Investigation on the genetic diversity of Sarcocheilichthys sinensis from diverse geographical populations and other species within the Sarcocheilichthys genus through the analysis of mitochondrial COI sequence segments

doi:10.3969/j.issn.1004-1524.20230874

Acta Agriculturae Zhejiangensis ›› 2024, Vol. 36 ›› Issue (8): 1779-1788.DOI: 10.3969/j.issn.1004-1524.20230874

• Animal Science • Previous Articles Next Articles

Investigation on the genetic diversity of Sarcocheilichthys sinensis from diverse geographical populations and other species within the Sarcocheilichthys genus through the analysis of mitochondrial COI sequence segments

HUANG Hui(), CHU Tianjiang, XIE Nan, LIU Kai()

Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China

Received:2023-07-24 Online:2024-08-25 Published:2024-09-06
Contact: LIU Kai

Abstract

Abstract:

The genus Sarcocheilichthys, commonly found in East Asia, comprises small freshwater fish species with potential for aquaculture and development. Gaining a thorough understanding of the genetic structure and geographic variation of Sarcocheilichthys fish is of great significance for scientifically formulating conservation plans and ensuring sustainable utilization of wild resources. The experimental subjects included S. parvus(XQ) of 20 individuals, S. kiangsiensis(JXQ) of 20 individuals, S. nigripinnis(HQQ) of 20 individuals, S. lacustris(DBQ) of 24 individuals, and multiple geographic populations of S. sinensis, including Huaihe population (HQ_HH) of 20 individuals, Minjiang population (HQ_MJ) of 17 individuals, Jiangxi population (HQ_JX) of 15 individuals, and Jiande population (HQ_JD) of 17 individuals. The mitochondrial cytochrome C oxidase subunit I (COI) sequence segments of each population were sequenced and analyzed. Among the 153 obtained sequence samples, there were 507 conserved sites, 154 variable sites, 150 parsimony informative sites, and 27 sites with base deletions or insertions, with an average transition/transversion ratio of 5.2. The H_d (haplotype diversity) of the HQQ population was the lowest (0.442), slightly higher in the HQ_HH population (0.574), and further increased in the DBQ population (0.707). The XQ population showed the highest H_d (0.963), while HQ_MJ and HQ_JX populations had slightly lower H_d values than XQ (0.860 and 0.848, respectively). Nucleotide diversity exhibited a similar trend to H_d results. A total of 153 individuals defined 56 haplotypes, and each population exhibited major haplotypes within their respective haplotype networks, such as Hap_2, Hap_33, and Hap_37, among others. The UPGMA molecular phylogenetic tree, hierarchical clustering tree, and NeighborNet molecular phylogenetic network constructed based on genetic distance indicated that the genetic relationships between XQ, HQQ, JXQ, and other Sarcocheilichthys fish were relatively distant. At the same time, DBQ had a closer genetic relationship with the HQ_HH population. This study used COI sequence segments to assess the genetic diversity of four geographic populations of S. sinensis and four other Sarcocheilichthys species. The research results contribute to understanding the current genetic diversity of different geographic populations of S. sinensis and four other Sarcocheilichthys species, providing valuable insights for the conservation and breeding of germplasm resources in S. sinensis and other Sarcocheilichthys fish in the future.

Key words: Sarcocheilichthys sinensis, Sarcocheilichthys genus, mitochondria, COI, genetic diversity

CLC Number:

HUANG Hui, CHU Tianjiang, XIE Nan, LIU Kai. Investigation on the genetic diversity of Sarcocheilichthys sinensis from diverse geographical populations and other species within the Sarcocheilichthys genus through the analysis of mitochondrial COI sequence segments[J]. Acta Agriculturae Zhejiangensis, 2024, 36(8): 1779-1788.

