Analysis of Chloroplast Genomes of Aleurites moluccana

doi:10.11983/CBB22026

Abstract

Abstract: Aleurites moluccana is an evergreen broad-leaved tree of the genus Aleurites in the family Euphorbiaceae, with energy, medicinal and ornamental values. To fill the gap in study of the chloroplast genome of A. moluccana, we assembled and annotated the chloroplast genome of A. moluccana by next-generation high-throughput whole genome sequencing, and performed genomic characterization and phylogenetic analysis. The results showed that the chloroplast genome of A. moluccana exhibited typical quadripartite and circular structures with a total length of 163 298 bp, the length of LSC, SSC, and IR was 91 301, 18 501, and 26 748 bp, respectively. It contains 131 genes, including 8 rRNA genes, 37 tRNA genes and 86 protein coding genes. A total of 145 SSR loci were found, with mononucleotide, dinucleotide, trinucleotide and tetranucleotide repeat units, and the numbers detected were 80, 53, 10, and 2, respectively. The results of collinearity analysis showed that the chloroplast genome of A. moluccana has the phenomenon of gene inversion and rearrangement. Phylogenetic trees were constructed using the maximum likelihood and Bayesian methods. It was found that A. moluccana was closely related to Vernicia fordii and Deutzianthus tonkinensis, and formed a sister group. The results of the dating analysis using fossil time showed that the differentiation time of the Aleurites, Vernicia and Deutzianthus was 25.94 Ma (95% HPD: 24.71-63.32 Ma). This study enriched the genomic information of A. moluccana and provided basic genetic data for the development and utilization of A. moluccana germplasm resources, as well as a reference for species identification and phylogenetic study of the Aleurites.

Key words: Aleurites moluccana, chloroplast genome, phylogeny

Jinbo Bao, Zhijie Ding, Haoyu Miao, Xueli Li, Shuxian Ren, Ruoyan Jiao, Hao Li, Qianqian Deng, Yingzi Li, Xinmin Tian. Analysis of Chloroplast Genomes of Aleurites moluccana[J]. Chinese Bulletin of Botany, 2023, 58(2): 248-260.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB22026

https://www.chinbullbotany.com/EN/Y2023/V58/I2/248

Figures/Tables 12

References 37

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Categories of genes	Group of genes	Name of genes
Genes for photosynthesis	Subunits of photosystem I	psaA, psaB, psaC, psaI, psaJ
	Subunits of photosystem II	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
	Subunits of ATP synthase	atpA, atpB, atpE, atpF, atpH, atpI
	Subunits of cytochrome	petA, petB, petD, petG, petL, petN
	ATP-dependent protease subunits P gene	clpP
	Large subunits of Rubisco	rbcL
	Subunits of NADH dehydrogenase	ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
Self replication	Small subunit of ribosome	rps2, rps3, rps4, rps7, rps8, rps11, rps12, rps14, rps15, rps16, rps18, rps19
	Large subunit of ribosome	rpl2, rpl14, rpl16, rpl20, rpl2, rpl23, rpl32, rpl33, rpl36, rpl22
	DNA dependent RNA polymerase	rpoA, rpoB, rpoC1, rpoC2
	Ribosomal RNA genes	rrn5, rrn4.5, rrn16, rrn23
	Transfer RNA genes	trnN-GUU, trnR-ACG, trnH-GUG, trnL-CAU, trnA-UGC, trnL-GAU, trnV-GAC, trnL- CAA, trnL-CAU, trnP-UGG, trnW-CCA, trnM-CAU, trnV-UAC, trnF-GAA, trnL-UAA, trnT-UGU, trnS-GGA, trnfM-CAU, trnG-GCC, trnS-UGA, trnT-GGU, trnE-UUC, trnY-GUA, trnD-GUC, trnC-GCA, trnR-UCU, trnS-GCU, trnQ-UUG, trnK-UUU, trnL-CAA, trnV-GAC, trnL-GAU, trnR-UGC, trnL-UAG, trnR-ACG, trnN-GUU
Other genes	Maturase	matK
	Envelop membrane protein	cemA
	Translation initiation factor IF-1	infA
	C-type cytochrome synthesis gene	ccsA
Unknown function	Conserved open reading frames	ycf1, ycf2, ycf3, ycf4, ycf15

