Next-generation sequencing yields the complete chloroplast genome of <i>C. goeringii</i> acc. smg222 and phylogenetic analysis

Wang, Heng; Park, So‐Yeon; Lee, Ah-Rim; Jang, Seong-Ho; Im, Da-Eun; Jun, Tae-Hwan; Lee, Joohyun; Chung, Jong‐Wook; Ham, Tae-Ho; Kwon, Soon Jae

doi:10.1080/23802359.2018.1437812

Cited by 7 publications

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“…The complete chloroplast genome sequence of C. goeringii acc. smg222 was 37.1% overall GC content (Wang et al 2018), similar to those of other Cymbidium species. These indicates that the wholegenome sequencing approach for the chloroplast of C. goeringii acc.…”

Section: Chloroplast Genome Sequencingsupporting

confidence: 64%

“…The 70 protein-coding, 30 transfer RNA, and 4 ribosomal RNA genes were composed as 104 unique genes in the C. goeringii acc. smg222 chloroplast genome (Wang et al 2018). Among the 70 protein-coding genes, 21 ribosomal subunit genes consist of 12 small subunits and 9 large subunits and DNA-directed RNA polymerase genes were 4.…”

Section: Features Of the C Goeringii Acc Smg222 Chloroplast Genomementioning

confidence: 99%

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Analysis of complete chloroplast genome sequence of Korean landrace Cymbidium goeringii

et al. 2020

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The complete chloroplast genome sequence of Korean Cymbidium goeringii acc. smg222 was analyzed. Based on a comparison with Chinese C. goeringii, losses of nine ndh subunits (ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhH, ndhJ, and ndhK), three protein-coding genes (ycf 1-like, ycf 15, and ycf 68), six transfer RNAs, and one conserved open reading frame (orf 42). In addition, 219 InDels (insertion or deletion) and 171 simple sequence repeats were observed. Twenty-Five of which InDel markers have been evaluated, that useful for distinguishing Korean and Chinese Cymbidium associations based on the polymorphisms of chloroplast genomes between Korean Cymbidium goeringii acc. smg222 and Chinese C. goeringii and evaluation of genetic diversity. Finally, the phylogenetic relationships of the 39 Korean and 22 Chinese species was constructed based on the five InDel markers of them and obtained high support, indicating that our data may be useful in resolving relationships in this genus. The information about chloroplast DNA structure and gene variants of C. goeringii acc. smg222 chloroplast genome will provide sufficient phylogenetic information for resolving evolutionary relationships. The molecular markers developed in here will contribute to further research of Cymbidium species and conservation of endemic Cymbidium species.

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Section: Chloroplast Genome Sequencingsupporting

confidence: 64%

Section: Features Of the C Goeringii Acc Smg222 Chloroplast Genomementioning

confidence: 99%

Analysis of complete chloroplast genome sequence of Korean landrace Cymbidium goeringii

et al. 2020

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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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“…A complete cp genome is a valuable resource of information for studying plant taxonomy, phylogenetic reconstruction, and historical biogeographic inference. Next-generation sequencing (NGS) technologies have enabled a rapid expansion in the database of whole cp genomes [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

Liu

Kong

Zhou

et al. 2018

IJMS

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The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted. The whole cp genome of C. chuniana was found to be 158,433 bp long with a total of 114 genes, 81 of which code for proteins. Nucleotide substitutions and length variation are present, particularly at the boundaries among large single copy (LSC), inverted repeat (IR) and small single copy (SSC) regions. Nucleotide diversity among all species was estimated to be 0.03, the average dn/ds ratio 0.3177, and the average K2P value 0.0372. Ninety-one SSRs were identified in C. chuniana, with the highest proportion in the LSC region. Ninety-seven species from the old Caesalpinioideae were selected for phylogenetic reconstruction, the analysis of which strongly supports the monophyly of Cercidoideae based on the new classification of the Fabaceae. Our study provides genomic information for further phylogenetic reconstruction and biogeographic inference of Cercis and other legume species.

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Next-generation sequencing yields the complete chloroplast genome of C. goeringii acc. smg222 and phylogenetic analysis

Abstract: View related articles View Crossmark data Citing articles: 4 View citing articles MITOGENOME ANNOUNCEMENT Next-generation sequencing yields the complete chloroplast genome of C. goeringii acc. smg222 and phylogenetic analysis

Cited by 7 publications

References 8 publications

Analysis of complete chloroplast genome sequence of Korean landrace Cymbidium goeringii

Analysis of complete chloroplast genome sequence of Korean landrace Cymbidium goeringii

Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

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