Characterization of the mitochondrial genome and phylogenetic implication of Schistosoma japonicum featured with “nocturnal cercarial emergence”

doi:10.12140/j.issn.1000-7423.2023.06.006

Abstract

Abstract:

Objective This study aimed to determine the complete mitochondrial genome sequence of Schistosoma japonicum featured with nocturnal cercarial emergence pattern and to explore its phylogenetic relationship with other S. japonicum geographical isolates from mainland China, providing new reference data for further study on population genetic structure and genetic diversity. Methods Field Oncomelania hupensis snails were collected from Shitai County of Anhui in 2020, and the infected snails were separated in the laboratory. ICR mice were infected with cercariae shed from the infected snails using abdominal patch method. The worms were obtained by perfusion from hepatic portal and mesenteric vein and randomly sampled for sequencing. The worm genomic DNA was extracted with blood/tissue DNA extraction Kit, and sequenced at paied-end using Illumina NovaSeq 6000 sequencing platform. The mitochondrial genome was assembled using GetOrganelle tool, and its structural features and base composition were analyzed using MEGA 11 software. The phylogenetic tree was constructed using the neighbour-joining (NJ) and maximum likelihood (ML) method based on 17 published mitochondrial genome sequences of S. japonicum from other parts of China. Results The complete circular mitochondrial genome of S. japonicum with nocturnal cercarial emergence pattern isolated from Shitai County of Anhui was 14 085 bp in length(Genbank accession no. ON637109), encoding 36 genes, consisting of 12 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, with the AT content of 71.35%. There were two gene-overlapping regions and 29 intergenic regions in the mitochondrial genome. Among the 22 tRNA genes, except for trnaC and trnaS1 genes, which missed the dihydrouridine (DHU) arm, the rest were able to form a typical cloverleaf secondary structure. Among the PCGs, the stop codon of cytb, nad4, nad2 and nad6 was TAA, which differed from other geographical strains in China with TAG as the stop codon. Phylogenetic trees constructed based on NJ and ML had similar topologies. The isolated strain of S. japonicum featured with “nocturnal cercarial emergence” in Shitai County, forms a single strain. S. japonicum strains from Taiwan, China and other regions of Chinese Mainland are separated to form one branch. Conclusion The stop codons of S. japonicum isolate from Shitai area of Anhui Province differed from those of other geographical isolates in China. Additionally, based on the phylogenetic analysis, the isolate featured with nocturnal cercarial emergence exhibited a more distant relationship with other regional isolates, showing greater

Key words: Mitochondrial genome, Sequence analysis, Phylogenetic relationship, Schistosoma japonicum, Nocturnal cercarial emergence

CLC Number:

R383.24

WANG Ning, PENG Hanqi, GAO Changzhe, CHENG Yuheng, LYU Dabing. Characterization of the mitochondrial genome and phylogenetic implication of Schistosoma japonicum featured with “nocturnal cercarial emergence”[J]. CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES, 2023, 41(6): 699-707.

