Genetic Analysis of Chloroplast Genome Characteristics of Potato‘Cooperation 88’Selfing Population

doi:10.16420/j.issn.0513-353x.2022-0721

Acta Horticulturae Sinica ›› 2023, Vol. 50 ›› Issue (8): 1649-1663.doi: 10.16420/j.issn.0513-353x.2022-0721

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Genetic Analysis of Chloroplast Genome Characteristics of Potato‘Cooperation 88’Selfing Population

WANG Rongyan¹^,², LI Qing¹^,², XU Ling¹, WANG Qiujie¹, SONG Yu¹^,², MU Changran¹, TANG Wei¹^,²^,^*(), HAO Dahai¹^,²^,^*()

¹ School of Life Sciences，Yunnan Normal University，Kunming 650500，China
² Key Laboratory for Potato Biology of Yunnan Province，Kunming 650500，China

Received:2023-03-09 Revised:2023-04-28 Online:2023-08-25 Published:2023-08-23
Contact: TANG Wei, HAO Dahai

Abstract

Abstract:

In order to analyze the chloroplast genome polymorphism and genetic diversity of potato ‘Cooperation 88’at the genome level and to understand the genetic composition and variation of the chloroplast genome of the selfing population of‘Cooperation 88’，this study assembled the chloroplast genomes of‘Cooperation 88’and 30 selfing progenies and comparatively analyzed them with the chloroplasts genomes of 11 other Solanaceae species，Arabidopsis thaliana and Oryza sativa. The results showed that the assembled chloroplast genome of the‘Cooperation 88’was a typical circular structure with a length of 160 323 bp and the GC content of 38.6%，including a total of 29 annotated tRNA genes and 77 protein-coding genes. The size of the chloroplast genome of the 30 selfing progenies ranged from 160 331 bp to 162 120 bp，the number of genes predicted was 95-106，and the GC content was 36.7%-38.6%. Further analysis showed that the chloroplast types of the parent and 30 selfing progeny were all W-type，showing no polymorphism. Both parent and selfing progenies prefer to use codons ending with A/U，and the progenies chloroplasts genomes codon pairs used different frequencies of the four bases，indicating that the relative synonymous codon usage and effective codons in the chloroplast genome of selfing progenies variations in the number of codons and high-frequency codons were caused by random mutation and translational natural selection in the chloroplast genome. In addition，12 repeats existing in the parent were also present in all progenies but four repeats were new appeared in progeny. UPGMA analysis and collinearity analysis also found that the evolutionary level of the Solanum chloroplast genome was highly conserved, but the appearance of repeats and the loss of genes changed the size of the progeny chloroplast genome and increased their genetic diversity.

Key words: potato, selfing population, chloroplast genome, repeat sequence, codon bias

WANG Rongyan, LI Qing, XU Ling, WANG Qiujie, SONG Yu, MU Changran, TANG Wei, HAO Dahai. Genetic Analysis of Chloroplast Genome Characteristics of Potato‘Cooperation 88’Selfing Population[J]. Acta Horticulturae Sinica, 2023, 50(8): 1649-1663.

Figures/Tables 11

References 58

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物种 Species	基因组大小/bp Genome size	反向重复长度/bp IR size	GC含量/% GC content	基因数 Number of genes	登录号 Accession No.
马铃薯Potato
合作88 Cooperation 88	160 323	25 575	38.6	106	ON921079
大西洋 Atlantic	155 296	25 593	37.9	134	GWHAORW01000000
底西瑞 Desiree	155 312	25 595	37.0	130	DQ231562
夏波蒂Shepody	155 296	25 593	37.9	132	MW307949
费乌瑞它 Favorita	155 296	25 593	37.9	132	MW307948
番茄 Solanum lycopersicum	155 461	25 611	37.9	134	DQ347959
龙葵 Solanum nigrum	155 432	25 589	38.0	125	KM489055
茄子 Solanum melongena	154 289	25 566	37.9	125	KU682719
烟草 Nicotiana debneyi	156 073	25 410	38.4	129	MT985319
枸杞 Lycium ruthenicum	154 996	25 395	37.9	111	MG976805
辣椒 Capsicum annuum	156 781	25 783	37.7	135	JX270811
黄灯笼辣椒 Capsicum chinense	156 807	25 803	37.7	134	KU041709
拟南芥 Arabidopsis thaliana	154 478	26 264	37.9	131	AP000423
水稻 Oryza sativa	134 503	20 804	39.0	148	MG252500

