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Comparative and phylogenetic analysis of the complete chloroplast genomes of ten Pittosporum species from East Asia

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Abstract

Pittosporum (Pittosporaceae) is famous as the ornamental and medical values, which is distributed tropical and subtropical regions of Eastern Hemisphere. The few phylogenetic studies have included samples from the Pacific Island, but the phylogenetic relationships of Asian species has not been studied. Here, the complete chloroplast (cp) genomes of ten Pittosporum species from East Asia were first sequenced and compared with those of the published species of this genus. Our results indicated that cp genomes of these species had a typical and conserved quadripartite structure. 131 genes were identical in order and orientation and no changes of inverted repeat (IR) occurred. However, the comparative analysis of cp genomes suggested that sequence divergence mainly appeared in non-coding or intergenic regions, in which several divergence hotspots were identified. By contrast, protein-coding genes showed the lowest variance under strong purifying selection. Phylogenetic analysis based on the cp genome sequences showed that the tested Pittosporum species were clustered into two major clades, in which the Asian species formed Clade I and the remaining species from Australia and New Zealand formed Clade II with high support values, which was consistent with the results of ITS data with low support values. These results suggested that cp genome is a robust phylogenetic indicator for deep nodes in the phylogeny of Pittosporum. Meanwhile, these results will provide the valuable information to better understand the phylogeny and biogeography of Pittosporum.

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Data availability

The data that support the findings of this study are openly available in the Science Data Bank at https://doi.org/https://doi.org/10.57760/sciencedb.08615 [https://doi.org/10.57760/sciencedb.08615].

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Acknowledgements

We thank Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences for providing the samples.

Funding

This research was funded by the National Natural Science Foundation of China, grant number 31860052, Science and Technology Program of Liupanshui, grant number 52020-2020-PT-20 and Program for Training Innovation and Entrepreneurship of University Graduates of Liupanshui Normal University, grant number 2021cxcy101.

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  1. School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, 553004, China

    Shu-Dong Zhang, Li-Zhen Ling & Qi-Hui Zhang

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  1. Shu-Dong Zhang
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  2. Li-Zhen Ling
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Contributions

L.Z. L conceived and designed the study. S.D. Z, Q.H. Z and L.Z. L performed the experiments, analyzed the data and wrote the manuscript. L.Z. L revised the manuscript.

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Correspondence to Li-Zhen Ling.

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Zhang, SD., Ling, LZ. & Zhang, QH. Comparative and phylogenetic analysis of the complete chloroplast genomes of ten Pittosporum species from East Asia. Funct Integr Genomics 24, 64 (2024). https://doi.org/10.1007/s10142-024-01344-9

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