Structure of Chloroplast Genome and its Characteristics of Sphaerophysa salsula

doi:10.7525/j.issn.1673-5102.2022.03.014

Abstract

Abstract:

The whole chloroplast genome of Sphaerophysa salsula was sequenced and assembled based on Illumina high-throughput sequencing platform. The assembly result indicated that the whole chloroplast genome of S. salsula had a total length of 123 327 bp， with a loss of IR region. The chloroplast genome encoded a total of 108 genes， including 74 protein-coding genes， 4 rRNA genes and 30 tRNA genes. and 99 SSR loci were found， and among them the number of mononucleotide， dinucleotide and trinucleotide repeat motifs was 75， 17 and 7， respectively. The phylogenetic analysis results showed that S. salsula and Alhagi sparsifolia were sister species， which had the closest genetic relationship. The results would lay the foundation for the genetic diversity， population genetic structure and speciation mechanism of S. salsula in the future.

Key words: Sphaerophysa salsula, chloroplast genome, simple sequence repeats, codon preference, phylogeny

CLC Number:

Q949.4

Dandan SU, Yuping LIU, Tao LIU, Changyuan ZHENG, Yu ZHANG, Yanan WANG, Na QIN, Xu SU. Structure of Chloroplast Genome and its Characteristics of Sphaerophysa salsula[J]. Bulletin of Botanical Research, 2022, 42(3): 446-454.

Figures/Tables 6

Fig.1

Table 1

Gene annotation of the chloroplast genome of S. salsula

基因类别

Gene category

基因分组

Gene group

基因名称

Gene name

光合作用基因

Genes for

photosynthesis

光系统Ⅰ亚基

Subunits of Photosystem I

psaA、psaB、psaC、psaI、psaJ

光系统Ⅱ亚基

Subunits of Photosystem II

psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbJ、

psbK、psbL、psbM、psbN、psbT、psbZ

细胞色素b/f复合体亚基

Subunit of cytochrome b/f complex

PetA、petB^a、petD^a、petG、petN、petL、petN

ATP合成酶亚基

Subunits of ATP synthase

atpA、atpB、atpE、atpF、atpH、atpI

NADH脱氢酶亚基

Subunits of NADH dehydrogenase

ndhA^a、ndhB、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK

二磷酸核酮糖羧化酶大亚基

Large subunit of Rubisco

rbcL

自我复制基因

Self replication

DNA依赖性RNA聚合酶

DNA dependent RNA polymerase

rpoA、rpoB、rpoC1、rpoC2

核糖体小亚基

Small subunit of ribosome

rps2、rps3、rps4、rps7、rps8、rps11、rps12^b、rps14、rps15、rps16、rps18、rps19

核糖体大亚基

Large subunit of ribosome

rpl2^a、rpl14、rpl16^a、rpl20、rpl23、rpl32、rpl33、rpl36

转运RNA

Transfer RNA gene

trnA-UGC、trnC-GCA、trnD-GUC、trnE-UUC、trnF-GAA、trnG-GCC、trnH-GUG、trnI-CAU、trnI-GAU、trnK-UUU、trnL-CAA、trnL-UAA、trnL-UAG、trnfM-CAU、trnM-CAU、trnN-GUU、trnP-GGG、trnQ-UUG、trnR-ACG、trnR-UCU、trnS-GGA、trnS-GGA、trnS-UGA、trnT-CGU^a、trnT-GGU^c、trnT-UGU、trnV-GAC、trnV-UAC、trnW-CCA、trnY-GUA

