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1.
Syst Biol ; 69(1): 91-109, 2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31127939

RESUMO

Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.


Assuntos
Orchidaceae/classificação , Orchidaceae/genética , Filogenia , Diploide , Europa (Continente) , Tetraploidia
2.
Int J Mol Sci ; 20(17)2019 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-31480267

RESUMO

Phalaenopsis cultivar 'Panda' is a beautiful and valuable ornamental for its big flower and unique big spots on the petals and sepals. Although anthocyanins are known as the main pigments responsible for flower colors in Phalaenopsis, and the anthocyanins biosynthetic pathway in Phalaenopsis is generally well known, the detailed knowledge of anthocynins regulation within the spot and non-spot parts in 'Panda' flower is limited. In this study, transcriptome and small RNA libraries analysis from spot and non-spot sepal tissues of 'Panda' were performed, and we found PeMYB7, PeMYB11, and miR156g, miR858 is associated with the purple spot patterning in its sepals. Transcriptome analyses showed a total 674 differentially expressed genes (DEGs), with 424 downregulated and 250 upregulated (Non-spot-VS-Spot), and 10 candidate DEGs involved in anthocyanin biosynthetic pathway. The qPCR analysis confirmed that seven candidate structure genes (PeANS, PeF3'H, PeC4H, PeF3H, PeF3H1, Pe4CL2, and PeCHI) have significantly higher expressing levels in spot tissues than non-spot tissues. A total 1552 differentially expressed miRNAs (DEMs) were detected with 676 downregulated and 876 upregulated. However, microRNA data showed no DEMs targeting on anthocyanin biosynthesis structure gene, while a total 40 DEMs target transcription factor (TF) genes, which expressed significantly different level in spot via non-spot sepal, including 2 key MYB regulator genes. These results indicated that the lack of anthocyanidins in non-spot sepal may not directly be caused by microRNA suppressing anthocyanidin synthesis genes rather than the MYB genes. Our findings will help in understanding the role of miRNA molecular mechanisms in the spot formation pattern of Phalaenopsis, and would be useful to provide a reference to similar research in other species.


Assuntos
Flores/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , MicroRNAs/genética , Orchidaceae/genética , Antocianinas/biossíntese , Antocianinas/metabolismo , Mapeamento Cromossômico , Flores/anatomia & histologia , Biblioteca Gênica , Genoma de Planta , MicroRNAs/metabolismo , Modelos Biológicos , Anotação de Sequência Molecular , Orchidaceae/anatomia & histologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
3.
Plant Sci ; 287: 110173, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31481204

RESUMO

Anthocyanins are responsible for red, purple, and pink pigmentation of flowers in Cymbidium hybrids. Although anthocyanin content in all floral organs increases with flower development, they increase markedly in the tepals compared with the labella or columns. Using next-generation sequencing technology, we identified three anthocyanin biosynthesis regulatory genes, CyMYB1, CybHLH1, and CybHLH2, from Cymbidium 'Mystique'. Yeast two-hybrid analysis showed that the CyMYB1 protein can form a heterodimer with either CybHLH1 or CybHLH2. In the tepals, the expression level of CyMYB1 increased as the flower developed, whereas the high expression level of CyMYB1 was detected at the early flower developmental stages in the labella and columns, remaining constant until increasing at the late developmental stage. These expression profiles of CyMYB1 positively correlated with the profiles of anthocyanin accumulation in the tepals. When Cymbidium Sazanami 'Champion' was grown at 30 °C/25 °C, reduced anthocyanin levels were observed, specifically in the tepals, compared with those in flowers grown at 20 °C/15 °C. The transcription of CyMYB1 in the tepals was suppressed at high temperatures, and the expressions of CyDFR and CyANS were also synchronously suppressed. This study revealed that CyMYB1 activates the transcription of CyDFR and CyANS and regulates the temporal- and temperature-dependent anthocyanin accumulation in Cymbidium tepals.


