Structural and Comparative Analysis of the Complete Chloroplast Genome of the Aronia melanocarpa and Its Phylogenetic Inference

doi:10.11983/CBB24146

Abstract

Abstract: INTRODUCTION Aronia melanocarpa also known as black chokeberry, belongs to the genus Aronia (Rosaceae). In addition to A. melanocarpa, Aronia includes A. arbutifolia or red chokeberry and A. prunifolia or purple chokeberry, both distributed naturally in North American, and an additional cultivated taxon, A. mitschurinii or Mitschurin’s chokeberry, originating from Europe. However, the species boundaries and relationships among the species of Aronia are not clear. Moreover, the taxonomic history of Aroniais complex, as species of this genus have formerly been placed in many different genera, such as Mespilus, Pyrus, Adenorachis, Sorbus, and Photinia. In the present study, we first sequenced and characterized the complete chloroplast (cp) genome of A. melanocarpa and compared its sequence with those of the cp genomes from 13 species of the family Rosaceae. The aims of this study were: (1) to increase our understanding of the structural patterns of complete cp genome of A. melanocarpa; (2) to investigate the phylogenetic relationships of A. melanocarpa with other Rosaceae species based on their cp genomes. RATIONALE The chloroplast is a unique and essential organelle in green plants with vital roles in photosynthesis and carbon fixation. Comparative analyses of cp genomes between different plant species reveal intra- and inter-species rearrangements that have occurred during evolution, such as inverted repeat (IR) contraction and expansion. Based on these characteristics, the cp genome has been wildly used for species identification, phylogenetic analysis, and exploring the genetic basis of environmental adaptation.RESULTS The complete A. melanocarpa cp genome was sequenced, analyzed, and compared with that from 13 other species in the Rosaceae. The cp genome is 159 772 bp and has a total guanine-cytosine (GC) content of 36.6%. It exhibits a typical quadripartite structure with four separate regions, including a large single copy (LSC) region of 87 810 bp and a small single copy (SSC) region of 19 200 bp separated by two inverted repeats (IRa and IRb) regions of 26 381 bp each. A total of 132 genes were annotated, including 87 protein-coding genes, 37 tRNAs, and eight rRNAs, with 22 duplicates in the IR regions. In total, 76 simple sequence repeats (SSRs) and 50 long repeats were detected. Phylogenetic analysis indicated that A. melanocarpa is most closely related to A. arbutifolia and forms a sister clade to Cydonia oblonga with weak support.CONCLUSION We analyzed the complete cp genome of A. melanocarpa by using Illumina high-throughput sequencing technology. The sequence of A. melanocarpa cp genome could be further used for the development of molecular markers. Highly variable regions were detected in intergenic regions, such as trnK-rps16, rps16-trnQ, trnG-atpA, petN-psbM, trnT-psbD, psbZ-trnG, trnT-trnL, ndhC-trnV and accD-psaI, which might be useful for broad applications in genetic research studies as well as phylogenetic studies. Phylogenetic construction results strongly supported that A. melanocarpa was closest related to A. arbutifolia, followed by C. oblonga with weak support. This newly available genomic data for A. melanocarpa will provide a basis for future research on the population genetics and phylogenomics and will benefit the breeding studies and utilization of the genus Aronia.
Map of the chloroplast genome of Aronia melanocarpa and phylogenetic analyses among the 60 Rosaceae species using their complete chloroplast genomes. Aronia formed a clade with Dichotomanthes and Pourthiaea based on cpDNA tree. Moreover, A. melanocarpa is most closely related to A. arbutifolia and forms a sister clade to Cydonia oblonga with weak support.