核糖体RNA

Ribosomal RNA gene

rrn4.5 ^c、rrn5、rrn16 ^d、rrn23^a^c

翻译起始因子

Translation initiation factor

infA

其他基因

Other genes

成熟酶Maturase

matK

包膜蛋白

Envelop membrane protein

cemA

c型细胞色素合成基因

c-type eytochrome synthesis gene

ccsA

乙酰辅酶A羧化酶亚基

Submit of acetyl-CoA-carboxylase

accD

ATP依赖的蛋白酶亚基p

ATP-dependent protease subunit P

clpP

未知功能基因

Genes of unknown

function

开放阅读框

Conserved open reading frame

ycf3、ycf4

Table 1

Fig.2

Table 2

Table 3

Distribution of SSR in the chloroplast genome of S. salsula

编号 No.	SSR类型 SSR type	SSR	大小 Size	起始 Start	终止 End	位置 Location
1	p2	（TA）8	16	311	326	IGS
2	p1	（A）11	11	1 654	1 664	IGS
3	c	（T）16aaaccagtcgtagtagttctagcggtcgactcgcttttttcaaa（T）11	71	1 782	1 852	rps18
4	p3	（TTA）4	12	3 390	3 401	IGS
5	p1	（A）11	11	8 370	8 380	IGS
6	p1	（T）13	13	9 253	9 265	IGS
7	p3	（TTA）4	12	10 147	10 158	IGS
8	p1	（T）12	12	10 426	10 437	IGS
9	p2	（TA）5	10	10 557	10 566	IGS
10	p1	（A）13	13	10 821	10 833	IGS
11	p1	（T）14	14	12 899	12 912	IGS
12	c	（ATT）4cacaacaacaataaatagattagaatttagaataaaaaag（A）10tcgagttgcttatgaatattcataagcgactcactttagattagagacgaatgat（A）11	128	13 214	13 341	IGS
13	p3	（TTA）4	12	13 922	13 933	IGS
14	c	（A）10gcaaaaatacaattca（T）10	36	14 201	14 236	IGS
15	p1	（A）11	11	15 005	15 015	IGS
16	c	（A）10gccttctttatatc（T）10	34	15 216	15 249	IGS
17	p1	（A）11	11	15 436	15 446	IGS
18	P1	（T）11	11	16 166	16 176	Intron
19	p1	（A）10	10	16 329	16 338	Intron
20	p1	（A）14	14	19 461	19 474	IGS
21	p1	（T）12	12	20 366	20 377	IGS
22	p1	（T）10	10	21 907	21 916	rps2
23	p1	（T）10	10	22 155	22 164	IGS
24	p1	（T）10	10	22 473	22 482	rpoC2
25	c	（T）13accgttctgggtggtatcaagatggcactgggtcgggatatcttatcaatttctccgggaaaat ggatatttccagaaaatatttttaattcca（T）13	120	24 251	24 370	rpoC2
26	p2	（TA）5	10	25 733	25 742	rpoC2
27	p1	（T）13	13	28 790	28 802	IGS
28	p2	（AT）5	10	30 274	30 283	rpoB
29	p1	（T）10	10	35 740	35 749	IGS
30	c	（TA）5aataagaaacgacgaagaaagaaat（A）10	45	36 204	36 248	IGS
31	p1	（T）10	10	36 425	36 434	IGS
32	c	（A）10gactc（T）10	25	36 606	36 630	IGS
33	p1	（T）11	11	37 859	37 869	IGS
34	c	（A）10ttaaatacaaaaaaatattcgaatttcttacctcgatctgcaaaaaagtatattggagtttttttaa tctg（A）13	94	38 304	38 397	IGS
35	p1	（T）13	13	41 339	41 351	IGS
36	c	（ATA）4tataatattatagaatataatactattttcaattcaattcgattatcg（A）10	70	42 430	42 499	IGS
37	p2	（TC）5	10	43 355	43 364	rps14
38	p1	（T）13	13	49 768	49 780	IGS
39	p1	（A）10	10	50 147	50 156	Intron
40	p1	（A）12	12	50 719	50 730	Intron
41	p1	（A）10	10	52 216	52 225	IGS
42	p1	（A）10	10	52 718	52 727	IGS
43	p2	（TA）5	10	52 829	52 838	IGS
44	p3	（ATT）4	12	52 955	52 966	IGS
45	p1	（T）11	11	53 650	53 660	IGS
46	p1	（T）10	10	54 408	54 417	Intron
47	p1	（A）11	11	54 750	54 760	IGS
48	p1	（T）12	12	58 301	58 312	IGS
49	c	（T）12caaaaaatttggaaatcaagaaaaaaatgttcgacaacaaagcaagttgatcggttaattgaa tatttaattttttaatttaataagaa（AT）5gtaagttaata（AT）5	132	60 248	60 379	IGS
50	p2	（AT）7	14	60 763	60 776	IGS
51	p1	（A）12	12	62 667	62 678	IGS
52	c	（TA）6atttatataatatataatttaatatataa（T）11	52	63 002	63 053	IGS
53	p1	（A）10	10	63 826	63 835	Intron
54	p1	（A）11	11	65 500	65 510	matK
55	p1	（T）11	11	67 532	67 542	IGS
56	p1	（A）10	10	70 175	70 184	IGS
57	p2	（TA）5	10	70 399	70 408	IGS
58	p1	（A）11	11	70 791	70 801	rpl32
59	p3	（AAT）4	12	71 096	71 107	IGS
60	c	（A）10caagaatacgacttaacttcgtattgaaatcgaaacgttc（T）11	61	71 363	71 423	IGS
61	p2	（TA）5	10	71 803	71 812	IGS
62	p2	（AT）5	10	72 778	72 787	IGS
63	p1	（T）10	10	72 897	72 906	IGS
64	p1	（T）11	11	77 205	77 215	IGS
65	p1	（A）10	10	77 959	77 968	Intron
66	p1	（A）10	10	80 730	80 739	IGS
67	p1	（T）12	12	81 210	81 221	IGS
68	p1	（A）11	11	81 337	81 347	IGS
69	p1	（T）10	10	84 154	84 163	ycf1
70	p1	（T）10	10	84 535	84 544	ycf1
71	p1	（T）10	10	85 095	85 104	ycf1
72	p1	（A）10	10	85 215	85 224	ycf1
73	c	（AT）6tattatttccatatatttaattattatttccatatatttacatatataaata（AT）5	74	96 229	96 302	IGS
74	p2	（TA）5	10	107 601	107 610	IGS
75	p1	（T）11	11	111 743	111 753	IGS
76	p1	（A）14	14	112 699	112 712	IGS
77	c	（A）10tagaattctgaattcta（T）10	37	113 143	113 179	IGS
78	p1	（A）10	10	116 162	116 171	IGS
79	p1	（T）14	14	118 638	118 651	Intron
80	p1	（A）12	12	119 300	119 311	IGS
81	p1	（A）10	10	121 728	121 737	IGS
82	p1	（T）14	14	122 695	122 708	Intron
83	p1	（A）11	11	122 869	122 879	Intron

