Open Access

Analysis of 14 BAC sequences from the Aedes aegyptigenome: a benchmark for genome annotation and assembly

  • Neil F Lobo1Email author,
  • Kathy S Campbell2,
  • Daniel Thaner1,
  • Becky deBruyn1,
  • Hean Koo3,
  • William M Gelbart2,
  • Brendan J Loftus3,
  • David W Severson1 and
  • Frank H Collins1
Contributed equally
Genome Biology20078:R88

DOI: 10.1186/gb-2007-8-5-r88

Received: 21 December 2006

Accepted: 22 May 2007

Published: 22 May 2007

Abstract

Background

Aedes aegypti is the principal vector of yellow fever and dengue viruses throughout the tropical world. To provide a set of manually curated and annotated sequences from the Ae. aegypti genome, 14 mapped bacterial artificial chromosome (BAC) clones encompassing 1.57 Mb were sequenced, assembled and manually annotated using a combination of computational gene-finding, expressed sequence tag (EST) matches and comparative protein homology. PCR and sequencing were used to experimentally confirm expression and sequence of a subset of these transcripts.

Results

Of the 51 manual annotations, 50 and 43 demonstrated a high level of similarity to Anopheles gambiae and Drosophila melanogaster genes, respectively. Ten of the 12 BAC sequences with more than one annotated gene exhibited synteny with the A. gambiae genome. Putative transcripts from eight BAC clones were found in multiple copies (two copies in most cases) in the Aedes genome assembly, which point to the probable presence of haplotype polymorphisms and/or misassemblies.

Conclusion

This study not only provides a benchmark set of manually annotated transcripts for this genome that can be used to assess the quality of the auto-annotation pipeline and the assembly, but it also looks at the effect of a high repeat content on the genome assembly and annotation pipeline.

Background

Ae. aegypti is the primary vector for both dengue and yellow fever viruses. In an effort to better understand this important disease vector and to provide tools to facilitate new avenues of research, whole-genome sequencing has been initiated. The 1.3 Gb genome (strain LVPib12) has been sequenced to 8× coverage in a joint effort by the Broad Institute [1] and The Institute for Genomic Research (TIGR) [2]. The trace reads were assembled with the ARACHNE genome-assembly package [3] into 4,758 supercontigs (assembly AaegL1). A collaborative annotation of the genome by VectorBase and TIGR has resulted in Genebuild 1.0 (designated AaegL1.1) consisting of 15,419 transcripts [4].

In this era of whole-genome sequencing, assembly and annotation, only a single animal genome - Caenorhabditis elegans - has been completely sequenced, resulting in five fully contiguous telomere-to-telomere chromosomal sequences with more than 90% of annotations supported by experimental evidence [5]. This unusually complete animal genome provides a solid set of data for the scientific community. At present, large genomes are usually sequenced as draft versions, resulting in the automatic production of an assembled genome. These consist of sets of contigs (contiguous sequence) that are oriented and ordered (when possible) across gaps with the sequences from the ends of cloned DNA (mate pair information) into supercontigs or scaffolds. These scaffolds are the basis of various analyses such as gene annotation and physical mapping.

Genome assembly can be complicated by the presence of haplotype polymorphisms present in the strain used for genome sequencing, high repeat content, cloning biases, and regions that are duplicated in the genome. The genome of D. melanogaster [6] and A. gambiae [7] have been through several rounds of assembly and gene annotation, which have each successively resulted in a better and more complete version of the genome consisting of mapped sequence with fewer gaps and an improved set of gene models [68].

The quality of a genome annotation depends on factors such as the gene prediction algorithm, the presence of high-quality comparative data such as expressed sequence tags (ESTs) and experimentally validated gene models, and effective masking of repeat and transposon open reading frames (ORFs). The dataset of gene models used to 'train' the algorithm to the specific genome is particularly important. Currently, the highest-quality gene models are those made by expert curators who manually examine all sources of evidence to make a gene prediction (such as that done with model-organism genomes like that of Drosophila).

In an effort to provide manually curated regions of the Ae. aegypti genome that can be used to assess the automatic annotation of the Aedes genome, we have sequenced, assembled and analyzed 14 bacterial artificial chromosome (BAC) clones. This study provides a set of high-quality manually annotated Aedes transcripts that have been compared to the other sequenced dipteran genomes - A. gambiae and D. melanogaster. This study also addresses issues such as the high repeat content and the presence of possibly duplicated regions that may have complicated the assembly of the Aedes genome.