Key words: Aronia melanocarpa, chloroplast genome, structural variation, phylogenetic relationships

Chuanyong Wang, Dian Zhuang, Zhengda Song, Henghua Zhai, Naiwei Li, Fan Zhang. Structural and Comparative Analysis of the Complete Chloroplast Genome of the Aronia melanocarpa and Its Phylogenetic Inference[J]. Chinese Bulletin of Botany, 2025, 60(4): 573-585.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB24146

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Figures/Tables 8

References 48

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Genome features	A. melanocarpa	Genome features	A. melanocarpa
Genome size (bp)/GC content (%)	159772/36.6	Number of unique genes	110
LSC size (bp)/GC content (%)	87810/34.3	Protein-coding genes	87
SSC size (bp)/GC content (%)	19200/30.4	tRNAs	37
IR size (bp)/GC content (%)	52762/42.7	rRNAs	8
Total gene number	132	Genes duplicated in the IRs	22

Genome features	A. melanocarpa	Genome features	A. melanocarpa
Genome size (bp)/GC content (%)	159772/36.6	Number of unique genes	110
LSC size (bp)/GC content (%)	87810/34.3	Protein-coding genes	87
SSC size (bp)/GC content (%)	19200/30.4	tRNAs	37
IR size (bp)/GC content (%)	52762/42.7	rRNAs	8
Total gene number	132	Genes duplicated in the IRs	22

Category	Gene group	Name of gene	Number
Self-replication	Proteins of the large ribosomal subunit	rpl2^ab, rpl14, rpl16^b, rpl20, rpl22, rpl23^a, rpl32, rpl33, rpl36	11
	Proteins of the small ribosomal subunit	rps2, rps3, rps4, rps7^a, rps8, rps11, rps12^ac, rps14, rps15, rps16^b, rps18, rps19^ab	15
	Subunits of RNA polymerase	rpoA, rpoB, rpoC1^b, rpoC2	4
	rRNAs	rrn23S^a, rrn16S^a, rrn5S^a, rrn4.5S^a	8
	tRNAs	trnH-GUG, trnK-UUU^b, trnQ-UUG, trnS-GCU, trnG- GCC^ab, trnR-UCU, trnC-GCA, trnD-GUC, trnY-GUA, trnE- UUC, trnT-GGU, trnS-UGA, trnfM, trnS-GGA, trnS-GGA, trnT-UGU, trnL-UAA^b, trnF-GAA, trnV-UAC^b, trnM-CAU, trnW-CCA, trnP-UGG, trnI-CAU^a, trnL-CAA^a, trnV-GAC^a, trnI-GAU^ab, trnA-UGC^ab, trnR-ACG^a, trnN-GUU^a, trnL-UAG	37
Photosynthesis	Subunits of photosystem I	psaA, psaB, psaI^a, psaJ	5
	Subunits of photosystem II	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI^a, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ	15
	Subunits of NADH dehydrogenase	ndhA^b, ndhB^ab, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK	12
	Subunits of cytochrome b/f complex	petA, petB^b, petD^b, petG, petL, petN	6
	Subunits of ATP synthase	atpA, atpB, atpE, atpF^b, atpH, atpI	6
	Large subunit of Rubisco	rbcL	1
Biosynthesis	Maturase	matK	1
	Protease	clpP^c	1
	Envelope membrane protein	cemA	1
	Acetyl-CoA carboxylase	accD	1
	C-type cytochrome synthesis gene	ccsA	1
	Translation initiation factor	infA	1
Unknown function	Conserved hypothetical chloroplast reading frames	ycf1^a, ycf2^a, ycf3^c, ycf4	6