Figures/Tables 5

References 40

[1]	FROESE R, PAULY D. FishBase[EB/OL]. [2023-05-04]. https://fishbase.mnhn.fr/.
[2]	LU Y R, FANG C C, HE S P. Cnfishbase: a cyber Chinese fish database[J]. Zoological Research, 2023, 44(5): 950-953.
[3]	BETANCUR-R R, WILEY E O, ARRATIA G, et al. Phylogenetic classification of bony fishes[J]. BMC Evolutionary Biology, 2017, 17(1): 162.
[4]	TAN M, ARMBRUSTER J W. Phylogenetic classification of extant Genera of fishes of the order Cypriniformes (Teleostei: Ostariophysi)[J]. Zootaxa, 2018, 4476(1): 6-39.
[5]	刘思情, 唐琼英, 李小娟, 等. 基于线粒体细胞色素b基因的黑鳍鳈(Sarcocheilichthys nigripinnis)生物地理学过程分析[J]. 动物学研究, 2013, 34(5): 437-445.
	LIU S Q, TANG Q Y, LI X J, et al. Phylogeographic analyses of Sarcocheilichthys nigripinnis(Teleostei: Cyprinidae) based on mitochondrial DNA Cyt b gene sequences[J]. Zoological Research, 2013, 34(5): 437-445. (in Chinese with English abstract)
[6]	朱传坤, 潘正军, 常国亮, 等. 基于线粒体DNA标记对3个华鳈群体的遗传结构分析[J]. 江苏农业科学, 2020, 48(5): 50-56.
	ZHU C K, PAN Z J, CHANG G L, et al. Genetic structure analysis of three Sarcocheilichthys sinensis populations based on mitochondrial DNA markers[J]. Jiangsu Agricultural Sciences, 2020, 48(5): 50-56. (in Chinese with English abstract)
[7]	HICKERSON M J, CARSTENS B C, CAVENDER-BARES J, et al. Phylogeography’s past, present, and future: 10 years after Avise, 2000[J]. Molecular Phylogenetics and Evolution, 2010, 54(1): 291-301.
[8]	HEBERT P D N, CYWINSKA A, BALL S L, et al. Biological identifications through DNA barcodes[J]. Proceedings Biological Sciences, 2003, 270(1512): 313-321.
[9]	ZHANG L, TANG Q Y, LIU H Z. Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys[J]. Journal of Fish Biology, 2008, 72(5): 1122-1137.
[10]	GREEN M R, SAMBROOK J. Isolation of high-molecular-weight DNA from suspension cultures of mammalian cells using proteinase K and phenol[J]. Cold Spring Harbor Protocols, 2018, 2018(4): 317-321.
[11]	IVANOVA N V, ZEMLAK T S, HANNER R H, et al. Universal primer cocktails for fish DNA barcoding[J]. Molecular Ecology Notes, 2007, 7(4): 544-548.
[12]	MENG G L, LI Y Y, YANG C T, et al. MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization[J]. Nucleic Acids Research, 2019, 47(11): e63.
[13]	KATOH K, STANDLEY D M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability[J]. Molecular Biology and Evolution, 2013, 30(4): 772-780.
[14]	ALI R H, BOGUSZ M, WHELAN S. Identifying clusters of high confidence homologies in multiple sequence alignments[J]. Molecular Biology and Evolution, 2019, 36(10): 2340-2351.
[15]	PARADIS E, SCHLIEP K. Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R[J]. Bioinformatics, 2019, 35(3): 526-528.
[16]	KIMURA M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences[J]. Journal of Molecular Evolution, 1980, 16(2): 111-120.
[17]	OKSANEN J, BLANCHET FG, KINDT R, et al. Vegan: Community Ecology Package[EB/OL].(2013-01-04). R Package Version 22-1. http://vegan.r-forge.r-project.org/.
[18]	KAMVAR Z N, TABIMA J F, GRÜNWALD N J. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction[J]. PeerJ, 2014, 2: e281.
[19]	YU G C, SMITH D K, ZHU H C, et al. Ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data[J]. Methods in Ecology and Evolution, 2017, 8(1): 28-36.
[20]	SUZUKI R, SHIMODAIRA H. Pvclust: Hierarchical clustering with p-values via multiscale bootstrap resampling[EB/OL]. [2019-11-19]. R Package Version 2.2- 0: The R Foundation. Vienna, 2019. https://cran.r-project.org/web/packages/pvclust/.
[21]	HUSON D H, BRYANT D. Application of phylogenetic networks in evolutionary studies[J]. Molecular Biology and Evolution, 2006, 23(2): 254-267.
