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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.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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