Results

Assembly

Fourteen BAC clones from an Ae. aegypti genomic library were isolated using PCR primers specific to single-copy genetic markers [9]. Shotgun sequences from each BAC were assembled into scaffolds using both the TIGR assembler [2] and Seqman [10]. Scaffolds resulting from the different methods of assembly (see Materials and methods) were consistent with the others. Mate-pair inconsistencies were usually from sequences that were in repeat regions of the scaffolds. A small number of single-copy chimeric clones were observed and their elimination, along with other mate-pair inconsistencies, did not change the assembled sequences.

The majority of sequence gaps were filled using primers designed to the unique sequence flanking gaps. Some primers designed to close these gaps did not produce any PCR products and sequencing reactions with these primers using the BAC clones as template terminated at the same region or were unreadable due to polymerase slippage. All remaining gaps in the 14 BACs were flanked by highly repetitive sequence. Assembled BAC sequences were compared with the genome assembly (BLASTN) to see if they assembled in a similar manner. The gaps present in the BAC clone assemblies were either coincident with gaps present in the genome assembly or sequence diverged in the genome assembly when gaps were not present in the same region (as discussed below).

Contigs from each BAC clone were oriented on the basis of end sequences and mate-pairs. Three BACs (BAC4, BAC7 and BAC8) were each assembled into continuous sequences with no gaps. The remaining BAC sequences assembled into sets of oriented scaffolds with gaps (arbitrarily replaced by 100 Ns) (Table 1). The only BAC clones that showed differences with the assembly made at TIGR were BAC8 and BAC9. Assembled contigs seem to have been mixed during their assembly and a careful assembly (using Seqman) separated the two BAC clones into their respective scaffolds. This was verified with PCR spanning gaps and comparison to the genome assembly. The 14 BAC assemblies totaled 1,571,625 bp (approx 0.12% of the 1.3 Gb genome). The average G+C content of all scaffolds was 37.75%. Although all the sequences had a G+C around the average, BAC3 had the lowest at 27% and BAC2 had the highest at 47% (see Table 1).
Table 1

Summary of BAC assemblies

BAC number

Name of BAC

Chromosome arm

GenBank accession number

Genetic marker

Scaffolds in assembly

Total number of contigs

Length (bp)

G+C%

1

ND13I3

2q

EF173370

Rpl17A

1

2

82203

38.97

2

ND22N19

2q

EF173371

D6L600

1

2

146563

47.09

3

ND22N5

3p

EF173372

Mal1

1

2

116923

27.39

4

ND41B18

3p

EF173373

LF347

1

1

164547

37.94

5

ND41C6

2q

EF173374

VMP-15a3

1

7

89409

38.93

6

ND46O19

2q

EF173375

BA67

1

7

114988

38.19

7

ND48J19

2q

EF173376

D7

1

1

83496

36.99

8

ND56P6

3q

EF173377

Para

1

1

81099

37.14

9

ND67B23

3q

EF173378

LF106

2

2

136645

39.29

10

ND83P15

3p

EF173379

AEGI28

1

2

76584

35.15

11

105H24

1p

EF173366

LF178

1

2

140290

38.43

12

124C17

2q

EF173367

LF138

1

8

158121

38.25

13

26O21

2p

EF173368

LF342

1

2

87550

37.00

14

92LO9

3p

EF173369

LF253

1

3

93207

37.72

The 14 BAC clones were localized to chromosome arms with single-locus genetic markers previously determined.

Repeat content

Repeat masking resulted in the masking of approximately 20% of the sequence. As repeat masking here was based on protein homology, the total sequence consisting of transposon sequence is likely to be higher. Manual annotation and similarity searches with in silico predictions and EST hits with transcribed transposon sequences increased the repeat/transposon content to approximately 35%. The Feilai element [11] was the most common element, comprising approximately 38% of the repeats. Almost all transposons identified were retrotransposons.

Gene prediction

In silico gene prediction was performed initially on the raw assembled scaffolds. A preliminary (BLASTX) analysis of these predicted transcripts (data not shown) demonstrated that there was a significant amount of over-prediction, gene-splitting and incorporation of random and transposon-based ORFs into gene models. Masking of repeat sequences before gene prediction reduced the number of gene models and this dataset was used as evidence for manual annotation.

