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Table 6 Comparative genomics of Bemisia tabaci s.l. and related insects with OrthoFinder

From: Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors

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

  1. a INSDC International Nucleotide Sequence Database Collaboration
  2. b OGCs Orthologous gene clusters
  3. 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)
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BMC Genomics

ISSN: 1471-2164

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