Differences of eDNA metabarcoding fragments in relative fish species resolution

Chen Zhi; Ma Chunlai; Ye Le; Yang Chaojie; Wang Haishan

doi:10.12284/hyxb2022150

Volume 44 Issue 8

Aug. 2022

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Chen Zhi，Ma Chunlai，Ye Le, et al. Differences of eDNA metabarcoding fragments in relative fish species resolution[J]. Haiyang Xuebao，2022, 44(8)：51–65 doi: 10.12284/hyxb2022150

Citation:

Chen Zhi，Ma Chunlai，Ye Le, et al. Differences of eDNA metabarcoding fragments in relative fish species resolution[J]. Haiyang Xuebao，2022, 44(8)：51–65 doi: 10.12284/hyxb2022150

Citation:

Chen Zhi，Ma Chunlai，Ye Le, et al. Differences of eDNA metabarcoding fragments in relative fish species resolution[J]. Haiyang Xuebao，2022, 44(8)：51–65 doi: 10.12284/hyxb2022150

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Differences of eDNA metabarcoding fragments in relative fish species resolution

doi: 10.12284/hyxb2022150

Chen Zhi^{1, 2
,},
Ma Chunlai^{1, 2},
Ye Le^{1, 2},
Yang Chaojie^{1, 2},
Wang Haishan^{1, 2
,
,}

1.
Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Ministry of Education, Hainan Tropical Ocean University, Sanya 572022, China
2.
Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya 572022, China

Received Date: 2022-02-17
Rev Recd Date: 2022-03-25

Available Online: 2022-04-24

Publish Date: 2022-08-15

Abstract

Abstract

The applicability of environmental DNA (eDNA) metabarcoding fragments to relative fish species had not been compared. There was a risk of “species loss” in diversity surveys. In order to screen out the best fragments, we compared the resolution rate differences of 15 eDNA metabarcoding fragments in 106 genera (a total of 935 species). The results were as follows: (1) the protein-coding gene (COI, fragment 15) had the highest resolution rate, but the universality of its corresponding primer pairs was the worst; the overall mean distance based on primer pair sequence of fragment 09, fragment 11, fragment 07, fragment 03 and fragment 12 were obviously large, suggesting their eDNA amplification efficiency were possibly low. (2) The resolution rates were significantly affected by the length of fragments, and the fragment 05, fragment 06, fragment 01, fragment 02 and fragment 13 of ribosomal genes had a higher resolution rate except fragment 15. (3) Non-metric multidimensional scaling analysis (NMDS) showed that there were great differences among different genes and different fragments belonging to the same gene. Therefore, the combination application of multi-fragment and multi-gene should be considered; besides, fragment 01 and fragment 02, and fragment 05 and fragment 06 were close to each other in the NMDS plot. They function of fish resolution were overlapped. (4) Species groups affected the resolution results, and eDNA studies stilled need to develop fragments with higher resolution rates. Based on the resolution rate of relative species, the universality of primer pairs and NMDS analysis, this study recommended fragment 01 (Mifish-U) for 2×150 bp sequencing platform and fragment 05 (Ac12S) for 2×250 bp sequencing platform, supplemented by fragment 13 (Vert-16S-eDNA) to investigate the diversity of relative fish. This study provided some support for improving the accuracy of fish eDNA survey results.
- eDNA metabarcoding,
- relative fish species resolution,
- 12S,
- amplicon length,
- multi-fragments

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References(40)

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