The complete chloroplast genome of the rare and endangered herb Paphiopedilum dianthum (Asparagales: Orchidaceae)

Hou, Na; Wang, Gang; Zhu, Yayan; Wang, Lianhui; Xu, Jiajuan

doi:10.1007/s12686-017-0907-x

Cited by 18 publications

(24 citation statements)

References 11 publications

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“…All the setting of sequence alignment, ML and Bayesian analyses were the same with Kim et al (2015). In the present study, phylogenetic framework of Paphiopedilum as well as Orchidaceae were consistent with all the previous phylogenetic studies (Kim et al 2015;Lin et al 2015;Hou et al 2018).…”

supporting

confidence: 88%

“…Then, second generation sequencing was performed with an Illumina HiSeq 4000 platform at Novogene (http://www.novo gene.com, China). Chloroplast reads were selected out with map function of Geneious R11 (Kearse et al 2012) using published chloroplast genomes of Paphiopedilum as references (Kim et al 2015;Lin et al 2015;Hou et al 2018). Filtered reads were assembled using de novo method implemented in Geneious R11.…”

mentioning

confidence: 99%

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Complete chloroplast genome sequences of an important horticultural orchid: Paphiopedilum hirsutissimum (Orchidaceae)

Zhao

Cheng

et al. 2019

Mitochondrial DNA Part B

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Paphiopedilum hirsutissimum is an important ornamental orchid species with great horticultural value. The whole chloroplast genome was assembled using genome skimming data. The total length of the cp genome is 154,569 bp, comprising a large single-copy (LSC) region of 85198 bp, a small single-copy (SSC) region of 683 bp, and a pair of inverted repeat regions (IRs) of 34,344 bp each. The chloroplast genome consists of 125 functional genes, including 79 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. The systematic position of the species was also inferred based on plastid phylogenomic analyses.

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supporting

confidence: 88%

mentioning

confidence: 99%

Complete chloroplast genome sequences of an important horticultural orchid: Paphiopedilum hirsutissimum (Orchidaceae)

Zhao

Cheng

et al. 2019

Mitochondrial DNA Part B

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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

et al. 2020

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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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“…Among them, 38 genes are involved in photosynthesis, six genes are in substance metabolism, and 29 genes are related with self-replication. Three genes that are ndhA and ndhE are pseudogenized or lost in its cpDNA when compared with that of a closed species, P. dianthum and P. armeniacum (Liu et al 2006;Hou et al 2017 The analyzed species and corresponding Genbank accession numbers are as follows: Apostasia odorata (NC_030722.1), Apostasia wallichii (NC_036260.1), Bletilla ochracea (NC_029483.1), Bletilla striata (NC_028422.1), Cattleya crispata (NC_026568.1), Cattleya liliputana (NC_032083.1), Cymbidium aloifolium (NC_021429.1), Cymbidium ensifolium (NC_028525.1), Cypripedium formosanum(NC_026772.1), Cypripedium macranthos (NC_024421.1), Dendrobium aphyllum (NC_035322.1), Dendrobium chrysanthum (NC_035336.1), Dendrobium crepidatum (NC_035331.1), Epipactis mairei (NC_030705.1), Epipactis veratrifolia (NC_030708.1), Gastrochilus fuscopunctatus (NC_035830.1), Gastrochilus japonicus (NC_035833.1), Goodyera fumata (NC_026773.1), Goodyera procera (NC_029363.1), Habenaria pantlingiana (NC_026775.1), Habenaria radiata (NC_035834.1), Masdevallia coccinea (NC_026541.1), Masdevallia picturata (NC_026777.1), Neofinetia falcata (NC_036372.1), Neofinetia richardsiana (NC_036373.1), Paphiopedilum armeniacum (NC_026779.1), Paphiopedilum niveum (NC_026776.1), Phalaenopsis equestris (NC_017609.1), Phalaenopsis hybrid cultivar (NC_025593.1), Phragmipedium longifolium (NC_028149.1), Pleione bulbocodioides (NC_036342.1), Sobralia callosa (NC_028147.1), Thrixspermum japonicum (NC_035831.1), Vanilla aphylla (NC_035320.1), and Vanilla planifolia (NC_026778.1).…”

Section: Paphiopedilum Concolor; Chloroplast Genome; Microsatellites;mentioning

confidence: 99%

Characterization and SSR identify of the complete chloroplast genome of Paphiopedilum concolor (Orchidaceae)

Hua

Chen

2019

Mitochondrial DNA Part B

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Paphiopedilum concolor (Orchidaceae) is endemic to China with highly ornamental and horticultural value. However, its whole chloroplast (cp) genome has not been reported yet. Here, the first nucleotide sequence of P. concolor was identified using Illumina sequencing technology. The circular genome is 166,744 bp in size and comprises a pair of inverted repeat (IR) regions of 15,694 bp, a large single-copy (LSC) region of 139,351 bp, and a small single-copy (SSC) region of 11,729 bp. The total GC content is 34.6%, whereas the corresponding values of the LSC, SSC, and IR regions are 33.7%, 26.0%, and 41.6%, respectively. The chloroplast genome contains 137 genes, including 91 protein-coding genes, eight ribosomal RNA genes, and 38 transfer RNA genes. Moreover, we identified a total of 129 microsatellites (SSRs) within the P. concolor cp genome. These newly developed genomic resources will greatly important to the further conservation genetic studies of Paphiopedilum species. ARTICLE HISTORY

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The complete chloroplast genome of the rare and endangered herb Paphiopedilum dianthum (Asparagales: Orchidaceae)

Cited by 18 publications

References 11 publications

Complete chloroplast genome sequences of an important horticultural orchid: Paphiopedilum hirsutissimum (Orchidaceae)

Complete chloroplast genome sequences of an important horticultural orchid: Paphiopedilum hirsutissimum (Orchidaceae)

Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences

Characterization and SSR identify of the complete chloroplast genome of Paphiopedilum concolor (Orchidaceae)

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