物种 Species	基因组大小/bp Genome size	反向重复长度/bp IR size	GC含量/% GC content	基因数 Number of genes	登录号 Accession No.
马铃薯Potato
合作88 Cooperation 88	160 323	25 575	38.6	106	ON921079
大西洋 Atlantic	155 296	25 593	37.9	134	GWHAORW01000000
底西瑞 Desiree	155 312	25 595	37.0	130	DQ231562
夏波蒂Shepody	155 296	25 593	37.9	132	MW307949
费乌瑞它 Favorita	155 296	25 593	37.9	132	MW307948
番茄 Solanum lycopersicum	155 461	25 611	37.9	134	DQ347959
龙葵 Solanum nigrum	155 432	25 589	38.0	125	KM489055
茄子 Solanum melongena	154 289	25 566	37.9	125	KU682719
烟草 Nicotiana debneyi	156 073	25 410	38.4	129	MT985319
枸杞 Lycium ruthenicum	154 996	25 395	37.9	111	MG976805
辣椒 Capsicum annuum	156 781	25 783	37.7	135	JX270811
黄灯笼辣椒 Capsicum chinense	156 807	25 803	37.7	134	KU041709
拟南芥 Arabidopsis thaliana	154 478	26 264	37.9	131	AP000423
水稻 Oryza sativa	134 503	20 804	39.0	148	MG252500

基因分类 Category of genes	基因分组 Group of genes	基因名称 Gene name
光合作用相关 Photosynthesis related	光系统ⅠPhotosystemⅠ	psaJ，psaI，psaA，psaB，psaC
	光系统Ⅱ PhotosystemⅡ	psbA，psbB，psbC，psbD，psbE，psbF，psbH，psbI，psbJ，psbK，psbL，psbM，psbN，psbT，psbZ
	ATP合酶 ATP synthase	atpF，atpH，atpA，atpB，atpE，atpI
	细胞色素Cytochrome	petA，petL，petG，petB，petD，petN
	NADH脱氢酶NADH dehydrogenase	ndhJ，ndhK，ndhF，ndhE，ndhG，ndhI，ndhH，ndhC，ndhA
	二磷酸核酮糖羧化酶大亚基 Rubis CO large subunit	rbcL
转录和翻译相关 Transcription and translation related	RNA 聚合酶RNA polymerase	rpoA，rpoB，rpoC1，rpoC2
	ATP依赖性clp蛋白酶 ATP-dependent clp protease	clpP
	成熟酶K Maturase K	matK
	核糖体大亚基Large subunit of ribosome	rpl33，rpl20，rpl36，rpl14，rpl16，rpl22，rpl23⁽²⁾ ，rpl2，rpl32
	核糖体小亚基Small subunit of ribosome	rps16，rps4，rps18，rps11，rps8，rps3，rps19，rps7，rps15，rps2，rps14，rps12
	tRNA	trnL-CAA，trnI-CAU，trnR-ACG，trnV-GAC，trnL-UAG，trnN-GUU，trnV-GAC，trnR-ACG，trnN-GUU，trnI-CAU，trnL-CAA，trnP-UGG，trnW-CCA，trnF-GAA，trnM-CAU，trnT-UGU、trnS-GGA，trnfM-CAU，trnG-GCC，trnS-UGA，trnT-GGU，trnC-GCA，trnE-UUC，trnD-GUC，trnY-GUA，trnR-UCU，trnS-GCU，trnQ-UUG，trnH-GUG
其他基因 Other genes	假设叶绿体阅读框架 Hypothetical chloroplast reading frames (ycf)	ycf1，ycf2，ycf3，ycf4
	C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA
	包膜膜蛋白 Envelope membrane protein	cemA
	乙酰辅酶A羧化酶亚基 Subunit of Acetyl-CoA carboxylase	accD

基因分类 Category of genes	基因分组 Group of genes	基因名称 Gene name
光合作用相关 Photosynthesis related	光系统ⅠPhotosystemⅠ	psaJ，psaI，psaA，psaB，psaC
	光系统Ⅱ PhotosystemⅡ	psbA，psbB，psbC，psbD，psbE，psbF，psbH，psbI，psbJ，psbK，psbL，psbM，psbN，psbT，psbZ
	ATP合酶 ATP synthase	atpF，atpH，atpA，atpB，atpE，atpI
	细胞色素Cytochrome	petA，petL，petG，petB，petD，petN
	NADH脱氢酶NADH dehydrogenase	ndhJ，ndhK，ndhF，ndhE，ndhG，ndhI，ndhH，ndhC，ndhA
	二磷酸核酮糖羧化酶大亚基 Rubis CO large subunit	rbcL
转录和翻译相关 Transcription and translation related	RNA 聚合酶RNA polymerase	rpoA，rpoB，rpoC1，rpoC2
	ATP依赖性clp蛋白酶 ATP-dependent clp protease	clpP
	成熟酶K Maturase K	matK
	核糖体大亚基Large subunit of ribosome	rpl33，rpl20，rpl36，rpl14，rpl16，rpl22，rpl23⁽²⁾ ，rpl2，rpl32
	核糖体小亚基Small subunit of ribosome	rps16，rps4，rps18，rps11，rps8，rps3，rps19，rps7，rps15，rps2，rps14，rps12
	tRNA	trnL-CAA，trnI-CAU，trnR-ACG，trnV-GAC，trnL-UAG，trnN-GUU，trnV-GAC，trnR-ACG，trnN-GUU，trnI-CAU，trnL-CAA，trnP-UGG，trnW-CCA，trnF-GAA，trnM-CAU，trnT-UGU、trnS-GGA，trnfM-CAU，trnG-GCC，trnS-UGA，trnT-GGU，trnC-GCA，trnE-UUC，trnD-GUC，trnY-GUA，trnR-UCU，trnS-GCU，trnQ-UUG，trnH-GUG
其他基因 Other genes	假设叶绿体阅读框架 Hypothetical chloroplast reading frames (ycf)	ycf1，ycf2，ycf3，ycf4
	C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA
	包膜膜蛋白 Envelope membrane protein	cemA
	乙酰辅酶A羧化酶亚基 Subunit of Acetyl-CoA carboxylase	accD

