Characterization of the complete plastid genome of an endangered species Fortunearia sinensis (Hamamelidaceae)

Abstract

Fortunearia sinensis Rehder & E.H.Wilson, the only species of monotypic genus Fortunearia (Hamamelidaceae), is a native rare and vulnerable deciduous tree in China. In this study, the complete plastid genome of F. sinensis was determined using the Illumina paired-end sequencing data. The complete plastid genome of F. sinensis is 1,59,441 bp in length, consisting of a pair of inverted repeats (IR) regions (26,268 bp), a large-single copy (LSC) region (88,124 bp), and a small-single copy (SSC) region (18,781 bp). The plastid genome encodes 112 unique genes, including 80 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. The phylogenetic analysis demonstrates a close relationship between F. sinensis and Sinowilsonia henryi.

Keywords:

• Fortunearia sinensis
• plastome
• Illumina sequencing
• phylogenetic analysis

Fortunearia sinensis Rehder & E.H. Wilson is the only species of the monotypic genus Fortunearia in Hamamelidaceae. This species is an endemic medicinal plant in China, since its leaves contain bergenin, fortunearioside, and other medicinal ingredients (Wang 1996). In addition, F. sinensis is economically important because of its high oil content in seeds (Jia and Zhou 1987). It has been assessed as a vulnerable species in China (Qin et al. 2017). In this study, we characterized the complete plastid genome sequence of F. sinensis based on Illumina paired-end sequencing for further genetic studies, conservation, and utilization of the endangered and rare species.

Fresh leaves of F. sinensis were collected from Wuhan Botanical Garden and dried with silica gel. The voucher specimen (voucher number: wh271) was deposited in the Herbarium of South China Botanical Garden (IBSC). Total genomic DNA was extracted using the modified CTAB method (Doyle and Doyle 1987). The prepared Illumina paired-end library with an average insert size of 270 bp was sequenced on a Hiseq X Ten platform. After quality filtering and trimming, c. 3.0 Gb clean data was assembled with a reference plastid genome of Sinowilsonia henryi Hemsl. (GenBank accession number: NC_036069) using NOVOPlasty (Dierckxsens et al. 2017). We remapped the clean reads to the resulting circular sequence in BWA version 0.7.17 (Li 2013), and manually identified and fixed single nucleotide and small structural errors using Geneious version R11.1.5 (Biomatters Ltd., Auckland, New Zealand). The annotation of the plastome was performed through the online programme GeSeq – Annotation of organellar genomes (Tillich et al. 2017) with necessary manual adjustment in Geneious.

The plastome of F. sinensis (GenBank accession number MK533616) is 159,441 bp in length. The genome shows a typical quadripartite structure, containing two copies of inverted repeat (IR) regions (26,268 bp), a large-single copy (LSC) region (88,124 bp), and a small-single copy (SSC) region (18,781 bp). Its overall GC content is 38.1%, while the corresponding values of the LSC, SSC, and IR regions are 36.3, 32.9, and 43.1%, respectively. A total of 112 unique genes were annotated, containing 80 protein-coding genes, 28 tRNA genes, and 4 rRNA genes (Table 1).

Table 1. List of 112 unique genes in the plastome of Fortunearia sinensis.

Category	Groups of genes	Names of genes
Protein synthesis and DNA replication	Transfer RNAs	trnA-UGC^a	trnC-ACA^a	trnC-GCA	trnD-GUC
		trnE-UUC^a	trnF-GAA	trnfM-CAU	trnG-GCC
–	–	trnH-GUG	trnK-UUU^a	trnL-UAA^a	trnL-UAG
–	–	trnL-CAA	trnM-CAU	trnN-GUU	trnP-UGG
–	–	trnQ-UUG	trnR-ACG	trnR-UCU	trnS-CGA^a
–	–	trnS-GCU	trnS-GGA	trnS-UGA	trnT-GGU
–	–	trnT-UGU	trnV-GAC	trnW-CCA	trnY-GUA
–	Ribosomal RNAs	rrn4.5	rrn5	rrn16	rrn23
–	Ribosomal protein small subunit	rps2	rps3	rps4	rps7^a
–		rps8	rps11	rps12^b	rps14
–		rps15	rps16^a	rps18	rps19
–	Ribosomal protein large subunit	rpl2^a	rpl14	rpl16	rpl20
–		rpl22	rpl23^a	rpl32	rpl33
–		rpl36
–	Subunits of RNA polymerase	rpoA	rpoB	rpoC1^a	rpoC2
Photosynthesis	Photosystem I	psaA	psaB	psaC	psaI
–		psaJ	ycf3^b
–	Photosystem II	psbA	psbB	psbC	psbD
–		psbE	psbF	psbH	psbI
–		psbJ	psbK	psbL	psbM
–		psbN	psbT	psbZ
–	Cytochrome b/f complex	petA	petB^a	petD^a	petG
–		petL	petN
–	ATP synthase	atpA	atpB	atpE	atpF^a
–		atpH	atpI
–	NADH-dehydrogenase	ndhA^a	ndhB^a	ndhC	ndhD
–		ndhE	ndhF	ndhG	ndhH
–		ndhI	ndhJ	ndhK
–	Large subunit Rubisco	rbcL	–	–	–
Miscellaneous group	Translation initiation factor IF-1	infA	–	–	–
–	Acetyl-CoA carboxylase	accD	–	–	–
–	Cytochrome c biogenesis	ccsA	–	–	–
–	Maturase	matK	–	–	–
–	ATP-dependent protease	clpP^b	–	–	–
–	Inner membrane protein	cemA	–	–	–
Unknown function	Conserved open reading frames	ycf1	ycf2	ycf4	ycf15

^aGene containing a single intron.

^bGene containing two introns.

Seven published plastid genome sequences, belonging to five species in Hamamelidaceae and two outgroups (Daphniphyllum oldhamii and Cercidiphyllum japonicum), were downloaded from GenBank for inferring the phylogenetic position of F. sinensis. A total of 79 common protein-coding genes of all eight plastomes were aligned separately using MAFFT (Katoh and Standley 2013) and concatenated into a single matrix in Geneious. The maximum likelihood (ML) tree based on the combined matrix was reconstructed using RAxML version 8.2.9 (Stamatakis 2014) with a basis of 1000 bootstrap replicates (Figure 1). The result showed the species of Hamamelidaceae formed a monophyletic clade with 100% bootstrap value. As expected, F. sinensis and S. henryi were recovered as sister with high support (100%), which agreed with the phylogenetic result of Li and Bogle (2001).

Figure 1. Phylogenetic relationships of Hamamelidaceae inferred from maximum likelihood method based on 79 common protein-coding genes. Daphniphyllum oldhamii and Cercidiphyllum japonicum were used as outgroups. The node labels indicate the ML bootstrap (1000 replicates) support values.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This study was financially supported by the National Natural Science Foundation of China [Grant No. 31570210] and the International Partnership Program of Chinese Academy of Sciences [Grant No. GJHZ1620].