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<p>The genus <i>Pithecellobium</i> Mart. (Caesalpinioideae, Fabaceae) plays vital ecological roles, including nitrogen fixation and habitat stabilization, and holds significant medicinal and economic values. However, its genetic diversity and evolutionary relationships remain poorly understood. This study presents the first complete chloroplast (cp.) genome of <i>Pithecellobium dulce</i> (Roxb.) Benth., a widely distributed tropical tree. The complete cp. genome was assembled <i>de novo</i> using NOVOPlasty and annotated with GeSeq and Geneious Prime. Repeat elements and codon usage analyses were analyzed using REPuter, Phobos, and Geneious Prime. Comparative genomic analyses included structural comparisons, IR expansion/contraction, and nucleotide divergence. Phylogenetic relationships were inferred from protein-coding genes using IQ-TREE and MrBayes, with divergence times estimated via BEAST2. The cp. genome of <i>P. dulce</i> was 179,483&#xa0;bp long, exhibiting a typical quadripartite structure with a large single-copy (LSC) region of 91,513&#xa0;bp, a small single-copy (SSC) region of 4,560&#xa0;bp, and two inverted repeat regions (IRs) of 41,705&#xa0;bp each. It encoded 142 genes, including 97 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analysis revealed a conserved genomic structure within the Pithecellobium subclade, with notable IR expansion into SSC and LSC regions. Phylogenetic analysis placed <i>P. dulce</i> within the Pithecellobium subclade, closely related to <i>Ebenopsis ebano</i> Britton &amp; Rose and <i>Havardia acatlensis</i> (Benth.) Britton &amp; Rose. Divergence time estimates suggest that Pithecellobium subclade diverged in the late Miocene (~ 29.96&#xa0;Ma), with <i>P. dulce</i> and <i>E. ebano</i> separating around 16.79&#xa0;Ma. This study provides an essential genomic resource for resolving phylogenetic relationships and advancing taxonomic research in Caesalpinioideae.</p>

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Comparative chloroplast genomic analysis of Pithecellobium dulce (Roxb.) Benth 1844 and related species within Caesalpinioideae

  • 期刊论文

  • 发表日期：

    2025年5月6日

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  • Hoang Danh Nguyen,
  • Ngoc Han Vu,
  • Hoang Dang Khoa Do,
  • Minh Thiet Vu

摘要

The genus Pithecellobium Mart. (Caesalpinioideae, Fabaceae) plays vital ecological roles, including nitrogen fixation and habitat stabilization, and holds significant medicinal and economic values. However, its genetic diversity and evolutionary relationships remain poorly understood. This study presents the first complete chloroplast (cp.) genome of Pithecellobium dulce (Roxb.) Benth., a widely distributed tropical tree. The complete cp. genome was assembled de novo using NOVOPlasty and annotated with GeSeq and Geneious Prime. Repeat elements and codon usage analyses were analyzed using REPuter, Phobos, and Geneious Prime. Comparative genomic analyses included structural comparisons, IR expansion/contraction, and nucleotide divergence. Phylogenetic relationships were inferred from protein-coding genes using IQ-TREE and MrBayes, with divergence times estimated via BEAST2. The cp. genome of P. dulce was 179,483 bp long, exhibiting a typical quadripartite structure with a large single-copy (LSC) region of 91,513 bp, a small single-copy (SSC) region of 4,560 bp, and two inverted repeat regions (IRs) of 41,705 bp each. It encoded 142 genes, including 97 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analysis revealed a conserved genomic structure within the Pithecellobium subclade, with notable IR expansion into SSC and LSC regions. Phylogenetic analysis placed P. dulce within the Pithecellobium subclade, closely related to Ebenopsis ebano Britton & Rose and Havardia acatlensis (Benth.) Britton & Rose. Divergence time estimates suggest that Pithecellobium subclade diverged in the late Miocene (~ 29.96 Ma), with P. dulce and E. ebano separating around 16.79 Ma. This study provides an essential genomic resource for resolving phylogenetic relationships and advancing taxonomic research in Caesalpinioideae.