Complete Chloroplast Genome of Fokienia hodginsii (Dunn) Henry et Thomas: Insights into Repeat Regions Variation and Phylogenetic Relationships in Cupressophyta

Mingyue Zang,Yuhao Weng,Jinhui Chen,Renhua Zheng,Jisen Shi,Qian Su,Lu Lu,Daiquan Ye,Tielong Cheng,Xueyan Zheng

doi:10.3390/f10070528

Mingyue Zang, Yuhao Weng + Show 8 more

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https://doi.org/10.3390/f10070528

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Journal: Forests	Publication Date: Jun 26, 2019
Citations: 6	License type: CC BY 4.0

Affiliation: Nanjing Forestry University, Jiangxi Academy of Forestry

Abstract

Fokienia hodginsii (Dunn) Henry et Thomas is a relic gymnosperm with broad application value. It is a fit candidate when choosing species for the construction of artificial forests. We determined the complete chloroplast genome sequence of F. hodginsii, which is 129,534 bp in length and encodes 83 protein genes, 33 transfer RNA (tRNA) genes, as well as four ribosomal RNA genes. The GC content of the complete sequence and protein coding regions is 34.8% and 36.2%, respectively. We identified 11 tandem repeats, 11 forward repeats, and three palindromic repeats and classified them by size. Following our microsatellite analysis, a total number of 73 simple sequence repeats were detected, preferentially within the intergenic space. Being a member of Cupressophyta, F. hodginsii owns several common characters; the trnR-CCG gene has been deleted, while the trnI-CAU and trnQ-UUG genes have been duplicated. Moreover, the accD gene, which encodes acetyl-CoA carboxylase, contains 771 codons in F. hodginsii, similar to Cryptomeria japonica (L. F.) D. Don, further supporting the diversity of accD and its size expansion in Cupressophyta. Concerning the loss of inverted repeat (IR) regions, the 86-bp sequence with the duplicated trnI-CAU gene is inferred to be the footprint of IR contraction. Phylogenetically, F. hodginsii is placed as a sister taxon to Chamaecyparis hodginsii (Dunn) Rushforth. This work offers meaningful guidance as well as reference value to the breeding research and improvement of F. hodginsii. Moreover, it gives us a better understanding of the genomic structure and evolutionary history of gymnosperms, especially coniferales.

Highlights

Fokienia hodginsii (Dunn) Henry et Thomas, a relic gymnosperm from the tertiary period, is the only species of Fokienia Henry et Thomas
We determined the full length of the F. hodginsii cp genome (MK890147) to be 129,534 bp (Figure 1)
The complete cp DNA does not share the common quadripartite structure, which contains a pair of inverted repeat (IR) separated by the large single-copy region (LSC) and small single-copy region (SSC) regions

Summary

Introduction

Fokienia hodginsii (Dunn) Henry et Thomas, a relic gymnosperm from the tertiary period, is the only species of Fokienia Henry et Thomas. This threatened species was listed as vulnerable by the International Union for Conservation of Nature (IUCN) and was under the second class state protection recorded by China Species Red List. Forests 2019, 10, 528 subtropical zones, especially at altitudes from 500 to 1800 m above sea level; this species is naturally distributed in southern Chinese provinces like Fujian, Jiangxi, and Guangdong [1,2]. Gymnosperms, with typical exposed ovules, are divided into five groups: the cycads, Ginkgo, Pinaceae, gnetophytes, and Cupressophyta.

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