Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae

Figures & data

Figure 1. The chloroplast genome of Phalaenopsis zhejiangensis. From the center going outward, the four circles indicate scattered forward and reverse repeats, tandem repeats, microsatellite sequences identified, and gene structure of the plastome.

Table 1. List of genes in the chloroplast genome of Phalaenopsis zhejiangensis.

Group of genes	Name of genes	Total number
Large subunit of ribosomal proteins	rpl2 (×2)*, rpl14, rpl16*, rpl20, rpl22, rpl23 (×2), rpl32, rpl33, rpl36	11
Small subunit of ribosomal proteins	rps2, rps3, rps4, rps7 (×2), rps8, rps11, rps12 (×2)**, rps14, rps15, rps16*, rps18, rps19(×2)	15
DNA-dependent RNA polymerase	rpoA, rpoB, rpoC1*, rpoC2	4
Ribosomal RNA genes	rrn4.5 (×2), rrn5 (×2), rrn16 (×2), rrn23 (×2)	8
Transfer RNA genes	trnA-UGC (×2)*, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC*, trnG-GCC, trnH-GUG (×2), trnI-CAU (×2), trnI-GAU (×2)*, trnK-UUU*, trnL-CAA (×2), trnL-UAA*, trnL-UAG, trnM-CAU, trnN-GUU (×2), trnP-UGG, trnQ-UUG, trnR-ACG (×2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC (×2), trnV-UAC*, trnW-CCA, trnY-GUA	38
Photosystem I	psaA, psaB, psaC, psaI, psaJ, ycf3**	6
Photosystem II	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ	15
Cytochrome b6/f complex	petA, petB*, petD*, petG, petL, petN	6
NADH dehydrogenase	ψndhB (×2), ψndhD, ψndhG, ψndhI, ψndhK	6
ATP synthase	atpA, atpB, atpE, atpF*, atpH, atpI	6
Rubisco	rbcL	1
Translational initiation factor	infA	1
Maturase	matK	1
Protease subunit P	clpP**	1
Envelop membrane protein	cemA	1
Subunit acetyl-CoA carboxylate	accD	1
c-type cytochrome synthesis gene	ccsA	1
Conserved open reading frames	ycf1, ycf2 (×2), ycf4	4
Total		126

(ψ) pseudogene; *one intron; **two introns.

Figure 2. Structural variations at inverted-repeat and single-copy borders in nine Phalaenopsis chloroplast genomes. The figure features are not to scale regarding sequence length.

Table 2. Details of nine Phalaenopsis chloroplast genomes.

Plant species	Accession number in NCBI	Genome length (bp)	GC contents (%)	LSC (bp)	SSC (bp)	IR (bp)
Phalaenopsis aphrodite subsp. formosana	AY916449	148,964	36.7	85,957	11,543	25,732
Phalaenopsis equestris	JF719062	148,959	36.7	85,967	11,300	25,846
Phalaenopsis hybrid ‘Tiny Star’	NC_025593	148,918	36.7	85,885	11,523	25,755
Phalaenopsis japonica	NC_046808	146,942	36.8	84,882	10,568	25,746
Phalaenopsis lobbii	MT830847	144,607	36.6	83,482	11,687	24,719
Phalaenopsis lowii	NC_050652	146,834	36.9	84,616	10,473	25,633
Phalaenopsis mannii	NC_050940	148,596	36.7	85,300	11,640	25,828
Phalaenopsis wilsonii	MW218959	145,373	36.9	84,995	10,668	24,855
Phalaenopsis zhejiangensis	MZ326749	143,574	38.7	83,854	10,764	24,464

Table 3. Repeat sequences and their distribution within Phalaenopsis zhejiangensis chloroplast genome.

Number	Motif	Size	Start	End	Location
1	(T)10	10	4245	4254	IGS
2	(A)10	10	7693	7702	IGS
3	(T)10	10	9184	9193	IGS
4	(T)10	10	9599	9608	IGS
5	(T)17	17	14,113	14,129	IGS
6	(T)12	12	17,053	17,064	IGS
7	(A)16	16	27,913	27,928	IGS
8	(T)10	10	28,756	28,765	IGS
9	(A)11	11	32,765	32,775	IGS
10	(T)10	10	33,072	33,081	IGS
11	(A)10	10	33,357	33,366	IGS
12	(A)10	10	37,057	37,066	IGS
13	(A)11	11	47,194	47,204	IGS
14	(A)10	10	47,875	47,884	IGS
15	(A)11	11	56,140	56,150	IGS
16	(T)12	12	62,492	62,503	IGS
17	(A)10	10	64,380	64,389	IGS
18	(T)10	10	64,612	64,621	IGS
19	(T)10	10	71,393	71,402	IGS
20	(T)10	10	79,492	79,501	IGS
21	(T)10	10	83,505	83,514	IGS
22	(T)10	10	98,214	98,223	IGS
23	(A)11	11	108,703	108,713	IGS
24	(T)10	10	113,355	113,364	IGS
25	(A)10	10	129,180	129,189	IGS
26	(A)10	10	111,423	111,432	ψndhD
27	(A)10	10	111,579	111,588	ψndhD
28	(TA)8	16	111,722	111,737	ψndhD
29	(T)10	10	49,573	49,582	ψndhK
30	(A)12	12	74,999	75,010	petB intron
31	(T)10	10	82,386	82,395	rpl16 intron
32	(A)11	11	23,345	23,355	rpoC1 intron
33	(T)11	11	69,574	69,584	clpP
34	(A)10	10	69,867	69,876	rps12
35	(T)10	10	9805	9814	trnG-GCC intron
36	(T)12	12	114,415	114,426	ycf1
37	(T)11	11	115,271	115,281	ycf1
38	(T)13	13	116,348	116,360	ycf1
39	(T)10	10	117,578	117,587	ycf1
40	(T)10	10	117,695	117,704	ycf1
41	(A)13	13	45,453	45,465	ycf3

IGS: intergenic spacer region.

Figure 3. The maximum-likelihood tree inferred from 41 Orchidaceae complete chloroplast genomes under GTR + G+I model with maximum-likelihood value (Llk)=–604333.07383, Akaike information criterion (AIC)=1208844.14766, and Bayesian information criterion (BIC)=1209758.57750.

Data availability statement

The data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/nuccore/MZ326749. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA734444, SRR14710950, and SAMN19491762, respectively.