Table 3

Fig.3

References 33

1	GRAY J C.Genetic manipulation of the chloroplast genome ［J］.Plant Biotechnology，1989，12：317-335.
2	TONTI-FILIPPINI J， NEVILL P G， DIXON K，et al.What can we do with 1000 plastid genomes？［J］.The Plant Journal，2017，90（4）：808-818.
3	ZHOU J G， CHEN X L， CUI Y X，et al.Molecular structure and phylogenetic analyses of complete chloroplast genomes of two Aristolochia medicinal species［J］.International Journal of Molecular Sciences，2017，18（9）：1839.
4	YU X Q， DREW B， YANG J B，et al.Comparative chloroplast genomes of eleven Schima（Theaceae） species：Insights into DNA barcoding and phylogeny［J］.PLoS One，2017，12（6）：e0178026.
5	KAILA T， CHADUVLA P K， SAXENA S，et al.Chloroplast genome sequence of Pigeonpea（Cajanus cajan（L.） Millspaugh） and Cajanus scarabaeoides（L.） Thouars： genome organization and comparison with other Legumes［J］.Frontiers in Plant Science，2016，7：1847.
6	ZHA X， WANG X Y， LI J R，et al.Complete chloroplast genome of Sophora alopecuroides（Papilionoideae）：molecular structures，comparative genome analysis and phylogenetic analysis［J］.Journal of Genetics，2020，99（1）：13.
7	NI X L， LI B F， JIA G L，et al.Characterization of the complete chloroplast genome of Ammopiptanthus mongolicus（Papilionoideae），a rare and endangered plant to China［J］.Mitochondrial DNA Part B，2019，4（1）：1886-1887.
8	KAILA T， CHADUVLA P K， RAWAL H，et al.Chloroplast genome sequence of Clusterbean（Cyamopsis tetragonoloba L.）：genome structure and comparative analysis［J］.Genes，2017，8（9）：212.
9	OYEBANJI O， ZHANG R， CHEN S Y，et al.New insights into the plastome evolution of the Millettioid/Phaseoloid Clade （Papilionoideae，Leguminosae）［J］.Frontiers in Plant Science，2020，11：151.
10	LAVIN M， DOYLE J J， PALMER J D.Evolutionary significance of the loss of the chloroplast-DNA inverted repeat in the Leguminosae subfamily Papilionoideae［J］.Evolution，1990，44（2）：390-402.
11	TOBY PENINGTON R.Cladistic analysis of chloroplast DNA restriction site characters in Andira（Leguminosae：Dalbergieae）［J］.American Journal of Botany，1995，82（4）：526-534.
12	PALMER J D， THOMPSON W F.Rearrangements in the chloroplast genomes of Mung bean and pea［J］.Proceedings of the National Academy of Sciences of the United States of America，1981，78（9）：5533-5537.
13	BRUNEAU A， DOYLE J J， PALMER D J D.A chloroplast DNA inversion as a subtribal character in the Phaseoleae（Leguminosae）［J］.Systematic Botany，1990，15（3）：378-386.
14	中国植物志编辑委员会.中国植物志：第40卷［M］.北京：科学出版社，1998：80.
	China Plant Committee.Flora of China：Volume 40［M］.Beijing：Science Press，1998：80.
15	刘尚武.青海植物志：第2卷［M］.西宁：青海人民出版社，1999： 173.
	LIU S W.Flora of Qinghai：Volume 2［M］.Xining：Qinghai People’s Press，1999：173.
16	于婷，高新磊，韩冰，等.苦马豆化学成分及应用研究进展［J］.内蒙古农业科技，2010，（4）：93-95.
	YU T， GAO X L， HAN B，et al.Progress of research on the chemical composition and application of Spehaerophysa salsula［J］.Inner Mongolia Agricultural Science and Technology，2010，（4）：93-95.
17	马忠俊.苦马豆生物活性成分的研究［D］.沈阳：沈阳药科大学，2003.
