Table 6.
Comparative genomics of Bemisia tabaci s.l. and related insects with OrthoFinder
| Species | Common name | Annotation source | INSDCa assembly accession | Input genes | Unassigned genes | Genes in OGCsb | Genes in OGCs (%) | Number of OGCs incl. species | OGCs incl. species (%) | Speciesspecific OGCs | Genes in speciesspecific OGCs | Genes in speciesspecific OGCs (%) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Acyrthosiphon pisum | Pea aphid | Ensembl Metazoa (rel. 100) | GCA_000142985 | 36,195 | 3,031 | 33,164 | 91.6 | 10,228 | 46.0 | 891 | 4,410 | 12.2 |
| Anopheles gambiae | African malaria mosquito | Ensembl Metazoa (rel. 100) | GCA_000005575 | 13,057 | 756 | 12,301 | 94.2 | 7,792 | 35.1 | 219 | 1,229 | 9.4 |
| Bombus terrestris | Buff-tailed bumblebee | Ensembl Metazoa (rel. 100) | GCA_000214255 | 10,581 | 674 | 9,907 | 93.6 | 7,697 | 34.6 | 62 | 276 | 2.6 |
| Bombyx mori | Domestic silk moth | Ensembl Metazoa (rel. 100) | GCA_000151625 | 14,623 | 1,249 | 13,374 | 91.5 | 8,677 | 39.0 | 112 | 498 | 3.4 |
| B. tabaci SSA1-SG1-Ng | African cassava whitefly | Ensembl Metazoa (rel. 103) | GCA_902825415 | 13,661 | 104 | 13,557 | 99.2 | 7,822 | 35.2 | 9 | 19 | 0.1 |
| B. tabaci SSA1-SG1-Ug | African cassava whitefly | Ensembl Metazoa (rel. 103) | GCA_902825425 | 12,710 | 68 | 12,642 | 99.5 | 7,371 | 33.2 | 3 | 13 | 0.1 |
| B. tabaci SSA2-Ng | African cassava whitefly | Ensembl Metazoa (rel. 103) | GCA_903994125 | 12,928 | 70 | 12,858 | 99.5 | 7,682 | 34.6 | 5 | 11 | 0.1 |
| B. tabaci SSA3-Ng | African cassava whitefly | Ensembl Metazoa (rel. 103) | GCA_903994115 | 13,463 | 119 | 13,344 | 99.1 | 7,727 | 34.8 | 5 | 10 | 0.1 |
| B. tabaci Asia II-5 | Indian cassava whitefly | Ensembl Metazoa (rel. 103) | GCA_903994105 | 12,289 | 62 | 12,227 | 99.5 | 7,687 | 34.6 | 6 | 24 | 0.2 |
| B. tabaci Uganda-1 | Sweet-potato whitefly | Ensembl Metazoa (rel. 103) | GCA_903994095 | 12,749 | 347 | 12,402 | 97.3 | 6,853 | 30.8 | 40 | 85 | 0.7 |
| B. argentifolii | Silverleaf whitefly | Ensembl Metazoa (unreleased) | GCA_001854935 | 12,077 | 65 | 12,012 | 99.5 | 7,950 | 35.8 | 6 | 19 | 0.2 |
| B. tabaci s.s | Tobacco whitefly | Ensembl Metazoa (unreleased) | GCA_003994315 | 15,784 | 485 | 15,299 | 96.9 | 7,873 | 35.4 | 68 | 151 | 1.0 |
| Danaus plexippus | Monarch butterfly | Ensembl Metazoa (rel. 100) | GCA_000235995 | 15,128 | 1,597 | 13,531 | 89.4 | 9,088 | 40.9 | 121 | 369 | 2.4 |
| Daphnia pulex | Common water flea | Ensembl Metazoa (rel. 100) | GCA_000187875 | 30,590 | 4,437 | 26,153 | 85.5 | 9,034 | 40.6 | 1,601 | 10,616 | 34.7 |
| Diaphorina citri | Asian citrus psyllid | NCBI-RefSeq (06–2020) | GCF_000475195 | 21,517 | 1,892 | 19,625 | 91.2 | 8,698 | 39.1 | 919 | 2,479 | 11.5 |
| Drosophila melanogaster | Fruit fly | Ensembl Metazoa (rel. 100) | GCA_000001215 | 13,947 | 1,630 | 12,317 | 88.3 | 7,819 | 35.2 | 324 | 1,235 | 8.9 |
| Frankliniella occidentalis | Western flower thrips | NCBI-RefSeq (06–2020) | GCF_000697945 | 23,356 | 1,472 | 21,884 | 93.7 | 9,021 | 40.6 | 743 | 3,012 | 12.9 |
| Myzus persicae | Green peach aphid | NCBI-RefSeq (06–2020) | GCF_001856785 | 23,910 | 275 | 23,635 | 98.8 | 8,975 | 40.4 | 172 | 553 | 2.3 |
| Rhodnius prolixus | Kissing bug | Ensembl Metazoa (rel. 100) | GCA_000181055 | 15,061 | 1,803 | 13,258 | 88.0 | 7,733 | 34.8 | 310 | 1,739 | 11.5 |
| Strigamia maritima | Centipede | Ensembl Metazoa (rel. 100) | GCA_000239455 | 14,992 | 1,902 | 13,090 | 87.3 | 7,245 | 32.6 | 369 | 1,684 | 11.2 |
| Tetranychus urticae | Two-spotted spider mite | Ensembl Metazoa (rel. 100) | GCA_000239435 | 17,671 | 3,892 | 13,779 | 78.0 | 6,443 | 29.0 | 660 | 4,110 | 23.3 |
| Trialeurodes vaporariorum | Greenhouse whitefly | WhiteflyDB (06–2020) | GCA_011764245 | 18,275 | 1,467 | 16,808 | 92.0 | 8,277 | 37.2 | 276 | 1,509 | 8.3 |
| Tribolium castaneum | Red flower beetle | Ensembl Metazoa (rel. 100) | GCA_000002335 | 16,590 | 3,001 | 13,589 | 81.9 | 8,294 | 37.3 | 284 | 1,371 | 8.3 |
a INSDC International Nucleotide Sequence Database Collaboration
b OGCs Orthologous gene clusters
A comparison of 23 arthropod taxa including the six new B. tabaci s.l. new genomes. Analysis was performed via Orthofinder (v2.4.0) [51], by providing canonical protein-coding sequences as input. The Orthofinder pipeline implemented both MSA and phylogenetic gene tree reconstruction with default settings. All B. tabaci s.l. gene sets were generated via the Ensembl gene annotation pipeline. Newly generated B. tabaci s.l. were first released via Ensembl Metazoa (release e103) (https://metazoa.ensembl.org). For previously published B. argentifolii and B. tabaci s.s. re-annotated datasets see Additional File 5. The protein-coding gene (PCG) set of T. vaporariorum was obtained from WhiteflyDB (http://www.whiteflygenomics.org). Remaining PCG sets were obtained directly from Ensembl Metazoa (release e100), using the Ensembl Perl API or alternatively downloaded from NCBI-RefSeq (June—2020)