on each phylogenetic branch of the 16 species were estimated using CAFE [12] (Fig. 1B). We further carried out GO/KEGG enrichment analyses on the significantly expanded gene families in A. ramifera and found some functionally enriched pathways and terms, including 'Zeatin biosynthesis' (ko00908), Glycerophospholipid metabolism (ko00564), 'Flavin adenine dinucleotide binding' (GO:0050660), and 'UDP-Nacetylmuramate dehydrogenase activity' (GO:0008762) (Additional file 1, Table S15 and S16). In addition, the significantly contracted gene families were enriched in 'Homologous recombination' (ko03440), 'Glycosphingolipid biosynthesis' (ko00604), 'Transferase activity, transferring phosphorus-containing groups' (GO:0016772), and 'Transferase activity' (GO:0016740) (Additional file 1, Table S17 and S18). ...Context 8
... further carried out GO/KEGG enrichment analyses on the significantly expanded gene families in A. ramifera and found some functionally enriched pathways and terms, including 'Zeatin biosynthesis' (ko00908), Glycerophospholipid metabolism (ko00564), 'Flavin adenine dinucleotide binding' (GO:0050660), and 'UDP-Nacetylmuramate dehydrogenase activity' (GO:0008762) (Additional file 1, Table S15 and S16). In addition, the significantly contracted gene families were enriched in 'Homologous recombination' (ko03440), 'Glycosphingolipid biosynthesis' (ko00604), 'Transferase activity, transferring phosphorus-containing groups' (GO:0016772), and 'Transferase activity' (GO:0016740) (Additional file 1, Table S17 and S18). ...Context 9
... MADSbox gene family members are categorized as type I or type II based on their gene tree. Using HMMER software and a MADS-box domain profile (PF00319), we identified 30 putative MADS-box genes in the A. ramifera 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]. ...Context 10
... 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. equestris (Additional file 1, Table S19). ...Context 11
... 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. equestris (Additional file 1, Table S19). Type I MADS-box transcription factors are involved in plant reproduction and endosperm development [16]. ...Context 12
... 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. S2B). ...Context 13
... s h 0 0 0 6 9 9 the epiphytic orchid genomes (Fig. 6 and Additional file 1, Table S21). However, only one homologous gene was found in A. ramifera, and the LOX1/LOX5 homologs were completely lost in A. shenzhenica ( Fig. 6 and Additional file 1, Table S21). ...Context 14
... s h 0 0 0 6 9 9 the epiphytic orchid genomes (Fig. 6 and Additional file 1, Table S21). However, only one homologous gene was found in A. ramifera, and the LOX1/LOX5 homologs were completely lost in A. shenzhenica ( Fig. 6 and Additional file 1, Table S21). We also found one copy of the LOX1/LOX5 genes in the hemi-epiphytic orchid V. planifolia ( Fig. 6 and Additional file 1, Table S21). ...Context 15
... only one homologous gene was found in A. ramifera, and the LOX1/LOX5 homologs were completely lost in A. shenzhenica ( Fig. 6 and Additional file 1, Table S21). We also found one copy of the LOX1/LOX5 genes in the hemi-epiphytic orchid V. planifolia ( Fig. 6 and Additional file 1, Table S21). ...Context 16
... genome assembly, SOAPdenovo2 [34] was used for contig construction and scaffolding, and GapCloser was used for extending the length of the final contigs. In total, 57.4 Gb of clean reads derived from the DNA libraries with five insert sizes (Additional file 1, Table S1) were used by SOAPdenovo2 assembler and GapCloser for de novo genome assembly. ...Similar publications
Transposable elements (TEs) have long been known to be major contributors to plant evolution, adaptation and crop domestication. Stress-induced TE mobilization is of particular interest because it may result in novel gene regulatory pathways responding to stresses and thereby contribute to stress adaptation. Here, we investigated the genomic impact...
