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Table 3 Summary of Bemisia tabaci s.l. structural annotation with four comparative insect genomes

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

  

B. tabaci SSA1-SG1-Ug

B. tabaci SSA1-SG1-Ng

B. tabaci SSA2-Ng

B. tabaci SSA3-Ng

B. tabaci Asia II-5

B. tabaci Uganda-1

B. argentifolii

B. tabaci s.s

T. vap.a

A. pisum

A. gambiae

D. melanogaster

T. castaneum

Gene

Total genes

13,852

14,942

14,386

14,952

13,497

13,804

12,723

16,378

18,275

37,522

13,796

17,807

17,052

Protein coding

12,710

13,661

12,928

13,463

12,289

12,749

12,077

15,786

18,275

36,195

13,057

13,947

16,590

Transcript

Total transcripts

29,757

29,919

29,035

30,073

28,862

25,101

26,475

30,266

18,275

37,522

15,718

34,920

18,996

Protein coding

28,022

27,923

26,825

27,844

26,928

23,614

25,522

29,609

18,275

36,195

14,979

30,588

18,534

% Prot. coding

94.17

93.33

92.39

92.59

93.30

94.08

96.40

97.83

100.00

96.46

95.30

87.59

97.57

Avg coding length

1,893

1,805

1,604

1,575

2,019

1,383

2,255

1,506

1,382

1,983

2,508

2,280

1,765

Exon

Total coding exons

248,703

225,850

201,198

204,013

248,187

144,581

254,773

228,346

94,682

182,028

71,504

181,712

98,403

Avg translatable exon length

219.12

202.2

173.69

172.47

198.64

165.05

213.73

200.71

308

208.55

371.24

378.82

288.26

Avg exons per transcript

8.2

7.2

6.4

6.3

8.1

5.1

8.9

6.8

5.2

4.8

3.7

4.9

4.3

Intron

Total introns

220,681

197,927

174,373

176,169

221,259

120,967

229,251

198,737

92,160

145,833

56,525

151,124

79,869

Avg length

3,661

3,051

3,325

3,148

3,641

2,113

3,409

2,143

1,846

1,658

1,862

1,606

1,424

Total length

807,954,736

603,944,323

579,736,570

554,533,025

805,703,415

255,575,888

781,519,935

425,841,115

170,187,655

241,821,138

105,259,352

242,737,713

113,707,069

5'UTR (canonical)

Total 5'UTRs

5,496

7,587

7,572

8,017

7,398

7,218

8,670

9,130

10,877

32,115

10,118

13,394

13,522

Avg length

5,202

3,958

4,837

3,985

5,838

1,921

4,018

1,750

192

1,661

1,841

1,441

1,086

Complete length

28,591,304

30,027,509

36,622,299

31,951,687

43,192,086

13,862,775

34,834,074

15,973,160

2,091,440

53,344,412

18,630,451

19,296,959

14,683,753

3'UTR (canonical)

Total 3'UTRs

5,180

7,080

6,748

7,303

6,751

7,278

8,010

8,880

9,033

33,840

9,551

13,495

13,504

Avg length

983

950

1,000

968

1,141

864

869

530

323

1,186

789

517

282

Complete length

5,093,086

6,723,389

6,746,881

7,071,323

7,702,287

6,291,556

6,962,565

4,707,060

2,919,282

40,126,738

7,533,191

6,970,762

3,812,572

BUSCO (Insecta n = 1,367)

[%]

Complete BUSCO

91.8

94.8

95.1

93.6

95.0

78.0

98.0

93.3

94.7

96.8

98.0

99.6

99.3

Single copy

82.4

90.6

91.7

89.4

91.1

72.1

96.1

72.6

92.5

90.7

96.2

99.0

98.8

Duplicated

9.4

4.2

3.4

4.2

3.9

5.9

1.9

20.7

2.2

6.1

1.8

0.6

0.5

Fragmented

1.3

2.0

2.4

3.6

1.2

6.9

1.2

1.9

0.6

0.7

0.8

0.1

0.4

Missing

6.9

3.2

2.5

2.8

3.8

15.1

0.8

4.8

4.7

2.5

1.2

0.3

0.3

  1. aT. vap = T. vaporariorum, D. melan. = D. melanogaster
  2. Summary statistics for the B. tabaci s.l. genomes and four comparative insect genomes. The new B. tabaci s.l. genomes and those of B. argentifolii and B. tabaci s.s. were annotated using the same methodology (see M&M). Gene features were categorized according to gene, transcript, exon, intron and both 3’ and 5’ UTRs. A BUSCO analysis of single copy ortholog results for orthology set (OrthoDB v9)—Insecta (n = 1,658) was above 82% for all cassava whitefly populations. The B. tabaci Uganda-1 genome had the highest percentage of missing genes from the BUSCO ortholog set. See Additional file 1: Table S3 for additional BUSCO ortholog set analyses: Arthropoda (n = 1,066), Metazoa (n = 978) and Eukaryota (n = 303)]
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BMC Genomics

ISSN: 1471-2164

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