Figures/Tables 8

Table 1

Fig. 1

Table 2

Table 3

Table 4

Fig. 2

Fig. 3

Fig. 4

References 34

[1]	LoVerde PT. Schistosomiasis[J]. Adv Exp Med Biol, 2019, 1154: 45-70. doi: 10.1007/978-3-030-18616-6_3 pmid: 31297759
[2]	Lo NC, Bezerra FSM, Colley DG, et al. Review of 2022 WHO guidelines on the control and elimination of schistosomiasis[J]. Lancet Infect Dis, 2022, 22(11): e327-e335. doi: 10.1016/S1473-3099(22)00221-3 pmid: 35594896
[3]	Kura K, Ayabina D, Hollingsworth TD, et al. Determining the optimal strategies to achieve elimination of transmission for Schistosoma mansoni[J]. Parasit Vectors, 2022, 15(1): 55. doi: 10.1186/s13071-022-05178-x
[4]	Hassan AS, Perera DJ, Ward BJ, et al. Therapeutic activity of a Salmonella-vectored Schistosoma mansoni vaccine in a mouse model of chronic infection[J]. Vaccine, 2021, 39(39): 5580-5588. doi: 10.1016/j.vaccine.2021.08.031 pmid: 34412919
[5]	Caldwell N, Afshar R, Baragaña B, et al. Perspective on schistosomiasis drug discovery: highlights from a schistosomiasis drug discovery workshop at wellcome collection, london, September 2022[J]. ACS Infect Dis, 2023, 9(5): 1046-1055. doi: 10.1021/acsinfecdis.3c00081 pmid: 37083395
[6]	Mcmanus DP, Dunne DW, Sacko M, et al. Schistosomiasis[J]. Nat Rev Dis Primers, 2018, 4(1): 14. doi: 10.1038/s41572-018-0017-4 pmid: 30093694
[7]	Dong Y, Zhang Y, Du CH, et al. Emergency treatment of schistosomiasis outbreaks in transmission-inter-rupted mountainous and hilly areas[J]. Chin J Schisto Control, 2019, 31(3): 323-325, 328. (in Chinese)
	(董毅, 张云, 杜春红, 等. 山丘型传播阻断地区血吸虫病突发疫情的应急处置[J]. 中国血吸虫病防治杂志, 2019, 31(3): 323-325, 328.)
[8]	Zou HY, Yu QF, Qiu C, et al. Meta-analyses of Schistosoma japonicum infections in wild rodents across China over time indicates a potential challenge to the 2030 elimination targets[J]. PLoS Negl Trop Dis, 2020, 14(9): e0008652. doi: 10.1371/journal.pntd.0008652
[9]	Guo KW, Niu AO. Studies on the genetic variation of two mitochondrial DNA molecules of Schistosoma japonicum[J]. Chin J Parasitol Parasit Dis, 2004, 22(5): 300-302. (in Chinese)
	(郭凯文, 牛安欧. 日本血吸虫线粒体DNA两个分子的遗传变异[J]. 中国寄生虫学与寄生虫病杂志, 2004, 22(5): 300-302.)
[10]	Tao W, Chen XF, Wu MY, et al. Effect of cementing ditch-based project on schistosomiasis control in Dingshen River Basin in Shitai County[J]. Chin J Schisto Control, 2018, 30(2): 222-225. (in Chinese)
	(陶伟, 陈雪峰, 吴明耀, 等. 石台县丁莘河流域水库灌区水利血防工程血吸虫病防治效果分析[J]. 中国血吸虫病防治杂志, 2018, 30(2): 222-225.)
[11]	Lu DB, Wang TP, Rudge JW, et al. Contrasting Reservoirs for Schistosoma japonicum between marshland and hilly regions in Anhui, China: a two-year longitudinal parasitological survey[J]. Parasitology, 2010, 137(1): 99-110. doi: 10.1017/S003118200999103X
[12]	Lu DB, Wang TP, Rudge JW, et al. Evolution in a multi-host parasite: chronobiological circadian rhythm and population genetics of Schistosoma japonicum cercariae indicates contrasting definitive host reservoirs by habitat[J]. Int J Parasitol, 2009, 39(14): 1581-1588. doi: 10.1016/j.ijpara.2009.06.003
[13]	Jones BP, Norman BF, Borrett HE, et al. Author correction: divergence across mitochondrial genomes of sympatric members of the Schistosoma indicum group and clues into the evolution of Schistosoma spindale[J]. Sci Rep, 2021, 11(1): 1246. doi: 10.1038/s41598-021-81050-9 pmid: 33414475
[14]	Lawton SP, Hirai H, Ironside JE, et al. Genomes and geography: genomic insights into the evolution and phylogeography of the genus Schistosoma[J]. Parasit Vectors, 2011, 4: 131. doi: 10.1186/1756-3305-4-131 pmid: 21736723
[15]	Chen XX, Yuan ZW, Li C, et al. Structural features and phylogenetic implications of Cicadellidae subfamily and two new mitogenomes leafhoppers[J]. PLoS One, 2021, 16(5): e0251207. doi: 10.1371/journal.pone.0251207
[16]	Donath A, Jühling F, Al-Arab M, et al. Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes[J]. Nucleic Acids Res, 2019, 47(20): 10543-10552. doi: 10.1093/nar/gkz833 pmid: 31584075