Gene models predicted by Genscan [12] and FGENESH [13] before repeat masking often included exons derived from transposon ORFs. An Aedes gene was often split into two predictions, with the incorporation of unmasked transposon-based and other random ORFs. In addition, the ab initio generated sets of gene models (by Genscan and FGENESH) were different. However, some predicted exons did match Aedes ESTs. Several hundred ESTs were identified from the Aedes database (e < -100) as well as from the Drosophila and Anopheles datasets (e < -50). A preliminary BLAST analysis of Aedes ESTs (e = 0.0) demonstrated that a large portion of them (around 30%) mapped to transposon ORFs.

Manual annotation

The 14 BACs were manually annotated in Apollo [14] using various tiers of evidence like ESTs and comparison to other dipteran peptides (see Materials and methods). Transcripts from the Anopheles and Drosophila genomes were used in conjunction with Aedes ESTs to limit the number of exons to those that had similarity to gene models in the other dipteran genomes. Annotations that did not possess similarity to the two dipteran genomes were also analyzed to include ORFs that may be specific to the Aedes genome as well as those that may have diverged significantly from their Anopheles or Drosophila homologs.

There were a total of 51 manual annotations (Table 2) among the 14 BAC sequences, with BAC2 having no annotated transcripts. Fifty of 51 manual annotations were found in the Ae. aegypti 1.0 Genebuild (AaegL1.1) [4] and 41 of these were identical (see Table 2). The remaining varied in several ways including differences in the 3' or 5' exon (seven transcripts), different intron/exon structure (two transcripts) or the annotation was missing in that region of the genome (one transcript). In all cases, the differences in the manually annotated models were based on Aedes EST comparisons, comparisons to annotations and ESTs in the Drosophila and Anopheles genome as well as confirmation by sequencing of PCR amplicons in a few cases. A number of transcripts differed in the length of the 3' or 5 ' UTRs. These differences were usually 10-20 bp long and not considered discordant with the gene build unless they differed by entire exons. All annotations had nucleotide matches in the Aedes genome and most had hits to Aedes ESTs. The genomic region encompassing BAC11 had two extra transcripts (AAEL03517 and AAEL02535). A protein comparison revealed that both genome-annotated transcripts were exons from a rhabdovirus nucleocapsid protein. These were not included in the list of manual annotations.
Table 2

Summary of manual annotations

BAC number

Transcript number

Aedes transcript

Supercontig

Contig

Sequencing of cDNA

Differences in annotation between manual annotation (MA) and gene build

Replicated transcript in Aedes assembly

       

Aedes transcript

Supercontig

Contig

Notes

1

1

AAEL013103

1.789

24718

-

-

AAEL014498

1.1137

29191

-

 

2

AAEL013088

1.789

24718

-

-

AAEL014499

1.1137

29191

-

 

3

AAEL013092

1.789

24718

-

-

AAEL014500

1.1137

29189

-

 

4

AAEL013582

1.875

25903

Identical

Longer 5' in MA

AAEL015005

1.1393

31331

5' end of transcript matched MA

       

AAEL013099

1.789

24718

3' end of transcript matched MA

 

5*

AAEL015006

1.1393

31331

Identical

-

AAEL013097

1.789

24718

Identical to AAEL013097

       

AAEL013583

1.875

25903

Identical to AAEL013583

 

6

AAEL013098

1.789

24719

-

Only 3' coding region lines up

AAEL013098

1.789

24719

Only 3' coding region lines up

3

7*

AAEL009524

1.403

16729

-

-

AAEL000392

1.7

624

-

4

8

AAEL008104

1.301

13837

-

-

-

-

-

-

 

9

AAEL008110

1.301

13837

Identical

Different intron/exon structure

-

-

-

-

 

10

AAEL008114

1.301

13837

Identical

3' longer in MA

-

-

-

-

 

11

AAEL008115

1.301

13837

-

-

-

-

-

-

 

12

AAEL008103

1.301

13837

Identical

-

-

-

-

-

 

13

AAEL008100

1.301

13837

-

-

-

-

-

-

5

14*

AAEL014561

1.1166

29449

Identical

-

Transcript missing

1.216

10858

-

 

15

AAEL014559

1.1166

29447

Identical

-

AAEL006682

1.216

10863

-

6

16*

AAEL014711

1.1232

30069

Identical

Different intron/exon structure

AAEL014491

1.1132

29135

-

 

17

AAEL014712

1.1232

30070

-

-

AAEL014495

1.1132

29137

-

 

18

AAEL014709

1.1232

30070

Identical

-

AAEL014494

1.1132

29136

-

7

19

AAEL006423

1.204

10417

-

-

-

-

-

-

 

20

No transcript

1.204

10417

-

Similar to AAEL003685

-

-

-

-

 