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... Even within a specific range, the results may sometimes be erroneous or contradictory to traditional morphological classification. Moreover, the majority of studies [69][70][71][72][73] on orchid morphology or genetic evolution primarily focus on epiphytic orchids within the entire orchid family or subfamily, with limited analysis conducted on species diversity within Cymbidium species and particularly the evolutionary disparities among Cymbidium species from different regions. ...
The genus Cymbidium, with its intricate floral elements, pronounced endemicity, and patchy distribution, evolves a rich diversity of morphological forms and a wide variety of species while causing an indistinctness in the classification of its species. To elucidate the phylogenetic relationships among Cymbidium species and enhance their taxonomic classification by DNA barcoding, this study conducted amplification and sequence results of nuclear (ITS) and chloroplast genes (matK, rbcL, trnL-F, psbA-trnH) with phenotypic genetic diversity analysis, genetic distance analysis, and phylogenetic analysis from 48 samples of Cymbidium species. The comparison of genetic distance variations showed that psbA-trnH, ITS + psbA-trnH, and ITS + matK + psbA-trnH exhibit minimal overlap and significant genetic variation within Cymbidium species. The phylogenetic analysis indicated that the combination, ITS + matK + psbA-trnH, has the highest identification rate. Notably, both the phylogenetic analysis and the genetic diversity analysis of phenotypic traits consistently indicated a clear divergence between epiphytic and terrestrial orchids, with epiphytic orchids forming a distinct clade. This provides reference evidence for studying the ecological adaptations and evolutionary differences between epiphytic and terrestrial orchids, as well as a scientific basis for the classification and identification, germplasm conservation, resource utilization, and phylogenetic evolution of orchids.
... These genomes indicate the orchids have undergone two whole-genome duplication (WGD) events, the most recent of which was shared by all orchids, whereas the older event was shared by most monocots (Van de Peer et al., 2017;Zhang et al., 2017). Changes within MADSbox gene classes, identified through these genomes, might have contributed to variations in labellum and pollinium morphology and accessory structures (Chao et al., 2018;Ai et al., 2021;Sun et al., 2021;Zhang et al., 2021bZhang et al., , 2021c. ...
Orchidaceae are one of the largest families of angiosperms in terms of species richness. In the last decade, numerous studies have delved into reconstructing the phylogenetic framework of Orchidaceae, leveraging data from plastid, mitochondrial and nuclear sources. These studies have provided new insights into the systematics, diversification and biogeography of Orchidaceae, establishing a robust foundation for future research. Nevertheless, pronounced controversies persist regarding the precise placement of certain lineages within these phylogenetic frameworks. To address these discrepancies and deepen our understanding of the phylogenetic structure of Orchidaceae, we provide a comprehensive overview and analysis of phylogenetic studies focusing on contentious groups within Orchidaceae since 2015, delving into discussions on the underlying reasons for observed topological conflicts. We also provide a novel phylogenetic framework at the subtribal level. Furthermore, we examine the tempo and mode underlying orchid species diversity from the perspective of historical biogeography, highlighting factors contributing to extensive speciation. Ultimately, we delineate avenues for future research aimed at enhancing our understanding of Orchidaceae phylogeny and diversity.
... There are more than 28,000 species and 850 genera in Orchidaceae, represents approximately 10% of all flowering plants worldwide and has the largest number of species (Chase et al., 2015). Orchids are remarkable for shedding light on plant evolution, with more complete orchid genomes now available, researchers have gained significant insight into the genetic foundations of orchid biology (Zhang et al., 2021a). Extensive research has been conducted on CYP75s in model plants, but there is currently limited knowledge about the characteristics of these genes in the Orchidaceae. ...
