Comparative study on DNA barcoding of house oribatid mites based on the 18S and 28S ribosomal DNA gene

doi:10.12140/j.issn.1000-7423.2023.02.006

Abstract

Abstract: Objective To compare the validity and applicability of 18S and 28S rDNA genes in species identification of house oribatid mites. Methods Oribatid mite were isolated from the dust samples collected from residential houses, farmhouses and warehouses in 9 citiess of Anhui Province (Bozhou, Fuyang, Huainan, Chuzhou, Hefei, Wuhu, Tongling, Anqing, Huangshan) from February 2021 to October 2021, and the mite species were identified morphologically. The genomic DNA was extracted from each individual oribatid mite, and the 18S rDNA, 28S rDNA D3 and D8 genes were obtained by PCR, and sequenced. The sequences of house oribatid mites genes were downloaded from GenBank. The sequence feature analysis and genetic distance calculation were carried out based on MEGA X software, and the DNA barcoding gap analysis was performed through ABGD website. The phylogenetic tree was created using neighbor joining method. Results A total of 53 mites were collected and morphologically identified of species, which belongs to three families, five genera and five species, particularly for Scheloribates laevigatus (15), Oribatula sakamorii (9), Oppiella nova (10), Ramusella clavipectinata (10), Neoamerioppia interrogate (9). The 18S rDNA, 28S rDNA D3 and D8 gene haplotypes were obtained from these five mite species with 7, 5 and 11 haplotypes, respectively. A total of 42 sequences of house oribatid mites were downloaded from GenBank. Sequence analysis showed that the lengths of 18S rDNA, 28S rDNA D3 and D8 genes were 442-590, 247-331 and 270-283 bp, respectively, with GC contents of 45.6%, 52.2% and 57.5%, and variation rates of 17.6%, 21.4% and 21.7%, respectively. The mean intraspecies genetic distances of 18S rDNA, 28S rDNA D3 and D8 gene were 0.001, 0.001 and 0.005, respectively. The mean interspecies genetic distances were 0.064, 0.115 and 0.109, respectively, with the mean interspecies genetic distances greater than the mean intra-species genetic distances (more than 10-fold). The results of DNA barcode gap analysis showed that there were overlapping regions between the intraspecific and interspecific genetic distances of 18S rDNA and 28S rDNA D3 gene sequences, and there was an significant DNA barcode gap in 28S rDNA D8 gene sequences. The phylogenetic tree showed that the taxonomic order clustering of house oribatid mite family are consistent with the morphological clustering results, but Hypochthonius luteus and H. rufulus showed clustering together in the 18S rDNA gene systematic evolution tree and could not be separated. The 28S rDNA D3 gene systematic evolution tree showed cross-class clustering. Conclusion 18S rDNA and 28S rDNA D3 and D8 genes can be effectively used for species identification of house oribatid mites, of them, 28S rDNA D8 gene is suitable for the species identification of low-classification taxa, while 18S rDNA and 28S rDNA D3 genes are suitable for the species of high-classification taxa.

Key words: House oribatid mites, DNA barcode, 18S rDNA gene, 28S rDNA gene

CLC Number:

R384.429

CHEN Huilin, ZHU Yonghang, FAN Haiye, ZHAO Wei, LIU Luyao, CAO Yuxiang, YE Changjiang, SUN Entao. Comparative study on DNA barcoding of house oribatid mites based on the 18S and 28S ribosomal DNA gene[J]. CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES, 2023, 41(2): 163-169.

Figures/Tables 6

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科 Family	属 Genera	种 Species	采集地 Locality	样品数 No.sample	18S rDNA		28S rDNA D3		28S rDNA D8
科 Family	属 Genera	种 Species	采集地 Locality	样品数 No.sample	单倍型数No. haplotypes	登录号 GenBank accession no.	单倍型数 No. haplotypes	登录号 GenBank accession no.	单倍型数 No. haplotypes	登录号 GenBank accession no.
菌甲螨科Scheloribatidae	菌甲螨属 Scheloribates	滑菌甲螨 S. laevigatus	亳州市涡阳县	15	1	ON117321	1	ON117422	4	ON117427 - ON117430
若甲螨科 Oribatulidae	若甲螨属 Oribatula	盛若甲螨 O. sakamorii	芜湖市弋江区	9	1	ON117322	1	ON117423	2	ON117431 ON117432
奥甲螨科 Oppiidae	小奥甲螨属 Oppiella	新小奥甲螨 O. nova	明光市潘村镇	10	3	ON117324- ON117326	1	ON117425	2	ON117434 ON117435
	枝奥甲螨属 Ramusella	棒梳枝奥甲螨 R. clavipectinata	亳州市涡阳县	10	1	ON117327	1	ON117426	2	ON117436 ON117437
	新美奥甲螨属Neoamerioppia	间新美奥甲螨 N. interrogata	芜湖市弋江区	9	1	ON117323	1	ON117424	1	ON117433