[17]	Greiner S, Lehwark P, Bock R. Organellar Genome DRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes[J]. Nucle Acid Res, 2019, 47(W1): W59-W64. doi: 10.1093/nar/gkz238
[18]	He JC, Chen XF, Wang TP, et al. Investigation on prevalence of Schistosoma japonicum infections in wild mice in Shitai County, Anhui Province, 2018[J]. Chin J Schisto Control, 2022, 34(6): 622-625. (in Chinese)
	(何家昶, 陈雪峰, 汪天平, 等. 2018年安徽省石台县野鼠血吸虫感染调查[J]. 中国血吸虫病防治杂志, 2022, 34(6): 622-625.)
[19]	Li ZJ, Ge J, Dai JR, et al. Biology and control of snail intermediate host of Schistosoma japonicum in the People’s republic of China[J]. Adv Parasitol, 2016, 92: 197-236.
[20]	Wu W, Feng AC, Huang YX. Research and control of advanced schistosomiasis japonica in China[J]. Parasitol Res, 2015, 114(1): 17-27. doi: 10.1007/s00436-014-4225-x pmid: 25403379
[21]	Li XH, Xu YX, Vance G, et al. Evidence that Rhesus macaques self-cure from a Schistosoma japonicum infection by disrupting worm esophageal function: a new route to an effective vaccine?[J]. PLoS Negl Trop Dis, 2015, 9(7): e0003925. doi: 10.1371/journal.pntd.0003925
[22]	Luo F, Yin MB, Mo XJ, et al. An improved genome assembly of the fluke Schistosoma japonicum[J]. PLoS Negl Trop Dis, 2019, 13(8): e0007612. doi: 10.1371/journal.pntd.0007612
[23]	Zarowiecki MZ, Huyse T, Littlewood DTJ. Making the most of mitochondrial genomes: markers for phylogeny, molecular ecology and barcodes in Schistosoma (Platyhelminthes∶Digenea)[J]. Int J Parasitol, 2007, 37(12): 1401-1418. pmid: 17570370
[24]	Han LH, Ke XR, Qin XY, et al. Mitogenome characteristics and evolution of Cordyceps[J]. Southwest China J Agric Sci, 2022, 35(7): 1520-1528. (in Chinese)
	(韩利红, 柯欣茹, 秦相月, 等. 虫草属线粒体基因组特征及系统发育[J]. 西南农业学报, 2022, 35(7): 1520-1528.)
[25]	Nahum LA, Mourão MM, Oliveira G. New frontiers in schistosoma genomics and transcriptomics[J]. J Parasitol Res, 2012, 2012: 849132.
[26]	Littlewood DTJ, Lockyer AE, Webster BL, et al. The complete mitochondrial genomes of Schistosoma haematobium and Schistosoma spindale and the evolutionary history of mitochondrial genome changes among parasitic flatworms[J]. Mol Phylogenet Evol, 2006, 39(2): 452-467. pmid: 16464618
[27]	Yin MB, Zheng HX, Su J, et al. Co-dispersal of the blood fluke Schistosoma japonicum and Homo sapiens in the Neolithic Age[J]. Sci Rep, 2015, 5: 18058. doi: 10.1038/srep18058
[28]	Li J, Chen F, Sugiyama H, et al. A specific indel marker for the Philippines Schistosoma japonicum revealed by analysis of mitochondrial genome sequences[J]. Parasitol Res, 2015, 114(7): 2697-2704. doi: 10.1007/s00436-015-4475-2
[29]	Zhao QP, Jiang MS, Littlewood DTJ, et al. Distinct genetic diversity of Oncomelania hupensis, intermediate host of Schistosoma japonicum in mainland China as revealed by ITS sequences[J]. PLoS Negl Trop Dis, 2010, 4(3): e611. doi: 10.1371/journal.pntd.0000611
[30]	Yang K, Wang XH, Yang GJ, et al. An integrated approach to identify distribution of Oncomelania hupensis, the intermediate host of Schistosoma japonicum, in a mountainous region in China[J]. Int J Parasitol, 2008, 38(8/9): 1007-1016. doi: 10.1016/j.ijpara.2007.12.007
[31]	Turgeon J, Bernatchez L. Clinal variation at microsatellite loci reveals historical secondary intergradation between glacial races of Coregonus artedi (Teleostei∶Coregoninae)[J]. Evolution, 2001, 55(11): 2274-2286. pmid: 11794787
[32]	Hu BJ, Xie HL, Li SM, et al. Measures and achievements of schistosomiasis control in the Yangtze River Basin[J]. Chin J Schisto Control, 2018, 30(5): 592-595. (in Chinese)
	(胡本骄, 谢红玲, 李胜明, 等. 长江流域血吸虫病防治举措与成效[J]. 中国血吸虫病防治杂志, 2018, 30(5): 592-595.)
[33]	Yin MB, Li HY, McManus DP, et al. Geographical genetic structure of Schistosoma japonicum revealed by analysis of mitochondrial DNA and microsatellite markers[J]. Parasit Vectors, 2015, 8: 150. doi: 10.1186/s13071-015-0757-x
[34]	Ji RX, Yu X, Ren TM, et al. Genetic diversity and population structure of Caryopteris mongholica revealed by reduced representation sequencing[J]. BMC Plant Biol, 2022, 22(1): 297. doi: 10.1186/s12870-022-03681-y

