The complete chloroplast genome of a rare orchid species Liparis loeselii (L.)

Krawczyk, Katarzyna; Wiland-Szymańska, Justyna; Buczkowska, Katarzyna; Drapikowska, Maria; Maślak, Magdalena; Myszczyński, Kamil; Szczecińska, Monika; Ślipiko, Monika; Sawicki, Jakub

doi:10.1007/s12686-017-0809-y

Cited by 9 publications

(8 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The maximum likelihood (ML) tree was implemented by RAxML v 7.2.8 (Stamatakis 2006) with Iris sanguinea (NC_029227) and Narcissus poeticus (NC_039825) as outgroup. The phylogenetic tree indicates that Liparis japonica is sister to Liparis loeselii and the genus Liparis is closely related to Dendrobium as supported by the previous studies (Givnish et al 2015, Krawczyk et al 2018 (Figure 1).…”

supporting

confidence: 77%

The complete chloroplast genome sequence of Liparis japonica (Orchidaceae)

Yang

Liu

2019

Mitochondrial DNA Part B

View full text Add to dashboard Cite

The Orchidaceae contains numerous species with great ecological and economic values. In this study, the complete chloroplast genome of Liparis japonica was presented by next-generation sequencing technologies. The cpDNA is 152,084 bp in length with a large single copy region (LSC) of 85,398 bp, a small single copy region (SSC) of 14,774 bp, and a pair of inverted repeat regions (IRs) of 25,956 bp. It contains 132 genes, including 79 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 7 pseudogenes. The overall GC content is 37.0%, while the corresponding values in the LSC, SSC, and IR region are 34.3, 30.0, 43.5%, respectively. The phylogenetic analysis shows that Liparis japonica is sister to Liparis loeselii and the genus Liparis is closely related to Dendrobium.

show abstract

supporting

confidence: 77%

The complete chloroplast genome sequence of Liparis japonica (Orchidaceae)

Yang

Liu

2019

Mitochondrial DNA Part B

View full text Add to dashboard Cite

show abstract

“…The ML tree, reconstructed using RAxML v8.2.10 (Stamatakis 2014 ) with 1000 bootstraps under GTR model, showed that both of L. nervosa and L. loeselii were phylogenetically closer to Dendrobium officinale than others ( Figure 1 ), which was consistent with the prior phylogenetic study (Krawczyk et al. 2018 ; Li et al. 2019 ; Zhang et al.…”

supporting

confidence: 85%

“…For phylogenetic maximum-likelihood (ML) analysis, multiple alignment was carried using MAFFT v7.2 with 15 published cp genomes downloaded from Genbank (Katoh and Standley 2013). The ML tree, reconstructed using RAxML v8.2.10 (Stamatakis 2014) with 1000 bootstraps under GTR model, showed that both of L. nervosa and L. loeselii were phylogenetically closer to Dendrobium officinale than others (Figure 1), which was consistent with the prior phylogenetic study (Krawczyk et al 2018;Li et al 2019;Zhang et al 2019).…”

supporting

confidence: 78%

See 1 more Smart Citation

The first complete chloroplast genome of Liparis nervosa and its phylogenetic position within Orchidaceae

Wang¹,

Guo

Peng³

et al. 2019

Mitochondrial DNA Part B

View full text Add to dashboard Cite

Liparis nervosa is a plant of the family Orchidaceae and mainly distributed in subtropical and tropical regions of the world. In Chinese traditional medicine, it has been used for the treatment of hemostasis, carbuncle, and furuncle for centuries. The chloroplast (cp) genome of L. nervosa, sequenced based on next-generation platform (NEOSAT), is 157,274 bp in size. The cp genome encodes 130 genes, including eight rRNA genes, 85 protein-coding genes (PCGs), and 37 tRNA genes. Phylogenetic relationship analysis based on complete cp genome sequences exhibited that both of L. nervosa and L. loeselii were phylogenetically closer to Dendrobium officinale.

show abstract

“…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

View full text Add to dashboard Cite

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

show abstract

The complete chloroplast genome of a rare orchid species Liparis loeselii (L.)

Cited by 9 publications

References 8 publications

The complete chloroplast genome sequence of Liparis japonica (Orchidaceae)

The complete chloroplast genome sequence of Liparis japonica (Orchidaceae)

The first complete chloroplast genome of Liparis nervosa and its phylogenetic position within Orchidaceae

Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences

Contact Info

Product

Resources

About