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Main conclusion <p>Genomic characterization of <i>R. palembanica</i>'s chloroplast reveals key markers and evolutionary links, advancing molecular resources for conserving threatened Dipterocarpaceae species.</p> Abstract <p>The Dipterocarps have an important ecological and economical role and are a major component of tropical forests in Southeast Asia. They are well-known as sources both for their timber and non-timber products. Genome references become fundamental resource and can be used as best practice in achieving biodiversity conservation efforts and goals. This study aims to characterize chloroplast genome of <i>Rubroshorea palembanica</i> compared to other Dipterocarpaceae species, construct phylogenetic relationship, and identify potential molecular markers for inferring genetic diversity and phylogenetic analysis. The chloroplast genome of <i>R. palembanica</i> was 150,558&#xa0;bp in size. A typical quadripartite structure occurred, comprising a large single-copy region of 83,511&#xa0;bp, a small single-copy region of 19,839 bp, and a pair of inverted regions of 23,604&#xa0;bp each. There were 128 unique genes, including 84 protein coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. A total of 159 simple sequence repeats and 190 long repeats were identified. Eight highly variable loci were identified and they have the potential for genetic markers. Those genes were <i>rps</i>16<i>–trn</i>Q, <i>trn</i>Q<i>–psb</i>K, <i>psb</i>K<i>–psb</i>I, <i>psb</i>I<i>–trn</i>S, <i>psb</i>B<i>–psb</i>T, <i>psb</i>T<i>–psb</i>N, <i>psb</i>N<i>–psb</i>H, and <i>psb</i>H<i>–pet</i>B. The phylogenetic position of <i>R. palembanica</i> was nested in the <i>Rubroshorea</i> clade, which was more closely related to <i>R. macrophylla</i>. These findings provide genomic information that could support conservation studies.</p>

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Characterization and comparison of the complete chloroplast genome of Rubroshorea palembanica: an endemic and threatened dipterocarp

  • 期刊论文

  • 发表日期：

    2026年4月8日

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  • Siti R. Ariati,
  • Arief Priyadi,
  • Fitri Indriani,
  • Risha A. Pratiwi,
  • Aditya Nugroho,
  • Muhammad R. Hariri,
  • Irfan Martiansyah,
  • Didik Widyatmoko

摘要

Main conclusion

Genomic characterization of R. palembanica's chloroplast reveals key markers and evolutionary links, advancing molecular resources for conserving threatened Dipterocarpaceae species.

Abstract

The Dipterocarps have an important ecological and economical role and are a major component of tropical forests in Southeast Asia. They are well-known as sources both for their timber and non-timber products. Genome references become fundamental resource and can be used as best practice in achieving biodiversity conservation efforts and goals. This study aims to characterize chloroplast genome of Rubroshorea palembanica compared to other Dipterocarpaceae species, construct phylogenetic relationship, and identify potential molecular markers for inferring genetic diversity and phylogenetic analysis. The chloroplast genome of R. palembanica was 150,558 bp in size. A typical quadripartite structure occurred, comprising a large single-copy region of 83,511 bp, a small single-copy region of 19,839 bp, and a pair of inverted regions of 23,604 bp each. There were 128 unique genes, including 84 protein coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. A total of 159 simple sequence repeats and 190 long repeats were identified. Eight highly variable loci were identified and they have the potential for genetic markers. Those genes were rps16–trnQ, trnQ–psbK, psbK–psbI, psbI–trnS, psbB–psbT, psbT–psbN, psbN–psbH, and psbH–petB. The phylogenetic position of R. palembanica was nested in the Rubroshorea clade, which was more closely related to R. macrophylla. These findings provide genomic information that could support conservation studies.