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Characteristics of the Chloroplast Genome of Adinandra bockiana and Comparative Analysis with Species of Pentaphylacaceae Family

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Abstract

Adinandra bockiana E. Pritz. ex Diels is a potential plant of the Adinandra genus that contains bioactive. This study presents the results of assembly and annotation of the chloroplast (cp) genome of A. bockiana, a comparison of it with Adinandra cp genomes of several other species, and proposed candidate DNA barcoding from the cp genome. The A. bockiana cp genome was reconstructed by raw reads from total DNA, assembling reads (each read is 150 bp in length) into contigs, and then the contigs were assembled again to sequence the complete cp genome. The A. bockiana cp genome is 156,284 bp in length and consists of a large single-copy (LSC) region of 85,693 bp, a small single-copy (SSC) region of 18,411 bp, a pair of inverted repeats (IRa and IRb) of 26,090 bp each, 129 functional genes, 51 SSRs, and other 70 repeat structures. The functional genes of the A. bockiana cp genome contain 84 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. A comparative analysis of the A. bockiana cp genome with the rest of the public Adinandra genomes showed that the number of genes and their structure were highly conserved in the surveyed group. Based on complete cp genomes and matK and trnL sequences of some species of the Adinandra and other genera, molecular phylogenetic trees were established which show the genetic relationships of the species belonging to the Pentaphylacaceae family. Among the chloroplast genes of A. bockiana, the matK and trnL genes are better candidates for phylogenetic analysis.

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Funding

This research is funded by Vietnam National Foundation for Science and Technology Development (NAFOSTED) under grant number 106.02-2018.338; Vietnam Ministry of Education and Training under grant number B2022-TNA-43.

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Authors and Affiliations

  1. Thai Nguyen University of Education, Thai Nguyen, 250000, Vietnam

    Nga Thi Thu Nguyen, Hang Thi Thuy Pho, Quan Huu Nguyen, Lan Thi Ngoc Nguyen, Thuong Danh Sy & Mau Hoang Chu

  2. Thai Nguyen University of Medicine and Pharmacy, Thai Nguyen, 250000, Vietnam

    Hang Thi Thuy Pho

  3. Institute of Biotechnology, Vietnam , Academy of Science and Technology, Hanoi, 100000, Vietnam

    Nhung Thi Doan, Huong Mai Pham, Lam Tung Le & Ha Hoang Chu

  4. Institute of Theoretical and Applied Research, Duy Tan University, Hanoi, 100000, Vietnam

    Lien Thi Kim Vu

  5. Faculty of Natural Sciences, Duy Tan University, Da Nang, 550000, Vietnam

    Lien Thi Kim Vu

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  1. Nga Thi Thu Nguyen
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Key Message

• The complete chloroplast genome of Adinandra bockiana was sequenced, and its size is 156,284 bp, including an LSC, SSC, 129 functional genes, 51 SSRs, and 70 repeat structures.

• The phylogenetic reconstruction using comparative analysis with species of the Pentaphylacaceae family and the matK sequence is a better candidate for phylogenetic resolution.

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Nguyen, N.T.T., Pho, H.T.T., Nguyen, Q.H. et al. Characteristics of the Chloroplast Genome of Adinandra bockiana and Comparative Analysis with Species of Pentaphylacaceae Family. Plant Mol Biol Rep 41, 611–621 (2023). https://doi.org/10.1007/s11105-023-01389-3

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