	MA Z J.Research on the chemical constituents and biological activities of Sphaerophysa salsula（Pall.） DC［D］.Shenyang：Shenyang Pharmaceutical University，2003.
18	邓振山.西北地区苦马豆根瘤中内生细菌遗传多样性及其促植物生长特性的研究［D］.杨凌：西北农林科技大学，2010.
	DENG Z S.Genetic diversity of endophytic bacteria and their potential for promotion of plant growth within nodules of the Sphaerophysa salsula grown in Northwest China［D］.Yangling：Northwest A & F University，2010.
19	何雯.小花棘豆中苦马豆素对羊的毒性作用及大鼠星形胶质细胞影响的研究［D］.阿拉尔：塔里木大学，2016.
	HE W.Effect of swainsonine from Oxytropis glabra DC on toxic actions in sheep and astrocyte cell in rat［D］.Ala’er：Tarim University，2016.
20	DRIEMEIER D， COLODEL E M， GIMENO E J，et al.Lysosomal storage disease caused by Sida carpinifolia poisoning in goats［J］.Journal of Veterinary Pathology，2000，37（2）：153-159.
21	TAI T H， TANKSLEY S D.A rapid and inexpensive method for isolation of total DNA from dehydrated plant tissue［J］.Plant Molecular Biology Reporter，1990，8（4）：297-303.
22	DING B C， SUN Y， RONG F X，et al.The complete mitochondrial genome of Holothuria spinifera（Théel，1866）［J］.Mitochondrial DNA Part B，2020，5（2）：1679-1680.
23	TILLICH M， LEHWARK P， PELLIZZER T，et al.GeSeq-versatile and accurate annotation of organelle genomes［J］.Nucleic Acids Research，2017，45（W1）：W6-W11.
24	LOHSE M， DRECHSEL O， KAHLAU S，et al.OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets［J］.Nucleic Acids Research，2013，41（W1）：W575-W581.
25	SHIELDS D C， SHARP P M.Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases［J］.Nucleic Acids Research，1987，15（19）：8023-8040.
26	ZHANG D， GAO F L， JAKOVLIĆ I，et al.PhyloSuite：An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies［J］.Molecular Ecology Resources，2020，20（1）：348-355.
27	ZHANG T W， FANG Y J， WANG X M，et al.The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica：insights into the evolution of plant organellar genomes［J］.PLoS One，2012，7（1）：e30531．
28	叶友菊，倪州献，白天道，等.马尾松叶绿体基因组密码子偏好性分析［J］.基因组学与应用生物学，2018，37（10）：4464-4471.
	YE Y J， NI Z X， BAI T D，et al.The analysis of chloroplast genome codon usage bais in Pinus massoniana ［J］.Genomics and Applied Biology，2018，37（10）：4464-4471.
29	DU X Y， ZENG T， FENG Q，et al.The complete chloroplast genome sequence of yellow mustard（Sinapis alba L.） and its phylogenetic relationship to other Brassicaceae species［J］.Gene，2020，731：144340.
30	ASAF S， WAQAS M， KHAN A L，et al.The complete chloroplast genome of Wild Rice（Oryza minuta） and Its comparison to related species［J］.Frontiers in Plant Science，2017，8：304.
31	KUANG D Y， WU H， WANG Y L，et al.Complete chloroplast genome sequence of Magnolia kwangsiensis（Magnoliaceae）：implication for DNA barcoding and population genetics［J］.Genome，2011，54（8）：663-673.
32	KANE N C， CRONK Q.Botany without borders：barcoding in focus［J］.Molecular Ecology，2008，17（24）：5175-5176.
33	NOCK C J， WATERS D L E， EDWARDS M A，et al.Chloroplast genome sequences from total DNA for plant identification［J］.Plant Biotechnology Journal，2011，9（3）：328-333.

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