Table 3.
Resequenced corynespora cassiicola isolates and Whole Genome Shotgun (WGS) sequencing metrics.
| Isolate name | Geographical origin | Host plant | Sanitary status of host tissue | aToxin class | WGS mapping on CCP | WGS de novo assembly | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Properly mapped reads (%) | Assembled genome size | bContigs | cN50 | Used reads | Used reads (%) | Coverage depth | Number of predicted genes | |||||
| 777AA | Brazil (BR) | Glycine max (Gm) | Lesioned | Cas2 | 69,6 | 43,337,818 | 25,946 | 59,381 | 20,252,558 | 95,7 | 36 | 16,745 |
| ATI11 | Brazil (BR) | Cucumis sativus (Cs) | Lesioned | Cas2 | 69,7 | 42,232,695 | 18,580 | 55,794 | 18,402,338 | 96,0 | 34 | 17,533 |
| CBS129.25 | Brazil (BR) | Cucumis sativus (Cs) | Lesioned | Cas2 | 73,4 | 41,411,750 | 11,707 | 65,420 | 21,960,627 | 96,0 | 43 | 16,848 |
| CCAM1 | Cameroon (CA) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 81,4 | 43,770,965 | 25,726 | 44,219 | 15,395,570 | 96,2 | 28 | 20,398 |
| CCAM2 | Cameroon (CA) | Hevea brasiliensis (Hb) | Lesioned | Cas1 | 93,7 | 43,143,070 | 21,575 | 45,751 | 19,761,908 | 95,3 | 36 | 20,926 |
| CCAM3 | Cameroon (CA) | Hevea brasiliensis (Hb) | Lesioned | Cas1 | 91,5 | 44,706,950 | 34,046 | 44,020 | 25,509,053 | 95,2 | 43 | 23,231 |
| CCAM4 | Cameroon (CA) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 82,1 | 43,735,702 | 24,864 | 50,281 | 23,499,794 | 96,0 | 43 | 20,437 |
| CCI13 | Côte d'Ivoire (CI) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 68 | 43,462,677 | 26,299 | 57,107 | 20,289,471 | 95,8 | 35 | 17,139 |
| CCI6 | Côte d'Ivoire (CI) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 68,8 | 43,521,463 | 25,732 | 58,564 | 21,920,208 | 95,6 | 38 | 17,106 |
| CCP | Philippines (PH) | Hevea brasiliensis (Hb) | Lesioned | Cas 1 | 44,850,000 | 244 | 17,167 | |||||
| CGAB1 | Gabon (GA) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 70,9 | 42,622,471 | 23,001 | 54,421 | 15,652,205 | 96,2 | 29 | 17,143 |
| CGAB2 | Gabon (GA) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 70 | 42,753,115 | 25,233 | 56,175 | 15,803,351 | 96,1 | 29 | 17,320 |
| CIND3 | India (IN) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 68,4 | 43,142,275 | 25,446 | 55,647 | 18,552,642 | 95,9 | 33 | 17,065 |
| CLN16 | Malaysia (MA) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 69,6 | 43,236,492 | 26,480 | 49,745 | 14,478,070 | 95,8 | 26 | 17,203 |
| CSB16 | Malaysia (MA) | Hevea brasiliensis (Hb) | Lesioned | Cas5 | 66,9 | 41,090,012 | 8,172 | 58,209 | 17,911,142 | 95,2 | 34 | 15,160 |
| CSRI1 | Sri Lanka (SL) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 66,2 | 41,512,866 | 16,169 | 57,706 | 20,366,586 | 95,8 | 39 | 16,143 |
| CSRI2 | Sri Lanka (SL) | Hevea brasiliensis (Hb) | Lesioned | Cas5 | 65,4 | 42,036 764 | 22,858 | 57,382 | 19,938,115 | 95,7 | 37 | 16,247 |