Categories of genes	Group of genes	Name of genes
Genes for photosynthesis	Subunits of photosystem I	psaA, psaB, psaC, psaI, psaJ
	Subunits of photosystem II	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
	Subunits of ATP synthase	atpA, atpB, atpE, atpF, atpH, atpI
	Subunits of cytochrome	petA, petB, petD, petG, petL, petN
	ATP-dependent protease subunits P gene	clpP
	Large subunits of Rubisco	rbcL
	Subunits of NADH dehydrogenase	ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
Self replication	Small subunit of ribosome	rps2, rps3, rps4, rps7, rps8, rps11, rps12, rps14, rps15, rps16, rps18, rps19
	Large subunit of ribosome	rpl2, rpl14, rpl16, rpl20, rpl2, rpl23, rpl32, rpl33, rpl36, rpl22
	DNA dependent RNA polymerase	rpoA, rpoB, rpoC1, rpoC2
	Ribosomal RNA genes	rrn5, rrn4.5, rrn16, rrn23
	Transfer RNA genes	trnN-GUU, trnR-ACG, trnH-GUG, trnL-CAU, trnA-UGC, trnL-GAU, trnV-GAC, trnL- CAA, trnL-CAU, trnP-UGG, trnW-CCA, trnM-CAU, trnV-UAC, trnF-GAA, trnL-UAA, trnT-UGU, trnS-GGA, trnfM-CAU, trnG-GCC, trnS-UGA, trnT-GGU, trnE-UUC, trnY-GUA, trnD-GUC, trnC-GCA, trnR-UCU, trnS-GCU, trnQ-UUG, trnK-UUU, trnL-CAA, trnV-GAC, trnL-GAU, trnR-UGC, trnL-UAG, trnR-ACG, trnN-GUU
Other genes	Maturase	matK
	Envelop membrane protein	cemA
	Translation initiation factor IF-1	infA
	C-type cytochrome synthesis gene	ccsA
Unknown function	Conserved open reading frames	ycf1, ycf2, ycf3, ycf4, ycf15

SSR repeat type (number of copies)	SSR repeat sequence	Number of copies
SSR repeat type (number of copies)	SSR repeat sequence	5	6	7	8	9	10	11	12	13	14	15	16-30	Total
Mononucleotide (80)	A/T						24	17	7	14		3	3	68
Mononucleotide (80)	C/G						7	3		2				12
Dinucleotide (53)	AT/TA/AC/CA/AG/GA		18	7		6	4	6		2			2	45
Dinucleotide (53)	CG/GC		4	2		1	1							8
Trinucleotide (10)	CGG/AAG	2	2	1										5
	TGT/TTA	1		2										3
	ATT/AAT	1	1											2
Tetranucleotide (2)	TACA/TGGT	1			1									2

SSR repeat type (number of copies)	SSR repeat sequence	Number of copies
SSR repeat type (number of copies)	SSR repeat sequence	5	6	7	8	9	10	11	12	13	14	15	16-30	Total
Mononucleotide (80)	A/T						24	17	7	14		3	3	68
Mononucleotide (80)	C/G						7	3		2				12
Dinucleotide (53)	AT/TA/AC/CA/AG/GA		18	7		6	4	6		2			2	45
Dinucleotide (53)	CG/GC		4	2		1	1							8
Trinucleotide (10)	CGG/AAG	2	2	1										5
	TGT/TTA	1		2										3
	ATT/AAT	1	1											2
Tetranucleotide (2)	TACA/TGGT	1			1									2

Amino acid	Codon	No. of codon	RSCU	Amino acid	Codon	No. of codon	RSCU
Ala	GCU	431	1.20	Cys	UGU	698	1.20
	GCC	306	0.86	Cys	UGC	468	0.80
	GCA	427	1.19	Glu	GAA	1416	1.40
	GCG	267	0.75	Glu	GAG	611	0.60
Asp	GAU	1073	1.41	Gly	GGU	534	0.93
Asp	GAC	448	0.59		GGC	382	0.67
Phe	UUU	2457	1.26		GGA	803	1.40
Phe	UUC	1452	0.74		GGG	572	1.00
His	CAU	874	1.36	Ile	AUU	1927	1.19
His	CAC	412	0.64		AUC	1184	0.73
Lys	AAA	2578	1.38		AUA	1728	1.07
Lys	AAG	1162	0.62	Leu	UUA	1299	1.46
Trp	UGG	748	1.00		UUG	1125	1.26
Asn	AAU	2122	1.43		CUU	1021	1.15
Asn	AAC	843	0.57		CUC	577	0.65
Arg	CGU	341	0.58		CUA	844	0.95
	CGC	246	0.42		CUG	442	0.50
	CGA	590	1.00	Pro	CCU	568	1.02
	CGG	412	0.70		CCC	556	1.00
	AGA	1253	2.12		CCA	699	1.25
	AGG	702	1.19		CCG	408	0.73
Thr	ACU	683	1.18	Met	AUG	887	1.00
Thr	ACC	550	0.95	Gln	CAA	1041	1.38
	ACA	696	1.20		CAG	463	0.62
	ACG	383	0.66	Ser	UCU	1070	1.36
Val	GUU	737	1.34		UCC	840	1.07
	GUC	402	0.73		UCA	1002	1.27
	GUA	667	1.21		UCG	565	0.72
	GUG	393	0.71		AGU	720	0.92
Tyr	UAU	1842	1.43		AGC	521	0.66
Tyr	UAC	737	0.57