样本名称 Sample name	基因组大小/bp Genome size	基因数 Number of genes	蛋白质编码基因 Protein-coding gene	转移RNA tRNA gene	GC含量/% GC content	反向重复序列/bp Inverted repeat
样本名称 Sample name	基因组大小/bp Genome size	基因数 Number of genes	蛋白质编码基因 Protein-coding gene	转移RNA tRNA gene	GC含量/% GC content	IRA	IRB
合作88 Cooperation 88	160 323	106	77	29	38.6	25 583	25 567
C88-18	160 331	106	77	29	38.6	25 599	25 579
C88-20	161 341	100	76	24	36.7	25 735	26 053
C88-24	161 157	100	76	24	37.2	25 548	26 053
C88-35	161 150	99	76	23	36.9	25 532	26 049
C88-61	161 157	101	76	25	36.9	25 633	25 960
C88-68	161 387	100	74	26	36.9	25 659	26 177
C88-69	161 220	99	75	24	36.8	25 733	25 930
C88-71	161 418	99	75	24	37.0	25 804	26 041
C88-84	161 599	100	76	24	36.8	25 839	26 190
C88-88	161 663	101	76	25	36.9	25 856	26 196
C88-96	161 431	98	74	24	36.9	25 765	26 109
C88-106	161 349	99	76	23	36.9	25 687	26 107
C88-107	161 375	101	76	25	37.1	25 656	26 163
C88-109	161 343	101	76	25	36.9	25 587	26 207
C88-111	161 630	100	75	25	37.0	26 002	26 076
C88-115	161 226	100	75	25	37.1	25 426	26 197
C88-118	161 175	100	75	25	37.0	25 623	25 997
C88-119	161 706	99	75	24	36.9	25 901	26 162
C88-132	161 326	100	75	25	36.9	25 697	26 041
C88-138	161 880	101	74	27	36.8	25 943	26 361
C88-141	161 577	101	76	25	36.8	25 689	26 330
C88-143	161 832	102	76	26	36.8	26 095	26 163
C88-144	161 228	95	73	22	36.7	25 579	26 081
C88-151	161 527	101	75	26	36.8	25 693	26 286
C88-157	161 568	101	75	26	37.0	25 718	26 286
C88-160	161 418	103	77	26	37.0	25 719	26 102
C88-161	162 120	100	75	25	36.9	26 218	26 345
C88-182	161 806	96	72	24	37.2	25 768	26 492
C88-187	160 484	100	74	26	37.5	25 292	25 636
C88-209	161 259	99	74	25	37.2	25 551	26 158

Genetic Analysis of Chloroplast Genome Characteristics of Potato‘Cooperation 88’Selfing Population

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重复 Repeat	长度/bp Length	序列 Sequence
R1	146	AAAAGAAGACTACCTTTTTTTGTTGTGCTTCGCTAGGTCGAGGTAAGTAAGGTATACGAAGGAAAAGCCTATTTGACAATGAAAGTGACCAAAGATATTCATTTTTCAAAAAACTTTAGCTTGTACACAAATACAGCAGGCCTTTC
R2	27	ATTAGTACATCATTGAATATACAATTC
R3	42	CTGTTCAATTGAGACCTTATAATGCAATCGCATTCTCTGGTC
R4	36	TTCAATTGAGACCTTATAATGCAATCGCATTCTCTG
R5	33	GAAAGATTCATCTATTTCTTTCTACCATACTAT
R6	16	GAATCTAGATTTGAGT
R7	60	ATTAGTACATCATTGAATATACAATTCAAAATTAGTACATCATTGAATATACAATTCAAA
R8	27	ATTCAATTGAGACCTTATAATGCAATC
R9	27	TGAGATTTTCACCTCATACGGCTCCTC
R10	26	ATAAAAGAATCTAAAAATCAATATTC
R11	26	TTCAATTGAGACCTTATAATGCAATC
R12	25	TGTATTTTTGATTTATCATCCCTTC
R13	32	TGGTTTTTTCATGTTGTCAAAGATTTGAACAA
R14	38	CAATAACCCCTATTTTATTTTCATGTCTTCATAGGGCA
R15	64	CTTAAACATTGACTTTTACACATGTGCACAACCAAATTCTCCAGGTTCGGGTCCAATTACATAA
R16	36	AATAAAATAGGGGTTATTGTGCCCTATGAAGACATG

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