样品来源（缩写） Population location（Abbreviation）	经度 Longitude	纬度 Latitude	流行区类型 Types of ecological settings	GenBank登录号 GenBank accession no.
安徽石台 Shitai, Anhui（AHST）	117.49	30.21	山丘型 Hilly-type	ON637109（研究样品 Research sample）
安徽贵池 Guichi, Anhui（AHGC）	117.57	30.69	湖沼型 Lake-type	KU196299
安徽铜陵 Tongling, Anhui（AHTL）	117.80	30.95	湖沼型 Lake-type	KU196309
安徽枞阳 Zongyang, Anhui（AHZY）	117.25	30.71	湖沼型 Lake-type	KF279406
安徽无为 Wuwei, Anhui（AHWW）	117.90	31.31	湖沼型 Lake-type	KF279404
江苏无锡 Wuxi, Jiangsu（JSWX）	120.28	31.53	湖沼型 Lake-type	HM120843
浙江嘉善 Jiashan, Zhejiang（ZJJS）	120.93	30.84	湖沼型 Lake-type	HM120841
江西南昌 Nanchang, Jiangxi（JXNC）	115.95	28.55	湖沼型 Lake-type	KU196369
江西永修 Yongxiu, Jiangxi（JXYX）	115.83	29.02	湖沼型 Lake-type	HM120844
江西都昌 Duchang, Jiangxi（JXDC）	116.21	29.28	湖沼型 Lake-type	KU196360
湖南岳阳 Yueyang, Hunan（HNYY）	113.14	29.36	湖沼型 Lake-type	KU196338
湖南常德 Changde, Hunan（HNCD）	111.71	29.04	湖沼型 Lake-type	KU196328
湖北武汉 Wuhan, Hubei（HBWH）	114.31	30.60	湖沼型 Lake-type	HM120842
湖北沙市 Shashi, Hubei（HBSS）	112.25	30.31	湖沼型 Lake-type	KU196237
四川西昌 Xichang, Sichuan（SCXC）	102.20	27.50	山丘型 Hilly-type	KU196389
四川天全 Tianquan, Sichuan（SCTQ）	102.78	30.06	山丘型 Hilly-type	HM120846
云南洱源 Eryuan, Yunnan（YNEY）	99.95	26.12	山丘型 Hilly-type	KU196408
中国台湾 Taiwan, China（TW）	120.92	23.85	湖沼型 Lake-type	KU196407

