Table 2.
Statistics gathered from the genome assemblies of Hva individual isolates and the hybrid assembly.
| Sample IDs | Coffea species and genotypes | Raw reads | Clean readsa | Contigs | Assembly size | Completenessb |
|---|---|---|---|---|---|---|
| HvHybridc | 412,417,464 | 359,076,496 | 396,264 | 333,258,024 | 91.94% | |
| HvCat 454d | 5,860,446 | |||||
| HvCat Illumina | C. arabica var. Caturra | 48,396,016 | 43,704,716 | 254,645 | 122,820,521 | 57.26% |
| Hv387 | C. canephora CII56 | 58,593,986 | 50,782,526 | 211,495 | 150,707,107 | 44.35% |
| Hv494 | H89: C. arabica var. Bourbon resistant × C. arabica CaRCV3 | 55,326,774 | 47,738,686 | 211,728 | 138,293,025 | 35.08% |
| HvDQ952 | F2 – C. arabica var. Caturra × HdT 1343 (C. arabica × C. canephora) | 43,875,056 | 38,844,164 | 197,927 | 121,119,448 | 31.85% |
| HvH_179 | H3101: (C. arabica CaCV1 × Hdt (C. arabica × C. canephora) 1343 574CV2) × C. arabica CtyR | 49,025,718 | 42,033,780 | 203,770 | 131,574,289 | 31.05% |
| HvH_569 | H3041: (C. arabica × HarrarR3) × HdT(C. arabica × C. canephora) 1343 Africa 1386 | 51,960,392 | 45,000,606 | 202,168 | 133,358,100 | 37.50% |
| HvH_701 | H2094: (C. arabica MundoNovo) × F502 (C. arabica accession from Tanganica) | 60,634,018 | 53,080,264 | 215,628 | 158,292,515 | 56.86% |
| HvMar_1 | C. arabica var. Caturra | 44,605,504 | 39,408,690 | 203,360 | 125,814,765 | 22.18% |
a
Clean reads were obtained after quality trimming and removal of duplicates.
b
Completeness of the genome was calculated running the software CEGMA with a set of 248 ultra-conserved Core Eukaryotic Genes (CEGs) (Parra et al., 2007).
c
The hybrid assembly was generated by the combination of all short reads from the eight isolates.
d
Eight and a half plates were sequenced with 454 technology.