Complete chloroplast genome of the orchid <i>Cattleya crispata</i> (Orchidaceae:Laeliinae), a Neotropical rupiculous species

Perini, Violeta da Rocha; Leles, Bruno; Furtado, Carolina; Prosdocimi, Francisco

doi:10.3109/19401736.2014.1003850

Cited by 12 publications

(5 citation statements)

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“…For examples, extensive gene losses have been reported in several independent mycoheterotrophic orchid lineages-i.e., Aphyllorchis (Feng et al, 2016), Cyrtosia (Kim et al, 2019), Epipogium (Schelkunov et al, 2015), Gastrodia (Yuan et al, 2018), Hexalectris (Barrett and Kennedy, 2018) and Rhizanthella (Delannoy et al, 2011). In addition, ndh deletion and pseudogenization are assumed to be phenomena that occur independently in many orchid lineages such as Apostasia (Lin et al, 2017;Niu et al, 2017a), Calypso , Cattleya (da Rocha Perini et al, 2016), Cephalanthera (Feng et al, 2016), Cremastra (Dong et al, 2018), Cymbidium (Yang et al, 2013;Kim et al, 2018;Wang et al, 2018), Dendrobium (Niu et al, 2017b), Epipactis (Dong et al, 2018), Eulophia (Huo et al, 2017), Holcoglossum (Li et al, 2019), Limodorum (Lallemand et al, 2019), Liparis (Krawczyk et al, 2018), Neuwiedia (Niu et al, 2017a), Oncidium (Wu et al, 2010;Kim et al, 2015a), Paphiopedilum (Niu et al, 2017b;Hou et al, 2018), Phalaenopsis (Chang et al, 2006), Phragmipedium (Kim et al, 2015a), Platanthera (Dong et al, 2018), Vanilla (Lin et al, 2015), and Vanda (Li et al, 2019). On the other hand, full ndh genes have been reported in members of Anoectochilus (Yu et al, 2016), Calanthe (Dong et al, 2018), Cypripedium (Kim et al, 2015b;Lin et al, 2015), Habenaria…”

Section: Introductionmentioning

confidence: 99%

Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences

Kim

Cheon

et al. 2020

Front. Plant Sci.

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In order to understand the evolution of the orchid plastome, we annotated and compared 124 complete plastomes of Orchidaceae representing all the major lineages in their structures, gene contents, gene rearrangements, and IR contractions/expansions. Fortytwo of these plastomes were generated from the corresponding author's laboratory, and 24 plastomes-including nine genera (Amitostigma, Bulbophyllum, Dactylorhiza, Dipodium, Galearis, Gymnadenia, Hetaeria, Oreorchis, and Sedirea)-are new in this study. All orchid plastomes, except Aphyllorchis montana, Epipogium aphyllum, and Gastrodia elata, have a quadripartite structure consisting of a large single copy (LSC), two inverted repeats (IRs), and a small single copy (SSC) region. The IR region was completely lost in the A. montana and G. elata plastomes. The SSC is lost in the E. aphyllum plastome. The smallest plastome size was 19,047 bp, in E. roseum, and the largest plastome size was 178,131 bp, in Cypripedium formosanum. The small plastome sizes are primarily the result of gene losses associated with mycoheterotrophic habitats, while the large plastome sizes are due to the expansion of noncoding regions. The minimal number of common genes among orchid plastomes to maintain minimal plastome activity was 15, including the three subunits of rpl (14, 16, and 36), seven subunits of rps (2, 3, 4, 7, 8, 11, and 14), three subunits of rrn (5, 16, and 23), trnC-GCA, and clpP genes. Three stages of gene loss were observed among the orchid plastomes. The first was ndh gene loss, which is widespread in Apostasioideae, Vanilloideae, Cypripedioideae, and Epidendroideae, but rare in the Orchidoideae. The second stage was the loss of photosynthetic genes (atp, pet, psa, and psb) and rpo gene subunits, which are restricted to Aphyllorchis, Hetaeria, Hexalectris, and some species of Corallorhiza and Neottia. The third stage was gene loss related to prokaryotic gene expression (rpl, rps, trn, and others), which was observed in Epipogium, Gastrodia, Lecanorchis, and Rhizanthella. In addition, an intermediate stage between the second and third stage was observed in Cyrtosia (Vanilloideae). The majority of intron losses are associated with the loss of their corresponding genes. In some orchid taxa, however, introns have been lost in rpl16, rps16, and clpP(2) without their corresponding gene being lost. A total of 104 gene rearrangements were counted when comparing 116 orchid plastomes. Among them, many were concentrated near the IRa/b-SSC junction area. The plastome phylogeny of

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Section: Introductionmentioning

confidence: 99%

Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences

Kim

Cheon

et al. 2020

Front. Plant Sci.