Assuntos
Antocianinas/biossíntese , Flores/metabolismo , Regulação da Expressão Gênica de Plantas , Orchidaceae/metabolismo , Flavonoides/metabolismo , Genes de Plantas/genética , Sequenciamento de Nucleotídeos em Larga Escala , Orchidaceae/genética , Filogenia , Proteínas de Plantas/metabolismo , Reação em Cadeia da Polimerase em Tempo Real , Temperatura Ambiente , Fatores de Transcrição/metabolismo , Transcriptoma
4.
BMC Plant Biol ; 19(1): 337, 2019 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-31375064

RESUMO

BACKGROUND: Cymbidium goeringii belongs to the Orchidaceae, which is one of the most abundant angiosperm families. Cymbidium goeringii consist with high economic value and characteristics include fragrance and multiple flower colors. Floral scent is one of the important strategies for ensuring fertilization. However, limited genetic data is available in this non-model plant, and little known about the molecular mechanism responsible for floral scent in this orchid. Transcriptome and expression profiling data are needed to identify genes and better understand the biological mechanisms of floral scents in this species. Present transcriptomic data provides basic information on the genes and enzymes related to and pathways involved in flower secondary metabolism in this plant. RESULTS: In this study, RNA sequencing analyses were performed to identify changes in gene expression and biological pathways related scent metabolism. Three cDNA libraries were obtained from three developmental floral stages: closed bud, half flowering stage and full flowering stage. Using Illumina technique 159,616,374 clean reads were obtained and were assembled into 85,868 final unigenes (average length 1194 nt), 33.85% of which were annotated in the NCBI non redundant protein database. Among this unigenes 36,082 were assigned to gene ontology and 23,164 were combined with COG groups. Total 33,417 unigenes were assigned in 127 pathways according to the Kyoto Encyclopedia of Genes and Genomes pathway database. According these transcriptomic data we identified number of candidates genes which differentially expressed in different developmental stages of flower related to fragrance biosynthesis. In q-RT-PCR most of the fragrance related genes highly expressed in half flowering stage. CONCLUSIONS: RNA-seq and DEG data provided comprehensive gene expression information at the transcriptional level that could be facilitate the molecular mechanisms of floral biosynthesis pathways in three developmental phase's flowers in Cymbidium goeringii, moreover providing useful information for further analysis on C. goeringii, and other plants of genus Cymbidium.


Assuntos
Flores/metabolismo , Genes de Plantas/genética , Odorantes , Orchidaceae/genética , Acetatos/metabolismo , Ciclopentanos/metabolismo , Farneseno Álcool/metabolismo , Flores/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genes de Plantas/fisiologia , Orchidaceae/metabolismo , Oxilipinas/metabolismo , Filogenia , Análise de Sequência de RNA , Sesquiterpenos/metabolismo , Terpenos/metabolismo
5.
BMC Plant Biol ; 19(1): 223, 2019 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-31138149

RESUMO

BACKGROUND: MADS-box genes play crucial roles in plant floral organ formation and plant reproductive development. However, there is still no information on genome-wide identification and classification of MADS-box genes in some representative plant species. A comprehensive investigation of MIKC-type genes in the orchid Dendrobium officinale is still lacking. RESULTS: Here we conducted a genome-wide analysis of MADS-box proteins from 29 species. In total, 1689 MADS-box proteins were identified. Two types of MADS-box genes, termed type I and II, were found in land plants, but not in liverwort. The SQUA, DEF/GLO, AG and SEP subfamilies existed in all the tested flowering plants, while SQUA was absent in the gymnosperm Ginkgo biloba, and no genes of the four subfamilies were found in a charophyte, liverwort, mosses, or lycophyte. This strongly corroborates the notion that clades of floral organ identity genes led to the evolution of flower development in flowering plants. Nine subfamilies of MIKCC genes were present in two orchids, D. officinale and Phalaenopsis equestris, while the TM8, FLC, AGL15 and AGL12 subfamilies may be lost. In addition, the four clades of floral organ identity genes in both orchids displayed a conservative and divergent expression pattern. Only three MIKC-type genes were induced by cold stress in D. officinale while 15 MIKC-type genes showed different levels of expression during seed germination. CONCLUSIONS: MIKC-type genes were identified from streptophyte lineages, revealing new insights into their evolution and development relationships. Our results show a novel role of MIKC-type genes in seed germination and provide a useful clue for future research on seed germination in orchids.