With a great diversity of species, Orchidaceae stands out as an essential component of plant biodiversity, making it a primary resource for studying angiosperms evolution and genomics. This study focuses on 13 published orchid genomes to identify and analyze the CYP75 gene family belonging to the cytochrome P450 superfamily, which is closely related to flavonoid biosynthetic enzymes and pigment regulation. We found 72 CYP75s in the 13 orchid genomes and further classified them into two classes: CYP75A and CYP75B subfamily, the former synthesizes blue anthocyanins, while the latter is involved in the production of red anthocyanins. Furthermore, the amount of CYP75Bs (53/72) greatly exceeds the amount of CYP75As (19/72) in orchids. Our findings suggest that CYP75B genes have a more important evolutionary role, as red plants are more common in nature than blue plants. We also discovered unique conserved motifs in each subfamily that serve as specific recognition features (motif 19 belong to CYP75A; motif 17 belong to CYP75B). Two diverse-colored varieties of C. goeringii were selected for qRT-PCR experiments. The expression of CgCYP75B1 was significantly higher in the purple-red variant compared to the yellow-green variant, while CgCYP75A1 showed no significant difference. Based on transcriptomic expression analysis, CYP75Bs are more highly expressed than CYP75As in floral organs, especially in colorful petals and lips. These results provide valuable information for future studies on CYP75s in orchids and other angiosperms.
... Climate changes during the Quaternary glacial and interglacial periods directly in uenced the distribution of plant taxa and the size of plant habitats 24 . The RR and RH effective population sizes tended to decrease sharply during the glacial period and stabilized or increased during the interglacial period, which is in accordance with the related ndings for orchids 25 , Rhododendron 26,27 , and other plant groups. ...
Rose is an important aromatic plant and produces flowers that are used in medicine and food. We herein present a haplotype-resolved genome for Rosa rugosa cultivar Hanxiang. Analyses of allele-specific expression identified a potential mechanism underlying floral scent biosynthesis. Population genomic analyses involving 133 Rosa accessions elucidated evolutionary histories and a single R. rugosa domestication event. Pathways mediating the synthesis of scent-related metabolites were enriched according to the analyses of the transcriptomes, haplotype variations, and allelic imbalances during the flower development stages of Hanxiang and Guomeigui ( R. rugosa accessions with diverse fragrances). The enzyme-encoding ASE genes RrHX1G119800 and RrHX1G204700 (primary amine oxidases) and RrHX2G284700 (L-tryptophan decarboxylase) in the phenylethylamine pathway were tentatively designated as core genes useful for improving 2-phenylethanol production in rose flowers. Our results provide molecular insights into the formation of R. rugosa floral fragrances and genome-level data that are useful for enhancing rose traits via genetic engineering.
... Based on the morphological, genome size and molecular analyses, Yin et al. (2016) described a new species, A. fogangica with its genome size estimated as 931 Mb, and molecular evidence also suggested that A. shenzhenica, A. nipponica and A. ramifera are distinct species. Genome sizes of A. shenzhenica (471Mb) and A. ramifera (366Mb) have been reported in Zhang et al. (2017) and Zhang et al. (2021), respectively, by whole genome sequencing. ...
... Molecular phylogenetic analysis was conducted to determine its phylogenetic position. The estimated genome size of the new species was considerably smaller than that of other previously reported Apostasia species (Jersáková et al. 2013, Zhang et al. 2017, Zhang et al. 2021). ...
... Data analyses including the maximum parsimony (MP), Bayesian inference (BI) and maximum likelihood (ML) methods were conducted as previously described by Li et al. (2016). Genome size determination:-Holoploid genome size (1 C-values) was estimated by flow cytometry (Jersáková et al. 2013, Yin et al. 2016, whole-genome sequencing (Zhang et al. 2017, Zhang et al. 2021) and genome sequencing data (Zhong-Jian Liu, unpublished data). ...
After examining morphological, molecular and genome-size evidence, we here describe a new orchid species, Apostasia fujianica, from Fujian, China. Morphological comparisons indicated that A. fujianica is similar to A. shenzhenica and A. nipponica, whereas the former displayed distinct differences in habit, roots, leaves, inflorescences and fruit shape and size. Apostasia fujianica (341 Mb) has a smaller genome size than A. shenzhenica (471 Mb), A. ramifera (366 Mb) and A. fogangica (931 Mb). Molecular analyses from combined nuclear (ITS, Xdh, naD1) and plastid (matK, rbcL, psbA-trnH, trnL-trnF and trnS-trnG) datasets indicated that A. fujianica is sister to A. shenzhenica. These results support the status of A. fujianica as a new species, distinguished in many aspects from A. shenzhenica, A. ramifera and A. nipponica.
