Spreadsheet: 52c78c22-0bc5-4130-8a65-6eee5d54bb68
Sheet: Sheet1

Supplementary Table 2: T. hominis genes potentially containing introns. 'Classical intron motif' refers to the Microsporidia-conserved motif*, which we detected by searching for the regular expression GTA[AG]GT[ATGC]+?TAA[ATGC]TT[ATGC]{0,3}AG. The 'relaxed' intron motif was discovered following a comparison of intron-encoding genes in E. cuniculi and N. ceranae with T. hominis (Table S3), where a modified motif could be identified in the ribosomal protein S27. Without splicing, this would lead to a frameshift in the ribosomal protein, which is considered essential. We therefore adapted the search motif to GTA[AG]GT[ATGC]+?TAATT[ATGC]{0,4}AG and detected several putative introns in mainly ribosomal proteins. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5
 | classical intron motif
 | intron position
orf number | start | end | gene size | annotation | frameshift (phase 1 or 2)?
64 | 192 | 246 | 312 | RNA polymerase | no
159 | 246 | 598 | 639 | hypothetical protein | yes
193 | 487 | 589 | 1074 | acyltransferases | no
212 | 160 | 400 | 420 | Histones H3 and H4 | no
227 | 225 | 1114 | 1587 | tRNA modification enzyme | yes
247 | 63 | 675 | 798 | Protein involved in mRNA turnover and stability | no
360 | 63 | 589 | 744 | hypothetical protein | yes
424 | 391 | 312 | 636 | putative LRR containing protein | no
495 | 4081 | 4402 | 4701 | Vacuolar protein sorting-associated protein | no
575 | 232 | 779 | 918 | hypothetical protein | yes
622 | 339 | 418 | 1920 | Serine palmitoyltransferase | yes
627 | 3 | 30 | 1161 | Ribosomal protein L24E | no
698 | 1057 | 1362 | 2292 | putative LRR containing protein | yes
706 | 1599 | 1939 | 2826 | putative LRR containing protein | yes
796 | 315 | 583 | 1452 | DNA polymerase | yes
843 | 744 | 822 | 936 | hypothetical protein | no
845 | 788 | 1509 | 2037 | Predicted E3 ubiquitin ligase | yes
864 | 799 | 865 | 900 | Protein kinase | no
904 | 2318 | 2421 | 2484 | CTP synthase | yes
905 | 556 | 1585 | 2064 | Peptidase | no
920 | 1698 | 1816 | 2262 | tRNA synthetase | yes
1062 | 247 | 1686 | 1758 | protein containing Tetratricopeptide-like helical | yes
1087 | 63 | 382 | 1416 | Origin recognition complex, subunit 1, and related proteins | yes
1094 | 1446 | 1495 | 4416 | putative LRR containing protein | yes
1096 | 682 | 3100 | 3837 | putative LRR containing protein | no
1191 | 217 | 425 | 525 | hypothetical protein | yes
1236 | 356 | 494 | 2805 | ATP-dependent RNA helicase | no
1236 | 942 | 1413 |  |  | no
1273 | 1865 | 2043 | 2421 | hypothetical protein | yes
1275 | 1521 | 1689 | 2052 | protein containing Kinesin, motor domain | no
1286 | 299 | 495 | 735 | Cis-prenyltransferase | yes
1315 | 156 | 341 | 732 | protein containing Zinc finger | yes
1450 | 526 | 1166 | 1410 | endonuclease | yes
1472 | 715 | 1172 | 1935 | hypothetical protein | yes
1500 | 798 | 857 | 1224 | hypothetical protein | yes
1595 | 96 | 423 | 315 | 40s ribosomal protein S26 (similar to RPS26B; RPS26A;) | no
1611 | 378 | 821 | 1698 | hypothetical protein | yes
