Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The plastid genome of Vanillon (Vanilla pompona, Orchidaceae).

ABSTRACT: This study presents the complete sequence of Vanilla pompona chloroplast genome. This 148,009?bp long genome consist of 107 genes out of which 30 of them are tRNA, 4 rRNA. Fairly long inverted repeat regions (IR) and large single-copy (LSC) of length 29,807 and 86,358?bp, respectively, were detected. This means an exceptionally short single-copy (SSC) region with only 2037?bp. This truncation of the SSC is due to multiple translocation of ndh genes to the mitochondrion as in majority of the Orchidaceae and especially in the genus Vanilla. The phylogeny presented here meaningfully places Vanillon within the orchid family.

SUBMITTER: Amiryousefi A

PROVIDER: S-EPMC7800859 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The plastid genome of Vanillon (Vanilla pompona, Orchidaceae).

Amiryousefi Ali A Hyvönen Jaakko J Poczai Péter P

Mitochondrial DNA. Part B, Resources 20170929 2

This study presents the complete sequence of Vanilla pompona chloroplast genome. This 148,009 bp long genome consist of 107 genes out of which 30 of them are tRNA, 4 rRNA. Fairly long inverted repeat regions (IR) and large single-copy (LSC) of length 29,807 and 86,358 bp, respectively, were detected. This means an exceptionally short single-copy (SSC) region with only 2037 bp. This truncation of the SSC is due to multiple translocation of ndh genes to the mitochondrion as in majori ...[more]

PMID: 33473949

Similar Datasets

The complete chloroplast genome of Vanilla shenzhenica (Orchidaceae).

Project description:Vanilla shenzhenica Z.J.Liu & S.C.Chen is a new species of orchid found in Shenzhen, South China for the first time. Here we report the complete chloroplast (cp) genome sequence and the features of V. shenzhenica. Its cp genome sequence was 151,537?bp, including one large single-copy region (LSC, 87,487?bp), one small single-copy region (SSC, 19,172?bp), and two inverted repeat regions (IRs, 22,439?bp). It encoded 123 genes, of which 104 were unique genes (69 protein-coding genes, 31 tRNAs and 4 rRNAs). The phylogenetic relationships show that V. shenzhenica is sister with V. aphylla.

| S-EPMC7706789 | biostudies-literature

Plastid Genome Evolution in the Subtribe Calypsoinae (Epidendroideae, Orchidaceae).

Project description:Calypsoinae is a small subtribe in Orchidaceae (Epidendroideae) characterized by diverse trophic strategies and morphological characters. Calypsoinae includes 13 genera, four of which are leafless and mycoheterotrophic. Mycoheterotrophic species in the leafless genus Corallorhiza are well suited to studies of plastome evolution. However, the lack of plastome sequences for other genera in Calypsoinae limits the scope of comparative and phylogenetic analyses, in particular our understanding of plastome evolution. To understand plastid genome evolution in Calypsoinae, we newly sequenced the plastomes of 12 species in the subtribe, including representatives of three mycoheterotrophic genera as well as five autotrophic genera. We detected two parallel photosynthetic losses in Corallorhiza. Evolutionary analyses indicated that the transition to obligate mycoheterotrophy leads to the relaxation of selection in a highly gene-specific pattern.

| S-EPMC7313661 | biostudies-literature

Complete plastid genome of Dendrobium naungmungense (Orchidaceae).

Project description:Dendrobium is one of the most important genera in Orchidaceae. In this study, we used the next-generation sequencing technology and assembled a complete plastid genome of a recently published new species of Dendrobium, D. naungmungense. The plastome was 151,883 bp in length, containing a large single-copy region (LSC) of 87,189 bp, and a small single-copy region (SSC) of 12,150 bp, and two inverted repeat regions (IR) of 26,272 bp. A total of 123 genes were predicted, including 38 tRNA genes, 8 rRNA genes, and 77 protein-coding genes. Phylogenetic analysis of 44 representative plastome of the genus Dendrobium and outgroup suggested D. naungmungense to be sister to Dendrobium wardianum.

| S-EPMC7707356 | biostudies-literature

Complete plastid genome of Vanda concolor (Orchidaceae, Aeridinae).