Assuntos
Proteínas de Domínio MADS/análise , Proteínas de Plantas/análise , Estreptófitas/genética , Dendrobium/genética , Genes de Plantas , Estudo de Associação Genômica Ampla , Proteínas de Domínio MADS/classificação , Família Multigênica , Orchidaceae/genética , Proteínas de Plantas/classificação
6.
Mol Biol Evol ; 36(9): 1884-1901, 2019 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-31058965

RESUMO

Heterotrophic plants are evolutionary experiments in genomic, morphological, and physiological change. Yet, genomic sampling gaps exist among independently derived heterotrophic lineages, leaving unanswered questions about the process of genome modification. Here, we have sequenced complete plastid genomes for all species of the leafless orchid genus Hexalectris, including multiple individuals for most, and leafy relatives Basiphyllaea and Bletia. Our objectives are to determine the number of independent losses of photosynthesis and to test hypotheses on the process of genome degradation as a result of relaxed selection. We demonstrate four to five independent losses of photosynthesis in Hexalectris based on degradation of the photosynthetic apparatus, with all but two species displaying evidence of losses, and variation in gene loss extending below the species level. Degradation in the atp complex is advanced in Hexalectris warnockii, whereas only minimal degradation (i.e., physical loss) has occurred among some "housekeeping" genes. We find genomic rearrangements, shifts in Inverted Repeat boundaries including complete loss in one accession of H. arizonica, and correlations among substitutional and genomic attributes. Our unprecedented finding of multiple, independent transitions to a fully mycoheterotrophic lifestyle in a single genus reveals that the number of such transitions among land plants is likely underestimated. This study underscores the importance of dense taxon sampling, which is highly informative for advancing models of genome evolution in heterotrophs. Mycoheterotrophs such as Hexalectris provide forward-genetic opportunities to study the consequences of radical genome evolution beyond what is possible with mutational studies in model organisms alone.


Assuntos
Genomas de Plastídeos , Processos Heterotróficos/genética , Orchidaceae/genética , Fotossíntese/genética , Evolução Molecular , Variação Estrutural do Genoma , Filogenia
7.
Genes Genet Syst ; 94(2): 95-98, 2019 Apr 27.
Artigo em Inglês | MEDLINE | ID: mdl-30956254

RESUMO

We developed microsatellite markers to compare the genetic variation between the putatively cleistogamous Gastrodia takeshimensis (Orchidaceae) and its chasmogamous sister species G. nipponica. We expected low genetic variation in G. takeshimensis in view of its hypothesized cleistogamy. Eighteen primer pairs were developed from a G. takeshimensis genomic DNA library, and their characteristics were tested for G. takeshimensis and G. nipponica. Seven loci were polymorphic in G. nipponica, whereas all loci showed no polymorphism in G. takeshimensis. Genetic diversity was thus not detected in G. takeshimensis, and it seems to have been lost by repeated selfing in the completely closed flower. The 18 markers described here will be useful for investigating the genetic variation between a cleistogamous species and its chasmogamous sister species.


Assuntos
Técnicas de Genotipagem/normas , Repetições de Microssatélites , Orchidaceae/genética , Genoma de Planta , Técnicas de Genotipagem/métodos , Polimorfismo Genético
8.
PLoS One ; 14(3): e0213185, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30822337

RESUMO

The Orchidaceae family, which is one of the most species-rich flowering plant families, includes species with highly diversified and specialized flower shapes. The aim of this study was to analyze the MADS-box genes expressed in the inflorescence of Orchis italica, a wild Mediterranean orchid species. MADS-box proteins are transcription factors involved in various plant biological processes, including flower development. In the floral tissues of O. italica, 29 MADS-box genes are expressed that are classified as both class I and II. Class I MADS-box genes include one Mß-type gene, thereby confirming the presence of this type of MADS-box genes in orchids. The class II MIKC* gene is highly expressed in the column, which is consistent with the conserved function of the MIKC* genes in gametophyte development. In addition, homologs of the SOC, SVP, ANR1, AGL12 and OsMADS32 genes are expressed. Compared with previous knowledge on class II MIKCC genes of O. italica involved in the ABCDE model of flower development, the number of class B and D genes has been confirmed. In addition, 4 class A (AP1/FUL) transcripts, 2 class E (SEP) transcripts, 2 new class C (AG) transcripts and 1 new AGL6 transcript have been identified. Within the AP1/FUL genes, the sequence divergence, relaxation of purifying selection and expression profiles suggest a possible functional diversification within these orchid genes. The detection of only two SEP transcripts in O. italica, in contrast with the 4 genes found in other orchids, suggests that only two SEP genes could be present in the subfamily Orchidoideae. The expression pattern of the MIKCC genes of O. italica indicates that low levels at the boundary of the domain of a given MADS-box gene can overlap with the expression of genes belonging to a different functional A-E class in the adjacent domain, thereby following a "fading borders" model.


