CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES >

2023 , Vol. 41 >Issue 2: 163 - 169

DOI: https://doi.org/10.12140/j.issn.1000-7423.2023.02.006

ORIGINAL ARTICLES

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

  • CHEN Huilin ,
  • ZHU Yonghang ,
  • FAN Haiye ,
  • ZHAO Wei ,
  • LIU Luyao ,
  • CAO Yuxiang ,
  • YE Changjiang ,
  • SUN Entao
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  • Laboratory of Health Inspection and Quarantine, Wannan Medical College, Wuhu 241002, Anhui, China

Received date: 2022-06-22

  Revised date: 2022-10-10

  Online published: 2023-04-10

Supported by

National Natural Science Foundation of China(31870352);Anhui Province University Students Innovation and Entrepreneurship Education and Training Program Project(S202110368044);2021 University Students Scientific Research Grant Program of Wannan Medical College(WK2021XS20)

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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

Cite this article

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 . DOI: 10.12140/j.issn.1000-7423.2023.02.006

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