基因 Gene	位置/nt Position/nt	长度/bp Length/bp	基因间隔/bp Intergenic sequences/bp	起始/终止密码子 Start and stop codons	反密码子 Anticodons	氨基酸数目 No. amino acid	(A + T)/%
trnR	1~65	65	11		TCG		66.15
nad5	77~1 663	1 587	42	ATG/TAG		528	73.03
trnG	1 706~1 775	70	7		TCC		70.00
cox3	1 783~2 433	651	14	ATG/TAA		216	72.35
trnE	2 448~2 516	69	9		TTC		62.32
trnH	2 526~2 590	65	5		GCG		75.38
cob	2 596~3 711	1 116	34	ATG/TAA		371	71.06
nad4L	3 746~4 009	264	-37	ATG/TAA		87	73.48
nad4	3 973~5 247	1 275	31	ATG/TAA		424	70.67
trnQ	5 279~5 345	67	62		TTG		58.21
trnF	5 408~5 468	61	0		GAA		65.57
trnM	5 469~5 535	67	0		CAT		73.13
atp6	5 536~6 054	519	15	ATG/TAA		172	72.45
nad2	6 070~6 924	855	3	ATG/TAA		284	72.87
trnA	6 928~6 995	68	18		TGC		73.53
trnD	7 014~7 078	65	1		GTC		63.08
nad1	7 080~7 982	891	-1	ATG/TAG		296	70.93
trnN	7 982~8 046	65	22		GTT		67.69
trnP	8 069~8 134	66	37		GAA		77.27
trnI	8 172~8 237	66	12		GAT		57.58
trnK	8 250~8 320	71	3		CTT		76.06
nad3	8 324~8 683	360	9	ATG/TAG		119	76.94
trnW	8 693~8 763	71	19		TCA		63.38
trnV	8 783~8 848	66	8		TAC		69.7
trnS1	8 857~8 919	63	6		GCT		69.84
cox1	8 926~10 569	1 644	60	GTG/TAG		547	68.49
trnT	10 630~10 698	69	0		TGT		73.91
rrnL	10 699~11 714	1 016	0				68.9
trnC	11 715~11 776	62	1		GCA		72.58
rrnS	11 778~12 518	741	4				66.67
cox2	12 523~13 131	609	10	ATG/TAA		202	69.13
nad6	13 142~13 600	459	68	ATG/TAA		152	76.03
trnY	13 669~13 735	67	14		GTA		71.64
trnL1	13 750~13 819	70	0		TAG		67.14
trnS2	13 820~13 887	68	129		TAA		75
trnL2	14 017~14 084	68	1		CAA		61.76

基因序列 Nucleotide sequence	A/%	T (U)/%	G/%	C/%	(A + T)/%	(G + C)/%	AT-skew	GC-skew
全基因组 Overall	25.14	46.21	20.37	8.28	71.35	28.65	-0.296	0.422
蛋白编码基因 Protein-coding gene	23.31	48.26	20.60	7.83	71.57	28.43	-0.349	0.451
密码子第一位点 Codon 1	26.63	41.11	24.08	8.18	67.74	32.26	-0.214	0.493
密码子第二位点 Codon 2	19.01	48.65	19.94	12.40	67.65	32.35	-0.438	0.233
密码子第三位点 Codon 3	24.31	55.01	17.77	2.91	79.33	20.67	-0.387	0.720
tRNA基因 tRNA genes	29.20	39.48	20.97	10.35	68.69	31.31	-0.150	0.339
rRNA基因 rRNA genes	29.76	38.19	20.72	11.33	67.96	32.04	-0.124	0.293

基因 Gene	A/%	T/%	G/%	C/%	(G + C)/%	AT-skew	GC-skew
nad5	21.30	51.73	20.54	6.43	26.97	-0.417	0.523
cox3	23.35	49.00	19.35	8.30	27.65	-0.355	0.400
cob	23.48	47.58	20.34	8.60	28.94	-0.339	0.406
nad4L	25.38	48.10	19.70	6.82	26.52	-0.309	0.486
nad4	23.92	46.74	21.18	8.16	29.33	-0.323	0.444
atp6	23.32	49.13	18.88	8.67	27.55	-0.356	0.371
nad2	21.05	51.81	20.24	6.90	27.13	-0.422	0.491
nad1	25.03	45.90	22.00	7.07	29.07	-0.294	0.514
nad3	23.89	53.06	18.05	5.00	23.06	-0.379	0.566
cox1	22.57	45.92	21.96	9.55	31.51	-0.341	0.394
cox2	27.75	41.38	21.35	9.52	30.87	-0.197	0.383
nad6	24.18	51.86	18.08	5.88	23.97	-0.364	0.509