... Furthermore, as RNA-Seq decrease in cost, promoting the identification of new genes by obtaining massive amounts of sequence data with enormous depth and coverage. As a result, a large number of critical regulators related to important agronomic traits and environmental adaptation have been identified in orchid species, including Apostasia (Zhang et al., , 2021a, Cymbidium (Ai et al., 2021;Yang et al., 2021), Dendrobium (Niu et al., 2021;Zhang et al., 2021b), Gastrodia Phalaenopsis (Cai et al., 2015;Chao et al., 2018), and Vanilla (Hasing et al., 2020). ...
Transcription factors (TFs) of the WRKY family play pivotal roles in defense responses and secondary metabolism of plants. Although WRKY TFs are well documented in numerous plant species, no study has performed a genome-wide investigation of the WRKY gene family in Cymbidium sinense. In the present work, we found 64 C. sinense WRKY (CsWRKY) TFs, and they were further divided into eight subgroups. Chromosomal distribution of CsWRKYs revealed that the majority of these genes were localized on 16 chromosomes, especially on Chromosome 2. Syntenic analysis implied that 13 (20.31%) genes were derived from segmental duplication events, and 17 orthologous gene pairs were identified between Arabidopsis thaliana WRKY (AtWRKY) and CsWRKY genes. Moreover, 55 of the 64 CsWRKYs were detectable in different plant tissues in response to exposure to plant hormones. Among them, Group III members were strongly induced in response to various hormone treatments, indicating their potential essential roles in hormone signaling. We subsequently analyzed the function of CsWRKY18 in Group III. The CsWRKY18 was localized in the nucleus. The constitutive expression of CsWRKY18 in Arabidopsis led to enhanced sensitivity to ABA-mediated seed germination and root growth and elevated plant tolerance to abiotic stress within the ABA-dependent pathway. Overall, our study represented the first genome-wide characterization and functional analysis of WRKY TFs in C. sinense, which could provide useful clues about the evolution and functional description of CsWRKY genes.
Repetitive sequences can lead to variation in DNA quantity and composition among species. The Orchidaceae, the largest angiosperm family, is divided into five subfamilies, with Apostasioideae as the basal group and Orchidoideae and Epidendroideae showing high diversification rates. Despite their different evolutionary paths, some species in these groups have similar nuclear DNA content. This study focuses on one example to understand the dynamics of major repetitive DNAs in the nucleus. We used Next-Generation Sequencing (NGS) data from Apostasia wallichii (Apostasioideae) and Ludisia discolor (Orchidoideae) to identify and quantify the most abundant repeats. The repetitive fraction varied in abundance (27.5% in L. discolor and 60.6% in A. wallichii) and composition, with LTR retrotransposons of different lineages being the most abundant repeats in each species. Satellite DNAs showed varying organization and abundance. Despite the unbalanced ratio between single-copy and repetitive DNA sequences, the two species had the same genome size, possibly due to the elimination of non-essential genes. This phenomenon has been observed in other Apostasia and likely led to the proliferation of transposable elements in A. wallichii. Deep genome information in the future will aid in understanding the contraction/expansion of gene families and the evolution of sequences in these genomes.
There are nearly 30,000 species of orchids globally, of which over 1,700 species are found in China. Orchids share a profound and intimate connection with Chinese society. With the rapid development of science and technology, China's orchid industry has flourished with many scientific and technological achievements. Here, we summarize the developmental history, current situation, latest research achievements, and industrialization technology of the orchid industry in China, and present a discussion and outlook on the future development direction of orchid research in China. This review unveils new prospects for the high-quality advancement of China's orchid industry.
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