Assuntos
Flores/genética , Regulação da Expressão Gênica de Plantas , Proteínas de Domínio MADS/genética , Orchidaceae/genética , Proteínas de Plantas/genética , Evolução Molecular , Flores/crescimento & desenvolvimento , Flores/metabolismo , Proteínas de Domínio MADS/metabolismo , Orchidaceae/crescimento & desenvolvimento , Proteínas de Plantas/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
9.
Mol Phylogenet Evol ; 136: 21-28, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30914398

RESUMO

The orchid genus Nigritella is closely related to Gymnadenia and has from time to time been merged with the latter. Although Nigritella is morphologically distinct, it has been suggested that the separating characters are easily modifiable and subject to rapid evolutionary change. So far, molecular phylogenetic studies have either given support for the inclusion of Nigritella in Gymnadenia, or for their separation as different genera. To resolve this issue, we analysed data obtained from Restriction-site associated DNA sequencing, RADseq, which provides a large number of SNPs distributed across the entire genome. To analyse samples of different ploidies, we take an analytical approach of building a reduced genomic reference based on de novo RADseq loci reconstructed from diploid accessions only, which we further use to map and call variants across both diploid and polyploid accessions. We found that Nigritella is distinct from Gymnadenia forming a well-supported separate clade, and that genetic diversity within Gymnadenia is high. Within Gymnadenia, taxa characterized by an ITS-E ribotype (G. conopsea s.str. (early flowering) and G. odoratissima), are divergent from taxa characterized by ITS-L ribotype (G. frivaldii, G. densiflora and late flowering G. conopsea). Gymnigritella runei is confirmed to have an allopolyploid origin from diploid Gymnadenia conopsea and tetraploid N. nigra ssp. nigra on the basis of RADseq data. Within Nigritella the aggregation of polyploid members into three clear-cut groups as suggested by allozyme and nuclear microsatellite data was further supported.


Assuntos
Orchidaceae/genética , Filogenia , Mapeamento por Restrição , Análise de Sequência de DNA , Geografia , Funções Verossimilhança , Análise de Componente Principal
10.
Am J Bot ; 106(3): 334-351, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30845367

RESUMO

PREMISE OF THE STUDY: Bilateral symmetry in core eudicot flowers is established by the differential expression of CYCLOIDEA (CYC), DICHOTOMA (DICH), and RADIALIS (RAD), which are restricted to the dorsal portion of the flower, and DIVARICATA (DIV), restricted to the ventral and lateral petals. Little is known regarding the evolution of these gene lineages in non-core eudicots, and there are no reports on gene expression that can be used to assess whether the network predates the diversification of core eudicots. METHODS: Homologs of the RAD and DIV lineages were isolated from available genomes and transcriptomes, including those of three selected non-core eudicot species, the magnoliid Aristolochia fimbriata and the monocots Cattleya trianae and Hypoxis decumbens. Phylogenetic analyses for each gene lineage were performed. RT-PCR was used to evaluate the expression and putative contribution to floral symmetry in dissected floral organs of the selected species. KEY RESULTS: RAD-like genes have undergone at least two duplication events before eudicot diversification, three before monocots and at least four in Orchidaceae. DIV-like genes also duplicated twice before eudicot diversification and underwent independent duplications specific to Orchidaceae. RAD-like and DIV-like genes have differential dorsiventral expression only in C. trianae, which contrasts with the homogeneous expression in the perianth of A. fimbriata. CONCLUSIONS: Our results point to a common genetic regulatory network for floral symmetry in monocots and core eudicots, while alternative genetic mechanisms are likely driving the bilateral perianth symmetry in the early-diverging angiosperm Aristolochia.