[22]	LEIGH J W, BRYANT D. Popart: full-feature software for haplotype network construction[J]. Methods in Ecology and Evolution, 2015, 6(9): 1110-1116.
[23]	ROZAS J, FERRER-MATA A, SÁNCHEZ-DELBARRIO J C, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets[J]. Molecular Biology and Evolution, 2017, 34(12): 3299-3302.
[24]	EXCOFFIER L, LISCHER H E L. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows[J]. Molecular Ecology Resources, 2010, 10(3): 564-567.
[25]	TAMURA K, STECHER G, KUMAR S. MEGA11: molecular evolutionary genetics analysis version 11[J]. Molecular Biology and Evolution, 2021, 38(7): 3022-3027.
[26]	MIELKE P W, BERRY K J. Description of MRPP[M]// Permutation methods. New York: Springer, 2001: 9-65.
[27]	VAN SICKLE J, HUGHES R M. Classification strengths of ecoregions, catchments, and geographic clusters for aquatic vertebrates in Oregon[J]. Journal of the North American Benthological Society, 2000, 19(3): 370-384.
[28]	黄辉, 刘凯, 王宇希, 等. 不同群体日本沼虾的线粒体COI基因序列分析[J]. 湖北农业科学, 2023, 62(5): 179-182, 189.
	HUANG H, LIU K, WANG Y X, et al. Analysis of mitochondrial COI sequences from different populations of Macrobrachium nipponense japonicus[J]. Hubei Agricultural Sciences, 2023, 62(5): 179-182, 189. (in Chinese with English abstract)
[29]	刘士力, 卞玉玲, 贾永义, 等. 基于线粒体COⅠ基因序列的红螯螯虾养殖群体遗传结构分析[J]. 浙江农业学报, 2021, 33(8): 1385-1392.
	LIU S L, BIAN Y L, JIA Y Y, et al. Genetics analysis based on mitochondrial COⅠ sequences in five cultured populations of red-claw crayfish (Cherax quadricarinatus)[J]. Acta Agriculturae Zhejiangensis, 2021, 33(8): 1385-1392. (in Chinese with English abstract)
[30]	余科, 安苗, 黄胜, 等. 清水江斑鳜COI基因序列分析[J]. 贵州畜牧兽医, 2020, 44(5): 5-10.
	YU K, AN M, HUANG S, et al. Sequence analysis of COI gene of Qingshuijiang Siniperca scherzeri[J]. Guizhou Journal of Animal Husbandry & Veterinary Medicine, 2020, 44(5): 5-10. (in Chinese with English abstract)
[31]	陈琴, 彭超, 赵峰, 等. 基于COⅠ序列研究南海芋螺遗传多样性[J]. 基因组学与应用生物学, 2020, 39(9): 3955-3960.
	CHEN Q, PENG C, ZHAO F, et al. Study on genetic diversity of cone snail in South China Sea based on COⅠ sequences[J]. Genomics and Applied Biology, 2020, 39(9): 3955-3960. (in Chinese with English abstract)
[32]	STOLTZFUS A, NORRIS R W. On the causes of evolutionary transition: transversion bias[J]. Molecular Biology and Evolution, 2016, 33(3): 595-602.
[33]	LANAVE C, TOMMASI S, PREPARATA G, et al. Transition and transversion rate in the evolution of animal mitochondrial DNA[J]. Bio Systems, 1986, 19(4): 273-283.
[34]	KUMAR S. Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates[J]. Genetics, 1996, 143(1): 537-548.
[35]	FÉRAL J P. How useful are the genetic markers in attempts to understand and manage marine biodiversity?[J]. Journal of Experimental Marine Biology and Ecology, 2002, 268(2): 121-145.
[36]	GRANT W, BOWEN B. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation[J]. Journal of Heredity, 1998, 89(5): 415-426.
[37]	SKIBINSKI D O F. DNA tests of neutral theory: applications in marine genetics[M]// SOLÉ-CAVA A M, RUSSO C A M, THORPE J P. Marine genetics. Dordrecht: Springer, 2000: 137-152.
[38]	HOLSINGER K. Lecture notes in population genetics[EB/OL].(2014-11-08). https://darwin1.eeb.uconn.edu/eeb348-notes/Lecture-Notes-in-Population-Genetics.pdf.
[39]	TODISCO V, VODĂ R, PROSSER S W J, et al. Next generation sequencing-aided comprehensive geographic coverage sheds light on the status of rare and extinct populations ofAporiabutterflies (Lepidoptera: Pieridae)[J]. Scientific Reports, 2020, 10: 13970.
[40]	WU J, CAO D C, LV W H, et al. The complete mitochondrial genome sequence of Sarcochellichthys lacustris (Dybowski)[J]. Mitochondrial DNA, 2015, 26(5): 795-796.