1643 | 1050 | 1758 | 1953 | protein containing Ricin B-related lectin | no
1722 | 1272 | 1659 | 1776 | hypothetical protein | no
1728 | 375 | 1170 | 2373 | Nucleotide excision repair protein RAD16 | no
1804 | 462 | 561 | 582 | protein containing Bacterial surface antigen (D15) | no
1856 | 130 | 220 | 552 | hypothetical protein | no
1858 | 944 | 1894 | 3015 | GTP-binding protein AARP2 involved in 40S ribosome biogenesis (similar to BMS1;) | yes
1905 | 783 | 1203 | 2358 | protein containing WD40 repeat | no
1953 | 1362 | 1464 | 2028 | hypothetical protein | no
1999 | 535 | 905 | 1044 | hypothetical protein | yes
2024 | 387 | 1315 | 2187 | 5'-3' exonuclease | yes
2075 | 1807 | 2191 | 2889 | putative LRR containing protein | yes
2117 | 302 | 341 | 585 | hypothetical protein | no
2173 | 1019 | 1059 | 1200 | 26S proteasome | yes
2240 | 63 | 1187 | 3048 | Rho guanyl-nucleotide exchange factor activity | yes
2278 | 558 | 605 | 2322 | helicase | yes
2297 | 404 | 504 | 972 | hypothetical protein | yes
2327 | 759 | 1290 | 1887 | histone acetyltransferase | no
2364 | 72 | 148 | 366 | Dim1 spliceosomal complex | yes
2381 | 146 | 240 | 831 | hypothetical protein | yes
2412 | 320 | 501 | 1122 | hypothetical protein | yes
2414 | 187 | 215 | 924 | [NAME] | yes
2439 | 32 | 650 | 726 | Glyoxylase | no
2603 | 690 | 1275 | 2946 | putative LRR containing protein | no
2646 | 66 | 1371 | 2163 | RNA polymerase | no
2676 | 895 | 1700 | 2028 | putative LRR containing protein | yes
2690 | 240 | 1425 | 2661 | Predicted RNA-binding protein | no
2690 | 1566 | 1810 |  |  | yes
2718 | 907 | 1162 | 3417 | putative LRR containing protein | no
2772 | 885 | 2485 | 2850 | putative LRR containing protein | yes
2888 | 681 | 1274 | 3273 | [NAME] | yes
2912 | 2307 | 2781 | 2784 | protein containing Homeodomain-related, DNA binding | no
3011 | 295 | 4026 | 4866 | putative LRR containing protein | yes
3039 | 949 | 1348 | 2826 | putative LRR containing protein | no
3100 | 34 | 1320 | 1335 | mRNA decay | yes
3118 | 22 | 429 | 474 | Predicted nucleic acid binding protein | yes
3123 | 322 | 342 | 660 | 40S ribosomal protein S23 | yes
3177 | 236 | 983 | 1110 | hypothetical protein | no
3214 | 294 | 1254 | 4371 | RNA helicase | no
3221 | 1003 | 1837 | 2022 | trehalase | no
3226 | 1365 | 2068 | 2850 | putative LRR containing protein | yes
3230 | 903 | 1243 | 2667 | AAA ATPase | yes
3251 | 173 | 220 | 684 | predicted membrane protein | yes
3262 | 148 | 172 | 429 | DNA binding cold shock protein | no
 | relaxed intron motif
 | intron position
orf number | start | end | gene size | annotation (based on KOGs and InterPro domains) | frameshift (phase 1 or 2)?
629 | 3 | 28 | 421 | Ribosomal protein S17 | yes
3301 | 3 | 28 | 181 | Ribosomal protein L39 | yes
199 | 3 | 26 | 337 | Ribosomal protein L44 | yes
383 | 3 | 234 | 795 | HIT protein (mRNA capping) | no
3300 | 3 | 31 | 286 | Ribosomal protein S27 | yes
*This motif is based on the introns characterized in Lee, [NAME], [NAME] and Fast (2010) and [NAME], [NAME], [NAME], Street, Zhao et al (2009).