Assuntos
Aristolochia/genética , Evolução Biológica , Flores/genética , Redes Reguladoras de Genes , Genes de Plantas , Hypoxis/genética , Orchidaceae/genética , Perfilação da Expressão Gênica , Filogenia
11.
Genome Biol Evol ; 11(2): 565-571, 2019 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-30715335

RESUMO

Cyrtosia septentrionalis is an achlorophyllous mycoheterotrophic orchid in the subfamily Vanilloideae (Orchidaceae). This article reports C. septentrionalis's complete plastome sequence and compare it with other orchid plastomes with a same mycoheterotrophic nutritional mode. The C. septentrionalis plastome has decreased to 96,859 bp in length, but it still maintains a quadripartite structure. The C. septentrionalis plastome contains 38 protein-coding genes, 25 tRNA genes, and four ribosomal RNA genes. Most genes related to photosynthesis have been lost, whereas the majority of housekeeping genes remain; this pattern corresponds to the end of stage 3 gene degradation. The inverted repeat regions of the C. septentrionalis plastome have decreased to 10,414 bp and mainly contain the gene ycf2. A block consisting of four rrn genes and rps7 and rps12 has shifted to a small single-copy region. As a result, the small single-copy region was found to be expanded, despite the loss of all ndh genes in the region. Three inversion mutations are required to explain the C. septentrionalis plastome's current gene order. The species is endangered, and these results have implications for its conservation.


Assuntos
Genomas de Plastídeos , Orchidaceae/genética , Fotossíntese/genética , Espécies em Perigo de Extinção
12.
BMC Genomics ; 20(1): 125, 2019 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-30744548

RESUMO

BACKGROUND: Cymbidium faberi, one of the most famous oriental orchids, has a distinct flower scent, which increases its economic value. However, the molecular mechanism of the flower scent biosynthesis was unclear prior to this study. Methyl jasmonate (MeJA) is one of the main volatile organic compounds (VOC) produced by the flowers of C. faberi. In this study, unigene 79,363 from comparative transcriptome analysis was selected for further investigation. RESULTS: A transcriptome comparison between blooming and withered flowers of C. faberi yielded a total of 9409 differentially expressed genes (DEGs), 558 of which were assigned to 258 pathways. The top ten pathways included α-linolenic acid metabolism, pyruvate metabolism and fatty acid degradation, which contributed to the conversion of α-linolenic acid to MeJA. One of the DEGs, jasmonic acid carboxyl methyltransferase (CfJMT, Unigene 79,363) was highly expressed in the blooming flower of C. faberi, but was barely detected in leaves and roots. Although the ectopic expression of CfJMT in tomato could not increase the MeJA content, the expression levels of endogenous MeJA biosynthesis genes were influenced, especially in the wound treatment, indicating that CfJMT may participate in the response to abiotic stresses. CONCLUSION: This study provides a basis for elucidating the molecular mechanism of flower scent biosynthesis in C. faberi, which is beneficial for the genetically informed breeding of new cultivars of the economically valuable oriental orchids.


Assuntos
Flores/metabolismo , Perfilação da Expressão Gênica , Metiltransferases/genética , Odorantes , Orchidaceae/genética , Orchidaceae/metabolismo , Orchidaceae/enzimologia , Orchidaceae/fisiologia , Regiões Promotoras Genéticas/genética , Estresse Fisiológico , Regulação para Cima
13.
BMC Evol Biol ; 19(1): 63, 2019 02 26.
Artigo em Inglês | MEDLINE | ID: mdl-30808310

RESUMO

BACKGROUND: The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive. Holcoglossum is a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation. This made it an ideal group to explore the plastome mutation mode at the infrageneric or intraspecific level. RESULTS: In this paper, we reported 15 complete plastid genomes from 12 species of Holcoglossum and 1 species of Vanda. The plastid genomes of Holcoglossum have a total length range between 145 kb and 148 kb, encoding a set of 102 genes. The whole set of ndh-gene families in Holcoglossum have been truncated or pseudogenized. Hairpin inversion in the coding region of the plastid gene ycf2 has been found. CONCLUSIONS: Using a comprehensive comparative plastome analysis, we found that all the indels between different individuals of the same species resulted from the copy number variation of the short repeat sequence, which may be caused by replication slippage. Annotation of tandem repeats shows that the variation introduced by tandem repeats is widespread in plastid genomes. The hairpin inversion found in the plastid gene ycf2 occurred randomly in the Orchidaceae.