群体Populations	T/%	C/%	A/%	G/%	A+T/%	C+G/%	TS/TV
华鳈淮河群体, HQ_HH Huaihe population of S. sinensis	27.28	28.90	23.66	20.16	50.94	49.06	2.0
华鳈建德群体HQ_JD Jiande population of S. sinensis	27.79	28.21	24.02	19.98	51.81	48.19	1.7
华鳈江西群体HQ_JX Jiangxi population of S. sinensis	27.88	28.14	24.14	19.84	52.02	47.98	20.7
华鳈闽江群体HQ_MJ Minjiang population of S. sinensis	27.89	28.06	24.60	19.45	52.49	47.51	11.2
东北鳈 DBQ S. lacustris	27.29	28.87	23.69	20.15	50.98	49.02	1.8
黑鳍鳈HQQ S. nigripinnis	29.36	27.66	23.89	19.09	53.25	46.75	1.7
江西鳈JXQ S. kiangsiensis	27.96	29.05	23.53	19.46	51.49	48.51	4.5
小鳈XQ S. parvus	29.45	27.13	24.76	18.66	54.21	45.79	7.6

群体Populations	T/%	C/%	A/%	G/%	A+T/%	C+G/%	TS/TV
华鳈淮河群体, HQ_HH Huaihe population of S. sinensis	27.28	28.90	23.66	20.16	50.94	49.06	2.0
华鳈建德群体HQ_JD Jiande population of S. sinensis	27.79	28.21	24.02	19.98	51.81	48.19	1.7
华鳈江西群体HQ_JX Jiangxi population of S. sinensis	27.88	28.14	24.14	19.84	52.02	47.98	20.7
华鳈闽江群体HQ_MJ Minjiang population of S. sinensis	27.89	28.06	24.60	19.45	52.49	47.51	11.2
东北鳈 DBQ S. lacustris	27.29	28.87	23.69	20.15	50.98	49.02	1.8
黑鳍鳈HQQ S. nigripinnis	29.36	27.66	23.89	19.09	53.25	46.75	1.7
江西鳈JXQ S. kiangsiensis	27.96	29.05	23.53	19.46	51.49	48.51	4.5
小鳈XQ S. parvus	29.45	27.13	24.76	18.66	54.21	45.79	7.6

群体 Populations	变异位点数 Number of variation sites	单倍型数 Haplotype number	单倍型多样性H_d Haplotype diversity	核苷酸多样性π Nucleotide diversity	Tajima’s D	Fu’s Fs
华鳈淮河群体, HQ_HH	3	4	0.574	0.001 01	-0.526 40	-0.881 90
Huaihe population of S. sinensis
华鳈建德群体HQ_JD	5	6	0.794	0.001 96	-0.892 18	-1.793 11
Jiande population of S. sinensis
华鳈江西群体HQ_JX	18	9	0.848	0.007 90	-0.110 15	-0.130 98
Jiangxi population of S. sinensis
华鳈闽江群体HQ_MJ	26	9	0.860	0.013 80	0.908 58	2.052 88
Minjiang population of S. sinensis
东北鳈 DBQ S. lacustris	7	9	0.707	0.001 70	-1.210 45	-5.311 87^*
黑鳍鳈HQQ S. nigripinnis	4	5	0.442	0.000 98	-1.205 71	-2.218 43^*
江西鳈JXQ S. kiangsiensis	4	5	0.774	0.001 91	0.388 91	-0.487 48
小鳈XQ S. parvus	47	15	0.963	0.024 58	1.020 70	-1.012 20

群体 Populations	变异位点数 Number of variation sites	单倍型数 Haplotype number	单倍型多样性H_d Haplotype diversity	核苷酸多样性π Nucleotide diversity	Tajima’s D	Fu’s Fs
华鳈淮河群体, HQ_HH	3	4	0.574	0.001 01	-0.526 40	-0.881 90
Huaihe population of S. sinensis
华鳈建德群体HQ_JD	5	6	0.794	0.001 96	-0.892 18	-1.793 11
Jiande population of S. sinensis
华鳈江西群体HQ_JX	18	9	0.848	0.007 90	-0.110 15	-0.130 98
Jiangxi population of S. sinensis
华鳈闽江群体HQ_MJ	26	9	0.860	0.013 80	0.908 58	2.052 88
Minjiang population of S. sinensis
东北鳈 DBQ S. lacustris	7	9	0.707	0.001 70	-1.210 45	-5.311 87^*
黑鳍鳈HQQ S. nigripinnis	4	5	0.442	0.000 98	-1.205 71	-2.218 43^*
江西鳈JXQ S. kiangsiensis	4	5	0.774	0.001 91	0.388 91	-0.487 48
小鳈XQ S. parvus	47	15	0.963	0.024 58	1.020 70	-1.012 20

群体Populations	HQ_HH	HQ_JD	HQ_JX	HQ_MJ	DBQ	HQQ	JXQ	XQ
HQ_HH	0.001 03
HQ_JD	0.017 13	0.001 27
HQ_JX	0.017 19	0.011 93	0.007 80
HQ_MJ	0.028 84	0.024 98	0.025 11	0.013 56
DBQ	0.001 59	0.017 36	0.017 45	0.028 98	0.001 74
HQQ	0.135 76	0.134 12	0.133 94	0.131 88	0.135 99	0.001 00
JXQ	0.128 40	0.137 85	0.132 57	0.131 41	0.129 88	0.065 47	0.001 94
XQ	0.148 29	0.143 67	0.140 44	0.135 06	0.148 53	0.133 86	0.140 44	0.025 27

Investigation on the genetic diversity of Sarcocheilichthys sinensis from diverse geographical populations and other species within the Sarcocheilichthys genus through the analysis of mitochondrial COI sequence segments

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