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“…Today, more than 600 land plant species has its plastid genome sequence available in Genbank web page ( www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=2759&opt=plastid ). In this review, we highlight species of high interest to horticulture, as tomato (NC_007898; Daniell et al, 2006 ), potato (NC_008096; Chung et al, 2006 ), lettuce (NC_007578; Timme et al, 2007 ), spinach (NC_002202; Schmitz-Linneweber et al, 2001 ), onion (NC_024813), carrot (NC_008325; Ruhlman et al, 2006 ); ornamental species, as orchids, i.e., Phalaenopsis aphrodite (NC_007499; Chang et al, 2006 ), Cymbidium aloifolium (NC_021429; Yang et al, 2013 ), and Cattleya crispata (NC_026568; da Rocha Perini et al, 2015 ), Lilium (NC_026787), Magnolia kwangsiensis (NC_015892; Kuang et al, 2011 ); fruit crops, as strawberry (NC_015206; Shulaev et al, 2011 ), peach (NC_014697; Jansen et al, 2011 ), orange (NC_008334; Bausher et al, 2006 ), banana (HF677508; Martin et al, 2013 ); medicinal species, as Camellia grandibracteata (NC_024659; Huang et al, 2014 ), Salvia (NC_020431; Qian et al, 2013 ), Artemisia frigida (NC_020607; Liu et al, 2013 ); and forestry species, as Eucalyptus aromaphloia (NC_022396; Bayly et al, 2013 ), Pinus contorta (NC_011153; Cronn et al, 2008 ), Picea abies (NC_021456; Nystedt et al, 2013 ).…”

Section: Plastid Genome In Horticultural Speciesmentioning

confidence: 99%

Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology

et al. 2015

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During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ∼130 genes in a 100–220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field.

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“…Orchid plastomes show a wide range of gene contents. For example, Cattleya (Epidendreae), Cephalanthera (Neottieae), Cymbidium (Cymbidieae), Kuhlhasseltia (Cranichideae), Neofinetia (Vandeae), and Vanilla (Vanilleae) plastomes do not contain various ndh genes [ 18 , 19 , 20 , 21 , 22 ]. The mycoheterotrophic orchid plastomes that are founded in Corallorhiza (Epidendreae), Cyrtosia (Vanilleae), Epipogium (Nervilieae), Gastrodia (Gastrodieae), Neottia (Neottieae), and Rhizanthella (Diurideae) are smaller in size and have fewer genes than photosynthetic orchids [ 10 , 11 , 15 , 23 , 24 , 25 , 26 , 27 ].…”

Section: Introductionmentioning

confidence: 99%

Evolutionary Patterns of the Chloroplast Genome in Vanilloid Orchids (Vanilloideae, Orchidaceae)

Kim

Cheon

Hong

et al. 2023

IJMS

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The Vanilloideae (vanilloids) is one of five subfamilies of Orchidaceae and is composed of fourteen genera and approximately 245 species. In this study, the six new chloroplast genomes (plastomes) of vanilloids (two Lecanorchis, two Pogonia, and two Vanilla species) were decoded, and then the evolutionary patterns of plastomes were compared to all available vanilloid plastomes. Pogonia japonica has the longest plastome, with 158,200 bp in genome size. In contrast, Lecanorchis japonica has the shortest plastome with 70,498 bp in genome size. The vanilloid plastomes have regular quadripartite structures, but the small single copy (SSC) region was drastically reduced. Two different tribes of Vanilloideae (Pogonieae and Vanilleae) showed different levels of SSC reductions. In addition, various gene losses were observed among the vanilloid plastomes. The photosynthetic vanilloids (Pogonia and Vanilla) showed signs of stage 1 degradation and had lost most of their ndh genes. The other three species (one Cyrotsia and two Lecanorchis), however, had stage 3 or stage 4 degradation and had lost almost all the genes in their plastomes, except for some housekeeping genes. The Vanilloideae were located between the Apostasioideae and Cypripedioideae in the maximum likelihood tree. A total of ten rearrangements were found among ten Vanilloideae plastomes when compared to the basal Apostasioideae plastomes. The four sub-regions of the single copy (SC) region shifted into an inverted repeat (IR) region, and the other four sub-regions of the IR region shifted into the SC regions. Both the synonymous (dS) and nonsynonymous (dN) substitution rates of IR in-cooperated SC sub-regions were decelerated, while the substitution rates of SC in-cooperated IR sub-regions were accelerated. A total of 20 protein-coding genes remained in mycoheterotrophic vanilloids. Almost all these protein genes show accelerated base substitution rates compared to the photosynthetic vanilloids. Two of the twenty genes in the mycoheterotrophic species faced strong “relaxed selection” pressure (p-value < 0.05).

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Complete chloroplast genome of the orchid Cattleya crispata (Orchidaceae:Laeliinae), a Neotropical rupiculous species

Cited by 12 publications

References 12 publications

Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences

Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences

Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology

Evolutionary Patterns of the Chloroplast Genome in Vanilloid Orchids (Vanilloideae, Orchidaceae)

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