Assuntos
Genomas de Plastídeos , Orchidaceae/genética , Variações do Número de Cópias de DNA , Evolução Molecular , Mutação INDEL , Fases de Leitura Aberta , Orchidaceae/classificação , Filogenia , Plastídeos , Sequências Repetitivas de Ácido Nucleico
14.
BMC Genomics ; 20(1): 25, 2019 Jan 09.
Artigo em Inglês | MEDLINE | ID: mdl-30626325

RESUMO

BACKGROUND: Orchids produce a colorless protocorm by symbiosis with fungi upon seed germination. For mass production of orchids, the prevailing approaches are both generation of protocorm-like bodies (PLBs) from callus and multiplication of adventitious buds on inflorescence. However, somaclonal variations occur during micropropagation. RESULTS: We isolated the two most expressed transposable elements belonging to P Instability Factor (PIF)-like transposons. Among them, a potential autonomous element was identified by similarity analysis against the whole-genome sequence of Phalaenopsis equestris and named PePIF1. It contains a 19-bp terminal inverted repeat flanked by a 3-bp target site duplication and two coding regions encoding ORF1- and transposase-like proteins. Phylogenetic analysis revealed that PePIF1 belongs to a new P-lineage of PIF. Furthermore, two distinct families, PePIF1a and PePIF1b, with 29 and 37 putative autonomous elements, respectively, were isolated, along with more than 3000 non-autonomous and miniature inverted-repeat transposable element (MITE)-like elements. Among them, 828 PePIF1-related elements were inserted in 771 predicted genes. Intriguingly, PePIF1 was transposed in the somaclonal variants of Phalaenopsis cultivars, as revealed by transposon display, and the newly inserted genes were identified and sequenced. CONCLUSION: A PIF-like element, PePIF1, was identified in the Phalaenopsis genome and actively transposed during micropropagation. With the identification of PePIF1, we have more understanding of the Phalaenopsis genome structure and somaclonal variations during micropropagation for use in orchid breeding and production.


Assuntos
Elementos de DNA Transponíveis/genética , Orchidaceae/genética , Filogenia , Genoma de Planta/genética , Mutagênese Insercional/genética , Fases de Leitura Aberta , Sequências Repetidas Terminais/genética , Transposases/genética
15.
BMC Genomics ; 20(1): 53, 2019 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-30654752

RESUMO

BACKGROUND: Cymbidium goeringii is one of the most horticulturally important and popular ornamental plants in the orchid family (Orchidaceae). It blooms in winter during January-March and a period of low temperature is necessary for its normal flowering, otherwise there is flower bud abortion, which seriously affects the economic benefits. However, the molecular mechanism underlying winter-blooming behavior in C. goeringii is unclear. RESULTS: In this research, we firstly study the flowering physiology of C. goeringii by cytobiology observations and physiological experiments. Using comparative transcriptome analysis, we identified 582 differentially expressed unigenes responding to cold treatment that were involved in metabolic process, flowering time, hormone signaling, stress response, and cell cycle, implying their potential roles in regulating winter-blooming of C. goeringii. Twelve MADS-box genes among them were investigated by full-length cDNA sequence analysis and expression validation, which indicated that three genes within the SHORT VEGETATIVE PHASE (SVP) sub-group had the most significant repressed expression after cold treatment. Further analysis revealed that the SVP genes showed population variation in expression that correlated with cold-regulated flowering and responded to low temperature earlier than the flowering pathway integrators CgAP1, CgSOC1, and CgLFY, suggesting a potential role of CgSVP genes in the early stage of low-temperature-induced blooming of C. goeringii. Moreover, a yeast two-hybrid experiment confirmed that CgSVP proteins interacted with CgAP1 and CgSOC1, suggesting that they may synergistically control the process of C. goeringii flowering in winter. CONCLUSIONS: This study represents the first exploration of flowering physiology of C. goeringii and provides gene expression information that could facilitate our understanding of molecular regulation of orchid plant winter-flowering, which could provide new insights and practical guidance for improving their flowering regulation and molecular breeding.