科 Family	属 Genera	18S rDNA		28S rDNA D3
科 Family	属 Genera	种 Species	登录号 GenBank accession no.	种 Species	登录号 GenBank accession no.
菌甲螨科 Scheloribatidae	菌甲螨属 Scheloribates	白菌甲螨 S. pallidulus	AB818527	滑菌甲螨 S. laevigatus	KY686523 KY686524
		升菌甲螨 S. ascendens	EU432199	棒菌甲螨 S. latipes	KY686526 KY686527
				围脊菌甲螨 S. circumcarinatus	KY686515 KY686516
				原菌甲螨	KY686519
S. initialis	KY686520
奥甲螨科 Oppiidae	小奥甲螨属 Oppiella	新小奥甲螨 O. nova	KR081626 MH198176	新小奥甲螨 O. nova	KF293605 KF293609
		小奥甲螨 O. splendens	OL839303 MK630356	尼兰小奥甲螨 O. neerlandica	KY686441 KY686442
	球奥甲螨属 Globoppia	大球奥甲螨 G. maior	KR081613
贝奥甲螨属 Berniniella			哈氏贝奥甲螨 B. hauseri	KF293641
若甲螨科 Oribatulidae	若甲螨属 Oribatula	盛若甲螨 O. sakamorii	AB818530
若甲螨科 Oribatulidae	若甲螨属 Oribatula	盛若甲螨 O. sakamorii	AB818530				单奥甲螨属 Phauloppia	明亮单奥甲螨 P. lucorum	EU432198
大翼甲螨科 Galumnidae	大翼甲螨属 Galumna	矛大翼甲螨 G. lanceata	KX397630 EU432197				单奥甲螨属 Phauloppia	明亮单奥甲螨 P. lucorum	EU432198	矛大翼甲螨 G. lanceata	AY273519
大翼甲螨科 Galumnidae	大翼甲螨属 Galumna	矛大翼甲螨 G. lanceata	KX397630 EU432197							矛大翼甲螨 G. lanceata	AY273519	显大翼甲螨 G. obvia	KY681228 KY681229
	全大翼甲螨属 Pergalumna			脉全大翼甲螨 P. nervosa	KY686457 KY686458							显大翼甲螨 G. obvia	KY681228 KY681229
	全大翼甲螨属 Pergalumna			脉全大翼甲螨 P. nervosa	KY686457 KY686458	缝甲螨科 Hypochthoniidae	东缝甲螨属 Eohypochthonius	小东缝甲螨 E. gracilis	EF203777
	缝甲螨属 Hypochthonius	金黄缝甲螨 H. luteus	JQ000038 EU152475	金黄缝甲螨 H. luteus	JQ000345 EU152601	缝甲螨科 Hypochthoniidae	东缝甲螨属 Eohypochthonius	小东缝甲螨 E. gracilis	EF203777
	缝甲螨属 Hypochthonius	金黄缝甲螨 H. luteus	JQ000038 EU152475	金黄缝甲螨 H. luteus	JQ000345 EU152601			淡红缝甲螨 H. rufulus	KR081618 EF091427	淡红缝甲螨 H. rufulus	KY681249 KR081662
	天使甲螨属 Malacoangelia	浆天使甲螨 M. remigera	JN585911	浆天使甲螨 M. remigera	KR081665			淡红缝甲螨 H. rufulus	KR081618 EF091427	淡红缝甲螨 H. rufulus	KY681249 KR081662
	天使甲螨属 Malacoangelia	浆天使甲螨 M. remigera	JN585911	浆天使甲螨 M. remigera	KR081665	广缝甲螨科 Cosmochthoniidae	广缝甲螨属 Cosmochthonius	羊毛广缝甲螨 C. lanatus	JQ000040 JN585919

基因 Gene	种内遗传距离 Interspecific genetic distance			种间遗传距离 Intraspecific genetic distance
基因 Gene	最大值 Maximum	最小值 Minimum	平均值 Average	最大值 Maximum	最小值 Minimum	平均值 Average
18S rDNA	0.013	0	0.001	0.108	0	0.064
28S rDNA D3	0.004	0	0.001	0.231	0.002	0.115
28S rDNA D8	0.016	0	0.005	0.161	0.069	0.109