Biodiv Sci ›› 2022, Vol. 30 ›› Issue (12): 22252. DOI: 10.17520/biods.2022252
Special Issue: 土壤生物与土壤健康
• Technology and Methodology • Previous Articles Next Articles
Cong Xu1, Feiyu Zhang1, Daoyuan Yu2, Xin Sun3, Feng Zhang1,*()
Received:
2022-05-09
Accepted:
2022-08-18
Online:
2022-12-20
Published:
2022-11-25
Contact:
*E-mail: fzhang@njau.edu.cn
Cong Xu, Feiyu Zhang, Daoyuan Yu, Xin Sun, Feng Zhang. Performance evaluation of molecular taxonomy assignment tools for soil invertebrates[J]. Biodiv Sci, 2022, 30(12): 22252.
类群 Taxa | 分子标记 Markers | 物种数目 Species number | 属数目 Genus number | 科数目 Family number |
---|---|---|---|---|
弹尾纲 Collembola | COI | 1,211 | 157 | 22 |
16S | 387 | 81 | 18 | |
18S | 163 | 79 | 19 | |
蜱螨亚纲 Acari | COI | 1,675 | 460 | 190 |
16S | 456 | 76 | 28 | |
18S | 635 | 459 | 220 | |
环带纲 Clitellata | COI | 1,297 | 255 | 39 |
16S | 972 | 214 | 28 | |
18S | 342 | 203 | 42 | |
色矛纲 Chromadorea | COI | 939 | 249 | 86 |
16S | 170 | 64 | 28 | |
18S | 1,042 | 430 | 135 | |
4个类群合并 Merged | COI | 5,122 | 1,121 | 337 |
Table 1 The biodiversity showed in databases of different groups for COI, 16S and 18S
类群 Taxa | 分子标记 Markers | 物种数目 Species number | 属数目 Genus number | 科数目 Family number |
---|---|---|---|---|
弹尾纲 Collembola | COI | 1,211 | 157 | 22 |
16S | 387 | 81 | 18 | |
18S | 163 | 79 | 19 | |
蜱螨亚纲 Acari | COI | 1,675 | 460 | 190 |
16S | 456 | 76 | 28 | |
18S | 635 | 459 | 220 | |
环带纲 Clitellata | COI | 1,297 | 255 | 39 |
16S | 972 | 214 | 28 | |
18S | 342 | 203 | 42 | |
色矛纲 Chromadorea | COI | 939 | 249 | 86 |
16S | 170 | 64 | 28 | |
18S | 1,042 | 430 | 135 | |
4个类群合并 Merged | COI | 5,122 | 1,121 | 337 |
Fig. 4 Relative running speed and memory usage of five taxonomic assignment tools when applying reference databases with 1,000 sequences (a and b) and 5,000 sequences (c and d) respectively
分类预测软件 Tools | 推荐使用情况 Recommendation on application |
---|---|
EPA-NG | 以COI作为分子标记且参考数据库不大的场合 COI is used as the marker and the reference database is small |
VSEARCH | 以16S或18S作为分子标记或者参考数据库较大的场合 16S/18S is used as the marker; the reference database includes thousands of sequences or more |
HS-BLASTN | 同VSEARCH, 但优先级不如VSEARCH Similar to VSEARCH |
APPLES | 仅预测较高阶元的场合 Predicting higher taxonomical hierarchy |
RAPPAS | 目标序列间长度差异较大的场合 When sequence lengths differ greatly |
Table 2 The recommendation on application of five taxonomic assignment tools
分类预测软件 Tools | 推荐使用情况 Recommendation on application |
---|---|
EPA-NG | 以COI作为分子标记且参考数据库不大的场合 COI is used as the marker and the reference database is small |
VSEARCH | 以16S或18S作为分子标记或者参考数据库较大的场合 16S/18S is used as the marker; the reference database includes thousands of sequences or more |
HS-BLASTN | 同VSEARCH, 但优先级不如VSEARCH Similar to VSEARCH |
APPLES | 仅预测较高阶元的场合 Predicting higher taxonomical hierarchy |
RAPPAS | 目标序列间长度差异较大的场合 When sequence lengths differ greatly |
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