Supplementary data of chloroplast genome of a centennial olive tree from the Peruvian coast
Data files
Nov 12, 2024 version files 4.94 MB
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README.md
788 B
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Supplementary_Data_1.phy
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Abstract
Olive (Olea europaea Linaeus 1753) is one of the valuable fruit trees and very important edible oil plant in the world. The chloroplast (cp) genome of an olive tree (Olea europaea) from the southern Peruvian arid coast was obtained for the first time. Genomic DNA of high quality was used to generate librarieswith Illumina Hiseq paired-end methods. The cp genome is 155,886 pb in length and contains a large single-copy region (LSC) of 86,610 pb and a small single copy region (SSC) of 17,790 pb separated by two inverted repeat (IR) regions (25,741bp). The cp genome of olive contains 124 genes that consists of 80 protein-coding genes, 36 tRNA, eight rRNA. Phylogenetic analysis showed this olive tree is sister to O. europaea subsp. maroccana (Oleeae tribe). This study presents the first overview of the chloroplast genome organization and phylogenetics of O. europaea, offering valuable insights for genetic and evolutionary research in the genus Olea.
README
We submitted the following:
- Data. Aligned dataset (187,111 bp) used for phylogenetic analysis.
- Supplementary Figure 1. Average depth of coverage.
- Supplementary Figure 2. Cis-splicing genes.
- Supplementary Figure 3. Trans-splicing genes.
Descriptions
To understand the phylogenetic position of Olea europaea, a maximum likelihood (ML) tree of 19 genomes retrieved from GenBank was reconstructed. First, we employed MAFFT v.7.475 to align those genomes. Then, with a GTR + GAMMA model of evolution, we obtained the best-scoring ML tree, considering 1,000 bootstrap (BS) inferences with RAxML v8.2.11. We employed capirona (Calycophyllum spruceanum) cp genome as an outgroup (OK326865). The aligned data that was employed for the phylogenetic analysis consists of 187,111 bp.