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ORIGINAL RESEARCH article

Front. Ecol. Evol.
Sec. Evolutionary and Population Genetics
Volume 12 - 2024 | doi: 10.3389/fevo.2024.1416876

The Complete Chloroplast Genome of Psydrax latifolia: Evolutionary Dynamics, Comparative Genomics and Phylogeny

Provisionally accepted
Fatmah A. Safhi Fatmah A. Safhi 1Areej S. Jalal Areej S. Jalal 1*Rana Alshegaihi Rana Alshegaihi 2Rahma Alshamrani Rahma Alshamrani 3Amnah Alamri Amnah Alamri 3WESSAM FELEMBAN WESSAM FELEMBAN 3Amani O. Abuzaid Amani O. Abuzaid 3Mohammed A. Hussein Mohammed A. Hussein 4Nora M. Al Aboud Nora M. Al Aboud 5Mahmoud Magdy Mahmoud Magdy 6Diaa Abd El Moneim Diaa Abd El Moneim 7
  • 1 Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
  • 2 Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
  • 3 Department of Biological Sciences, King Abdulaziz University, Jeddah, Makkah, Saudi Arabia
  • 4 (Genetic Branch), Department of Botany, Faculty of Science, Suez Canal University, Ismailia, Ismailia, Egypt
  • 5 Department of Biology, College of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
  • 6 Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Beni Suef, Egypt
  • 7 (Genetic Branch), Department of Plant Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt

The final, formatted version of the article will be published soon.

    This study introduces the inaugural complete plastome (cpDNA) sequence of Psydrax latifolia. Classified within the Rubiaceae family, this flowering plant comprises small trees or smooth shrubs, occasionally also featuring a few lianas. Collected near the Red Sea coast in Jazan province, Saudi Arabia, this specimen thrives in the paleotropics areas within the Fifa Mountains. The plastome of P. latifolia was characterized and reconstructed using whole-genome next-generation sequencing (NGS). It was compared with other published plastomes from species within the same Rubiaceae family. The P. latifolia plastome size was 153,242 base pairs (bp), containing a single large copy (LSC) consisting of 83,603 bp, a small single copy (SSC) region of 18,115 bp, and separated by a pair of inverted repeats regions (IRs) containing 25,762 bp each. Psydrax latifolia consisted of 87 protein-coding genes, eight rRNA genes, 33 tRNA genes, and 37.30% overall GC content. In addition, a comparison between 16 Rubiaceae family species and P. latifolia plastome features was conducted. In P. latifolia, RSCU (Relative Synonymous Codon Usage) varies according to the region, with the plastome of the protein-coding region being more conservative than the intergenic spacer. Based on the complete plastome of Psydrax latifolia, a member of the Ixoroideae subfamily, was sequenced and analyzed to elucidate its evolutionary dynamics and phylogenetic relationships within the Rubiaceae family. Comparative analyses with 16 sequenced Rubiaceae species were conducted to highlight genomic features and evolutionary patterns. This study provided insight into the plastome of P. latifolia and its phylogenetic relationships.

    Keywords: Psydrax latifolia, Wild plants, applied genomics, phylogenomic analysis, Plastome

    Received: 13 Apr 2024; Accepted: 02 Sep 2024.

    Copyright: © 2024 Safhi, Jalal, Alshegaihi, Alshamrani, Alamri, FELEMBAN, Abuzaid, Hussein, Al Aboud, Magdy and Abd El Moneim. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Areej S. Jalal, Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia

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