| CSRI5 | Sri Lanka (SL) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 69 | 43,093,641 | 24,753 | 56,383 | 19,074,836 | 95,5 | 34 | 17,128 |
| CTHA1 | Thaïland (TH) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 84,4 | 42,179,887 | 16,615 | 44 014 | 19,483,933 | 95,7 | 38 | 19,069 |
| CTHA2 | Thaïland (TH) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 67 | 41,852,029 | 18,777 | 54 006 | 19,105,681 | 96,0 | 37 | 16,189 |
| CTHA3 | Thaïland (TH) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 84,2 | 40,558,447 | 6,035 | 33 197 | 12,008,130 | 95,5 | 24 | 15,705 |
| CTHA4 | Thaïland (TH) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 86,3 | 40,998,259 | 6,794 | 43 846 | 25,526,040 | 95,2 | 51 | 16,564 |
| CTHA5 | Thaïland (TH) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 71,8 | 41,979,272 | 19,267 | 65 277 | 15,226,899 | 95,7 | 29 | 17,056 |
| CTHA6 | Thaïland (TH) | Hevea brasiliensis (Hb) | Lesioned | Cas0 | 70,6 | 42,283,119 | 24,161 | 72 894 | 14,104,323 | 94,8 | 27 | 17,145 |
| E139 | Brazil (BR) | Hevea brasiliensis (Hb) | Healthy | Cas4 | 80,2 | 44,431,849 | 27,829 | 45,812 | 23,838,352 | 96,2 | 43 | 21,058 |
| E55 | Brazil (BR) | Hevea brasiliensis (Hb) | Healthy | Cas0 | 74,3 | 41,269,705 | 16,066 | 49,888 | 25,968,811 | 94,2 | 48 | 15,772 |
| E79 | Brazil (BR) | Hevea brasiliensis (Hb) | Healthy | Cas4 | 81,2 | 44,028,261 | 27,903 | 47,985 | 22,067,764 | 96,2 | 40 | 21,866 |
| EDIG | Brazil (BR) | Cucumis sativus (Cs) | Lesioned | Cas2 | 70,5 | 42,249,625 | 17,402 | 37,754 | 12,130,622 | 96,2 | 22 | 17,357 |
| GSO2 | Brazil (BR) | Vernonia cinerea (Vc) | Lesioned | Cas2 | 67,4 | 43,198,292 | 22,836 | 30,770 | 12,431,866 | 95,7 | 22 | 17,060 |
| IA | Brazil (BR) | Cucumis sativus (Cs) | Lesioned | Cas2 + 7 | 68,7 | 42,992,747 | 23,053 | 58,869 | 29,543,154 | 96,0 | 53 | 17,059 |
| JQ | Brazil (BR) | Cucumis sativus (Cs) | Lesioned | Cas2 + 7 | 70,5 | 42,862,184 | 20,611 | 55,346 | 17,233,530 | 96,1 | 32 | 17,001 |
| LPO7 | Brazil (BR) | Piper hispidinervum (Ph) | Lesioned | Cas0 | 71,8 | 43,904,214 | 30,661 | 49,813 | 25,807,090 | 95,3 | 47 | 19,014 |
| PB | Brazil (BR) | Cucumis sativus (Cs) | Lesioned | Cas2 + 7 | 69,4 | 42,924,591 | 21,830 | 55,818 | 22,793,115 | 96,1 | 41 | 16,977 |
| RUD | Brazil (BR) | Glycine max (Gm) | Lesioned | Cas2 + 6 | 70,8 | 42,698,174 | 18,250 | 49,215 | 15 754,738 | 95,8 | 29 | 16,905 |
| SS1 | Malaysia (MA) | Hevea brasiliensis (Hb) | Lesioned | Cas5 | 66,9 | 41,929,664 | 21,219 | 52,434 | 17,449,048 | 95,7 | 34 | 16,152 |
| TSB1 | Malaysia (MA) | Hevea brasiliensis (Hb) | Lesioned | Cas5 | 66,3 | 42,091,408 | 21,882 | 55,474 | 20,226,399 | 95,7 | 38 | 16,238 |
In bold characters: reference CCP isolate.
a
Toxin class according to this analysis.
b
Number of contigs in each genome (scaffolds in the case of CCP).
c
Contig length at which 50% of total bases in the assembly are in contigs of that length or greater.