Assuntos
Temperatura Baixa , Flores/genética , Flores/fisiologia , Genes de Plantas , Orchidaceae/genética , Orchidaceae/fisiologia , Transcriptoma/genética , Flores/ultraestrutura , Regulação da Expressão Gênica de Plantas , Anotação de Sequência Molecular , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Mapas de Interação de Proteínas/genética , Reprodutibilidade dos Testes , Fatores de Tempo
16.
Nat Commun ; 10(1): 63, 2019 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-30622247

RESUMO

Maintenance of polymorphism by overdominance (heterozygote advantage) is a fundamental concept in evolutionary biology. In most examples known in nature, overdominance is a result of homozygotes suffering from deleterious effects. Here we show that overdominance maintains a non-deleterious polymorphism with black, red and white floral morphs in the Alpine orchid Gymnadenia rhellicani. Phenotypic, metabolomic and transcriptomic analyses reveal that the morphs differ solely in cyanidin pigments, which are linked to differential expression of an anthocyanidin synthase (ANS) gene. This expression difference is caused by a premature stop codon in an ANS-regulating R2R3-MYB transcription factor, which is heterozygous in the red colour morph. Furthermore, field observations show that bee and fly pollinators have opposite colour preferences; this results in higher fitness (seed set) of the heterozygous morph without deleterious effects in either homozygous morph. Together, these findings demonstrate that genuine overdominance exists in nature.


Assuntos
Orchidaceae/fisiologia , Oxigenases/genética , Pigmentação/genética , Proteínas de Plantas/genética , Fatores de Transcrição/genética , Animais , Antocianinas/metabolismo , Abelhas/fisiologia , Códon sem Sentido , Cor , Dípteros/fisiologia , Flores/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genes Dominantes/genética , Aptidão Genética , Heterozigoto , Orchidaceae/genética , Oxigenases/metabolismo , Polinização , Polimorfismo Genético , Seleção Genética
17.
Ann Bot ; 123(2): 347-354, 2019 01 23.
Artigo em Inglês | MEDLINE | ID: mdl-29878057

RESUMO

Background and Aims: Selection exerted by pollinators on flowers is predicted to occur along two distinct axes. While pollinator attraction to flowers is governed by pollinator preferences, pollen transfer efficiency is mediated by the mechanical fit of pollinators to flower morphology. Although pollinator attraction in sexually deceptive orchids is typically underpinned by floral odour, morphological traits are expected to play a vital role in mechanical fit during floral contact with pollinators. Methods: Here we utilize a comprehensive and novel procedure to test for pollinator-mediated selection through mechanical fit with the flower labellum in the orchid Chiloglottis trapeziformis. This approach combines detailed pollinator observations related to plant reproductive fitness with complementary experimental manipulation and phenotypic selection analysis. Key Results: Experiments with virgin flowers revealed that pollen removal occurs only during vigorous pseudocopulation. This behaviour involves male wasps that grasp the insectiform callus structure on the labellum while probing the labellum tip in a forward orientation. Both orientation and duration of pseudocopulation were significant predictors of pollen removal, confirming a direct relationship between pollinator behaviour and plant fitness. Controlled floral manipulation that either shortened or elongated the distance between the callus and the labellum tip detected no change in pollinator attraction. The duration of pseudocopulation, however, was significantly reduced on flowers with shortened or elongated callus-tip distances, consistent with stabilizing selection. Phenotypic selection analysis confirmed this prediction in natural populations by uncovering evidence for stabilizing selection on the distance between the callus and the labellum tip. Conclusions: Our experimental manipulations and selection analysis in natural populations thus demonstrate stabilizing selection on the distance from the callus to the labellum tip, and illustrate the utility of employing multiple approaches to confirm selection exerted by pollinators on floral form.


Assuntos
Flores/genética , Orchidaceae/genética , Polinização/genética , Seleção Genética , Vespas/fisiologia , Animais , Aptidão Genética , Masculino , Comportamento Sexual Animal
18.
Plant Biol (Stuttg) ; 21(2): 259-266, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30388306

RESUMO

In angiosperms, a decrease in fruit production towards the apex of individual inflorescences is usually observed. Orchids are thought to be primarily pollination-limited species, and non-uniform pollination could cause this decrease pattern in several species. Fruit production was investigated in relation to flower position and floral display size in Orchis militaris (Orchidaceae), a deceptive species. Over 2 years, eight populations of O. militaris were studied and fruit position along the inflorescence was recorded. Generalised linear models were performed to examine the effect of population, year, flower position and floral display size on fruit production. The dominant pattern was characterised by a higher fruit set in the middle part of the inflorescence (parabolic pattern). A non-directional pattern of fruit production was also detected in some populations. Within a given population, patterns were generally consistent among years. In one of the two study years and in one of the eight populations specifically, the proximal-to-distal decrease in fruit production was dramatic in plants with a large floral display but weak or absent in small displays. Our study demonstrates the intraspecific diversity of fruit distribution patterns in O. militaris. Non-uniform pollination along the inflorescence is likely to be responsible for the parabolic pattern, while irregular visitation could explain the non-directional pattern of fruit production. Pattern variation among years and between populations could arise from spatiotemporal variation in pollinator assemblages. Resource competition effects could explain the interaction effect between display size and flower position.