Project description:Vanda is one of the five most horticulturally important genera in Orchidaceae. In this study, we assembled the complete plastid genome of an important cultivated species, V. concolor. The plastome was 149,474 bp in length, containing a large single-copy region (LSC) of 85,678 bp, a small single-copy region (SSC) of 12,002 bp, and two inverted repeat regions (IR) of 25,897 bp. A total of 127 genes were predicted, including 38 tRNA, 8 rRNA, and 74 protein-coding genes. Phylogenetic analysis of 21 representative plastome of the subtribe Aeridinae suggested V. concolor to be sister to V. brunnea and that this pair is sister to Neofinetia.

| S-EPMC7707440 | biostudies-literature

Complete plastid genome of Cheirostylis chinensis (Orchidaceae, Goodyerinae).

Project description:The first complete plastid genome of Cheirostylis, Ch. chinensis, was assembled and analyzed in this study. The total genome was 147,218 bp in length, consisting of a large single-copy region (LSC) of 81,081 bp, a small single-copy region (SSC) of 14,769 bp, and two inverted repeat regions (IRA and IRB) of 25,684 bp. The genome contained 131 genes, including 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes and 85 protein-coding genes. Phylogenomic analysis indicated that Ch. chinensis nested within Goodyerinae.

| S-EPMC7720991 | biostudies-literature

The complete plastid genome of Vanda xichangensis (Orchidaceae, Aeridinae).

Project description:The complete plastid genome of Vanda xichangensis was determined and analyzed in this work. The plastome was 146,681?bp in length with 83,920?bp of the large single-copy (LSC) region, 11,751?bp of the small single-copy (SSC) region and 25,505?bp of the inverted repeat (IR) regions. The genome contained 120 genes, 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis suggested V. xichangensis is sister to V. richardsiana plus V. falcata.

| S-EPMC7707680 | biostudies-literature

The complete plastid genome of Thrixspermum tsii (Orchidaceae, Aeridinae).

Project description:The complete plastid genome of Thrixspermum tsii was determined and analyzed in this work. The plastome was 149,689 bp in length with 86,778 bp of the large single-copy (LSC) region, 12,129 bp of the small single-copy (SSC) region and 25,391 bp of the inverted repeat (IR) regions. The genome contained 120 genes, 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of 17 Aeridinae plastomes suggested four groups were divided, and T. tsii was sister to T. japonicum.

| S-EPMC7748503 | biostudies-literature

The complete plastid genome of Holcoglossum singchianum (Orchidaceae, Vandeae).

Project description:The complete plastid genome of Holcoglossum singchianum was determined and analyzed in this work. The plastome was 147,715 bp in length with 84,094 bp of the large single-copy (LSC) region, 12,073 bp of the small single-copy (SSC) region and 25,774 bp of the inverted repeat (IRs) regions. The genome contained 120 genes, 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of 20 Aeridinae plastomes suggested three groups of Holcoglossum were divided, and H. singchianum was sister to H. lingulatum.

| S-EPMC7748776 | biostudies-literature

The complete plastid genome of Thrixspermum centipeda (Orchidaceae, Aeridinae).

Project description:The complete plastid genome of the type species of Thrixspermum, Th. centipeda, was determined and analyzed in this work. The plastome was 147,888 bp in length with 85,899 bp of the large single-copy (LSC) region, 11,055 bp of the small single-copy (SSC) region and 25,467 bp of the invert repeats (IR) regions. The genome contained 120 genes, including 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis divided 18 Aeridinae plastomes into four groups, and Th. centipeda was sister to Th. tsii.

| S-EPMC8008882 | biostudies-literature

Complete plastid genome of Holcoglossum tsii (Orchidaceae, Aeridinae) and phylogenetic analysis.

Project description:The complete plastid genome of Holcoglossum tsii was determined and analyzed in this work. The plastome was 146,897 bp in length with 83,366 bp of the large single-copy (LSC) region, 11,957 bp of the small single-copy (SSC) region, and 25,787 bp of the invert repeats (IR) regions. The genome contained 127 genes, 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis suggested H. tsii is sister to H. rupestre.

| S-EPMC7748626 | biostudies-literature