Category	Gene group	Name of gene	Number
Self-replication	Proteins of the large ribosomal subunit	rpl2^ab, rpl14, rpl16^b, rpl20, rpl22, rpl23^a, rpl32, rpl33, rpl36	11
	Proteins of the small ribosomal subunit	rps2, rps3, rps4, rps7^a, rps8, rps11, rps12^ac, rps14, rps15, rps16^b, rps18, rps19^ab	15
	Subunits of RNA polymerase	rpoA, rpoB, rpoC1^b, rpoC2	4
	rRNAs	rrn23S^a, rrn16S^a, rrn5S^a, rrn4.5S^a	8
	tRNAs	trnH-GUG, trnK-UUU^b, trnQ-UUG, trnS-GCU, trnG- GCC^ab, trnR-UCU, trnC-GCA, trnD-GUC, trnY-GUA, trnE- UUC, trnT-GGU, trnS-UGA, trnfM, trnS-GGA, trnS-GGA, trnT-UGU, trnL-UAA^b, trnF-GAA, trnV-UAC^b, trnM-CAU, trnW-CCA, trnP-UGG, trnI-CAU^a, trnL-CAA^a, trnV-GAC^a, trnI-GAU^ab, trnA-UGC^ab, trnR-ACG^a, trnN-GUU^a, trnL-UAG	37
Photosynthesis	Subunits of photosystem I	psaA, psaB, psaI^a, psaJ	5
	Subunits of photosystem II	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI^a, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ	15
	Subunits of NADH dehydrogenase	ndhA^b, ndhB^ab, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK	12
	Subunits of cytochrome b/f complex	petA, petB^b, petD^b, petG, petL, petN	6
	Subunits of ATP synthase	atpA, atpB, atpE, atpF^b, atpH, atpI	6
	Large subunit of Rubisco	rbcL	1
Biosynthesis	Maturase	matK	1
	Protease	clpP^c	1
	Envelope membrane protein	cemA	1
	Acetyl-CoA carboxylase	accD	1
	C-type cytochrome synthesis gene	ccsA	1
	Translation initiation factor	infA	1
Unknown function	Conserved hypothetical chloroplast reading frames	ycf1^a, ycf2^a, ycf3^c, ycf4	6

Amino acids	Codon	No.	RSCU	Amino acids	Codon	No.	RSCU
Phe	UUU	975	1.3	Ala	GCU	645	1.84
Phe	UUC	526	0.7	Ala	GCC	217	0.62
Leu	UUA	912	1.95	Ala	GCA	390	1.11
Leu	UUG	565	1.21	Ala	GCG	148	0.42
Leu	CUU	593	1.27	TER	UAA	51	1.76
Leu	CUC	186	0.4	TER	UAG	21	0.72
Leu	CUA	363	0.78	TER	UGA	15	0.52
Leu	CUG	181	0.39	His	CAU	493	1.55
Ile	AUU	1123	1.47	His	CAC	145	0.45
Ile	AUC	440	0.58	Gln	CAA	727	1.54
Ile	AUA	730	0.96	Gln	CAG	217	0.46
Met	AUG	627	1	Asn	AAU	987	1.53
Val	GUU	524	1.44	Asn	AAC	305	0.47
Val	GUC	167	0.46	Lys	AAA	1068	1.49
Val	GUA	552	1.52	Lys	AAG	364	0.51
Val	GUG	208	0.57	Asp	GAU	889	1.62
Ser	UCU	573	1.69	Asp	GAC	208	0.38
Ser	UCC	330	0.97	Glu	GAA	1035	1.48
Ser	UCA	408	1.2	Glu	GAG	363	0.52
Ser	UCG	190	0.56	Cys	UGU	226	1.49
Ser	AGU	411	1.21	Cys	UGC	77	0.51
Ser	AGC	128	0.38	Trp	UGG	458	1
Pro	CCU	421	1.56	Arg	CGU	340	1.27
Pro	CCC	201	0.74	Arg	CGC	112	0.42
Pro	CCA	310	1.15	Arg	CGA	370	1.38
Pro	CCG	149	0.55	Arg	CGG	121	0.45
Thr	ACU	551	1.6	Arg	AGA	493	1.84
Thr	ACC	251	0.73	Arg	AGG	173	0.65
Thr	ACA	423	1.23	Gly	GGU	589	1.31
Thr	ACG	153	0.44	Gly	GGC	183	0.41
Tyr	UAU	801	1.61	Gly	GGA	725	1.62
Tyr	UAC	194	0.39	Gly	GGG	295	0.66