TABLE I.
Summary of datasets including number of OTUs, number of analyzed sites (before slash), total number of sites (after slash), and the percentage of analyzed sites (in parentheses) for each gene separately, and combined, in comparison with datasets used in Miadlikowska et al. (2006). The 5-gene dataset includes taxa for which complete or partial data from all five genes (nucSSU, nucLSU, mitSSU, RPB1 and RPB2) were available. The 5+4-gene, 5+4+3-gene, and 5+4+3+2-gene datasets include taxa for which at least four, three, or two genes were included, respectively.
| Datasets | Newly added OTUs or sequences to GenBankc |
Missing sequencesc |
5-gene dataset/ 2006 |
5-gene dataset/ this study |
5+4-gene dataset/ 2006 |
5+4-gene dataset/ this study |
5+4+3-gene dataset/ 2006 |
5+4+3-gene dataset/ this study |
5+4+3+2- gene dataset/ this study |
|---|---|---|---|---|---|---|---|---|---|
| No. of OTUs/percent of missing data | NA | NA | 111/0% | 183 (+72)/0% | 188/26% | 388 (+200)/10% | 274/37% | 764 (+490)/25% | 1317 (+553)/54% |
| nucSSU | 143 OTUs | 701 | 1125/7445 (15%) | 1494/15913 (9%) | 1085/7228 (15%) | 1494/15913 (9%) | 1071/7215 (15%) | 1494/15913 (9%) | 1494/15913 (9%) |
| nucLSU | 162 OTUs | 127 | 1141/5162 (22%) | 1061/9363 (11%) | 1121/5151 (22%) | 1061/9363 (11%) | 1122/5096 (22%) | 1061/9363 (11%) | 1061/9363 (11%) |
| mitSSU | 174 OTUs | 127 | 471/2635 (17%) | 429/3642 (12%) | 437/2691 (16%) | 429/3642 (12%) | 445/2862 (15%) | 429/3642 (12%) | 429/3642 (12%) |
| RPB1 | 104 (114a) OTUs | 780 (2022a) | 2688/3159 (85%) | 2676/3172 (84%) | 2676/3243 (82%) | 2676/3172 (84%) | 2673/3229 (83%) | 2676/3172 (84%) | 2676/3172 (84%) |
| RPB2 | 59 (80b) OTUs | 879 (1924b) | 1932/2291 (84%) | 1773/2307 (77%) | 1851/2349 (79%) | 1773/2307 (77%) | 1803/2409 (75%) | 1773/2307 (77%) | 1773/2307 (77%) |
| Combined | 642 seq. | 2614 | 7357/20692 (35%) | 7433/34397 (22%) | 7170/20662 (35%) | 7433/34397 (22%) | 7114/20811 (34%) | 7433/34397 (22%) | 7433/34397 (22%) |
a
RPB1 (A–F) and RPB1 (F–G) separately
b
RPB2 (5–7) and RPB2 (7–11) separately
c
In the most inclusive (5+4+3+2-gene) dataset assembled for this study.