Assuntos
Frutas/anatomia & histologia , Inflorescência/anatomia & histologia , Orchidaceae/anatomia & histologia , Flores/anatomia & histologia , Flores/crescimento & desenvolvimento , Frutas/crescimento & desenvolvimento , Inflorescência/crescimento & desenvolvimento , Orchidaceae/genética , Polinização , Análise Espaço-Temporal , Fatores de Tempo
19.
Ann Bot ; 123(1): 69-77, 2019 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-30113635

RESUMO

Background and Aims: Orchidaceae is a large plant family, and its extraordinary adaptations may have guaranteed its evolutionary success. Flavonoids are a group of secondary metabolites that mediate plant acclimation to challenge environments. Chalcone synthase (CHS) catalyses the initial step in the flavonoid biosynthetic pathway. This is the first chromosome-level investigation of the CHS gene family in Phalaenopsis aphrodite and was conducted to elucidate if divergence of this gene family is associated with chromosome evolution. Methods: Complete CHS genes were identified from our whole-genome sequencing data sets and their gene expression profiles were obtained from our transcriptomic data sets. Fluorescence in situ hybridization (FISH) was conducted to position five CHS genes to high-resolution pachytene chromosomes. Key Results: The five Phalaenopsis CHS genes can be classified into three groups, PaCHS1, PaCHS2 and the tandemly arrayed three-gene cluster, which diverged earlier than those of the orchid genera and species. Additionally, pachytene chromosome-based FISH mapping showed that the three groups of CHS genes are localized on three distinct chromosomes. Moreover, an expression analysis of RNA sequencing revealed that the five CHS genes had highly differentiated expression patterns and its expression pattern-based clustering showed high correlations between sequence divergences and chromosomal localizations of the CHS gene family in P. aphrodite. Conclusions: Based on their phylogenetic relationships, expression clustering analysis and chromosomal distributions of the five paralogous PaCHS genes, we proposed that expansion of this gene family in P. aphrodite occurred through segmental duplications, followed by tandem duplications. These findings provide information for further studies of CHS functions and regulations, and shed light on the divergence of an important gene family in orchids.


Assuntos
Aciltransferases/genética , Duplicação Cromossômica , Evolução Molecular , Orchidaceae/genética , Proteínas de Plantas/genética , Aciltransferases/metabolismo , Família Multigênica , Filogenia , Proteínas de Plantas/metabolismo
20.
Hereditas ; 155: 35, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30459533

RESUMO

Background: Bletilla striata is a well-known traditional Chinese herb with varieties of functions. In China, the natural resources of Bletilla striata have been severely damaged because of the excessive exploitation and destruction of natural habitats. The aim of present study was to provide a reference for fully exploiting and utilizing the germplasm resources of Bletilla striata. Results: The genetic diversity of 50 varieties of Bletilla striata from different area in China was analyzed by SCoT and IRAP molecular marker technique. A total of 209 bands were amplified by 20 groups of SCoT primers, of which 201 (96.17%) were polymorphic, and 47 polymorphic bands (94%) were observed in 50 bands amplified by 8 groups of IRAP primers. The 50 populations of Bletilla striata were divided into two major groups by SCoT and IRAP at the genetic similarity coefficient value of 0.60 and 0.68 individually. The partition of clusters in the unweighted pair group method with arithmetic mean dendrogram and principal coordinate analysis plot based on the SCoT and IRAP markers was similar. Conclusions: Results indicated the abundant genetic diversity of Bletilla striata among different areas. Our results will provide useful information for resource protection.


Assuntos
Variação Genética , Genética Populacional , Orchidaceae/genética , Plantas Medicinais/genética , China , Marcadores Genéticos , Filogenia
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