Dataset Information

Characterization of the complete plastome of Ophrys aveyronensis, a Euro-Mediterranean orchid with an intriguing disjunct geographic distribution.

ABSTRACT: Ophrys aveyronensis is an orchid with disjunct geographic distribution. For biogeographic and conservation purpose, we sequenced its complete plastome using Illumina data. The complete plastome is 146,816?bp in length, consisting of a pair of inverted repeats (IRs) of 25,006?bp, a large single-copy (LSC) region and a small single-copy region (SSC) of 80,495 and 16,309?bp, respectively. It was found to contain 133 genes, including 86 protein-coding genes, up to 39 trRNA genes and 8 rRNA genes. The overall GC content of the plastid genome is 36.9%. Phylogenetic inference confirms that O. aveyronensis is very close to O. sphegodes.

SUBMITTER: Bertrand JAM

PROVIDER: S-EPMC7710315 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Characterization of the complete plastome of <i>Ophrys aveyronensis</i>, a Euro-Mediterranean orchid with an intriguing disjunct geographic distribution.

Bertrand Joris A M JAM Gibert Anaïs A Llauro Christel C Panaud Olivier O

Mitochondrial DNA. Part B, Resources 20190926 2

<i>Ophrys aveyronensis</i> is an orchid with disjunct geographic distribution. For biogeographic and conservation purpose, we sequenced its complete plastome using Illumina data. The complete plastome is 146,816 bp in length, consisting of a pair of inverted repeats (IRs) of 25,006 bp, a large single-copy (LSC) region and a small single-copy region (SSC) of 80,495 and 16,309 bp, respectively. It was found to contain 133 genes, including 86 protein-coding genes, up to 39 trRNA genes and 8 rRNA ge ...[more]

PMID: 33365944

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Project description:Proteomics data from a combind transcriptome/proteome study of three sexually deceptive orchids of the genus Ophrys. Data are from labella of mature, unpollinated flowers of (1) Ophrys exaltata subsp. archipelagi, (2) O. sphegodes, and (3) O. garganica. Proteomics data were searched against SwissProt and TAIR databases and further against organism-specific databases obtained from transcriptome sequencing (454, Sanger ESTs and Solexa data). Thirteen trypsinised gel slices per sample were subjected to electrospray ionisation-based LC-MS/MS analysis with a 2D linear ion trap Finnigan LTQ (Thermo Electron Corporation) equipped with an Ultimate Nano HPLC System (Dionex Corporation). Mass spectra were searched against SwissProt and Arabidopsis TAIR9 protein databases to identify peptides. Additionally, spectra were searched against protein databases created from the Ophrys reference transcriptome obtained in this study. Stringent criteria were used for the assignment of spectra to peptides (95% peptide identification probability) in Scaffold 3.3 (Proteome Software Inc., USA). In order to maximise the utility of proteomics data for uncovering proteins predicted by the orchid transcriptome, a minimum of one unique peptide was used for protein identification, while using two different stringency levels for the probabilistic assignment of peptides to proteins (99% for highest quality, HQ; 90% to maximise protein discovery, PD, in the absence of a fully sequenced genome). Concerning the sequencing and transcriptomics results: Three normalised cDNA libraries were constructed from three different Ophrys species, O. exaltata, O. garganica, and O. sphegodes. These libraries were 454 pyrosequenced and all the high quality reads generated in this study are available in the Sequence Read Archive (SRA) of the National Centre for Biotechnology Information (NCBI) with the accession number SRA060767. Additional sequencing of O. sphegodes flower labella yielded 1.7 Mbp of Sanger (dbEST library LIBEST_028084; dbEST IDs 77978749-77979571; GenBank accessions JZ163765-JZ164587) and 2.5 Gbp of Illumina Solexa (SRA060767) data.

Dataset Information

Characterization of the complete plastome of Ophrys aveyronensis, a Euro-Mediterranean orchid with an intriguing disjunct geographic distribution.

Publications

Characterization of the complete plastome of <i>Ophrys aveyronensis</i>, a Euro-Mediterranean orchid with an intriguing disjunct geographic distribution.

Similar Datasets

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