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High-throughput sequencing uncover Ficus tikoua Bur. chloroplast genome

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Abstract

Ficus tikoua Bur., called “di guo”, is a very important economic plant. However, we know little on its molecular mechanisms for a long time. In this study, three F. tikoua chloroplast genomes were first obtained through Illumina sequencing. The F. tikoua Bur. cp genomes exhibited a typical circular structure, including a pair of inverted repeats, a small single copy sequence, and a long single copy sequence. More than 100 genes and about 70 ncRNAs (rRNAs, tRNAs, snRNA, snoRNA, etc.) were identified in each cp genomes. Some repeats, including DNA element, long terminal repeat, small RNA, simple repeat and low complexity, were examined in the three complete cp genomes. In addition, phylogeny tree from six Ficus. species and five Morus. species in family Moracea were constructed for clarifying taxonomy. This data can help further the understanding of evolution and phylogenetic relationships in F. tikoua Bur.

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Abbreviations

Cp:

Chloroplast genomes

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

CDSs:

Coding sequences

SSR:

Simple sequence repeat

ISSC:

A small single copy sequence

LSC:

A long single copy sequence

IR:

Inverted repeats

snRNA:

Small nuclear RNA

RMB:

Renminbi

Bp:

Base pair

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Acknowledgements

This study was financed by the National Natural Science Foundation of China (No. 30971794), the Science and Technology Foundation of Guizhou Province, China (No. QKHJC[2017]1004), the Training Program for High-level Innovative Talents of Guizhou Province (No. QKHRC[2016]4020), the Program for First-class Discipline Construction in Guizhou Province (No. QJKYF[2017]85), the National Innovation Training Program for Undergraduate (Nos. 2018109760007 and 2018109 760008), the Innovative Training Program for Undergraduate in Guizhou Province (Nos. 2018520777, 2018520778, 2018520831, 20195200341, 20195201373 and 2018520861), educational incubation program of Guiyang university (GYU-KJT[2019]-06, GYU-KJT[2019]-07, Foundation of Guiyang science and technology bureau (GYU-KYZ[2019-2020]PT13-02) and the Project for Major Research by Innovation Group in Guizhou Education Department(No. QJHKY[2018]027).

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  1. Jiyue Wang and Denghong Shi are Co-first author.

Authors and Affiliations

  1. Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guiyang, 550005, China

    Jiyue Wang, Denghong Shi, Yu Bai & Yan Liu

  2. Graduate School, Guiyang University, Guiyang, 550005, China

    Jiyue Wang

  3. School of Biological and Environmental Engineering, Guiyang University, Guiyang, 550005, China

    Denghong Shi, Yu Bai & Yan Liu

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  1. Jiyue Wang
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Correspondence to Jiyue Wang.

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Wang, J., Shi, D., Bai, Y. et al. High-throughput sequencing uncover Ficus tikoua Bur. chloroplast genome. J. Plant Biochem. Biotechnol. 29, 171–182 (2020). https://doi.org/10.1007/s13562-019-00537-9

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