21*

AAEL006424

1.204

10417

Identical

-

-

-

-

-

 

22

AAEL006417

1.204

10417

Identical

-

-

-

-

-

8

23*

AAEL006019

1.186

9724

Identical

-

AAEL008297

1.312

14138

-

9

24*

AAEL010573

1.488

18854

Identical

-

AAEL000068

1.1

48

-

 

25

AAEL010594

1.488

18854

Identical

-

AAEL000046

1.1

48

-

 

26

AAEL010587

1.488

18855

Identical

-

AAEL000020

1.1

48

-

 

27

AAEL010575

1.488

18855

Identical

-

AAEL000076

1.1

48

-

 

28

AAEL000054

1.1

48

-

-

AAEL010578

1.488

18855

-

 

29

AAEL010595

1.488

18855

-

-

-

-

-

-

10

30

AAEL007897

1.288

13401

Identical

Extra 3' exon in MA

-

-

-

-

 

31

AAEL007893

1.288

13401

-

-

-

-

-

-

 

32

AAEL007907

1.288

13401

-

-

-

-

-

-

11

33

AAEL002503

1.59

3864

-

-

-

-

-

-

 

34

AAEL002532

1.59

3866

Identical

3' exon absent in MA

-

-

-

-

 

35

AAEL002534

1.59

3863

-

-

-

-

-

-

 

36

AAEL002523

1.59

3864

-

-

-

-

-

-

12

37

AAEL001205

1.25

1764

-

Longer 5' in MA

-

-

-

-

 

38

AAEL001215

1.25

1764

Identical

Longer 3' in MA

-

-

-

-

 

39

AAEL001215

1.25

1764

Identical

-

-

-

-

-

 

40

AAEL001198

1.25

1761

-

-

-

-

-

-

 

41

AAEL001201

1.25

1764

-

-

-

-

-

-

 

42

AAEL001210

1.25

1764

-

-

-

-

-

-

13

43

AAEL008780

1.348

15270

-

-

AAEL001693

1.39

2713

-

 

44

AAEL008781

1.348

15269

-

-

AAEL001703

1.39

2712

-

 

45

AAEL008769

1.348

15269

-

-

AAEL001701

1.39

2711

-

 

46

AAEL008778

1.348

15269

-

-

AAEL001681

1.39

2711

-

14

47

AAEL005065

1.140

7865

-

-

AAEL005223

1.146

8136

-

 

48

AAEL005085

1.140

7866

-

-

AAEL005220

1.146

8136

-

 

49

AEL005237

1.146

8136

-

-

AAEL005088

1.140

7865

-

 

50

AAEL005229

1.146

8136

-

-

AAEL005059

1.140

7865

-

 

51

AAEL005218

1.146

8136

-

-

No gene build annotation

1.140

7865

-

The 51 manually annotated transcripts (Transcript number) from each BAC clone (BAC number) along with their corresponding transcript (Gene build transcript) from the gene build (AaegL1) and their location (supercontig, contig) are listed along with cDNA amplicons if sequenced. Transcripts that were replicated in the genome are also listed along with their corresponding gene build transcript, location and differences with the manual annotation (MA) if any. Manual annotations marked with an asterisk indicate single-copy cDNA-derived genetic markers used to isolate the BAC.

To confirm the annotation and expression of a subset of these annotations, primers were designed to all manually annotated transcripts where the prediction lacked necessary evidence. PCR was performed on cDNA obtained from all stages of the mosquito (see Materials and methods). These sequences were utilized to correct or confirm manual annotations when the curator presented multiple possible gene models or splice sites for a particular sequence. All 20 amplicons sequenced were identical to a curated gene model (see Table 2).

Replicated segments

Eight of the 14 BAC clones had annotations present more than once in the genome assembly. This was unexpected as these BACs were specifically isolated using validated single-locus genetic markers [9]. These replicated transcripts present in AaeL1.1 were virtually identical and usually present along with the same flanking transcripts in different supercontigs. To see if intergenic sequence were also replicated, the assembled BAC scaffolds were compared to the Aedes genome assembly scaffolds containing the identical transcripts. Though replicated transcripts were virtually identical, intergenic/intron sequences were usually identical on one replicate while they varied slightly on the other. These eight blocks of sequence were present in complete or partially replicated segments in different parts of the Aedes genome assembly, with only one replicate possessing identical intergenic sequence and the rest having slightly variable intergenic sequences.

Some replicated blocks were 'hybrids' of the BAC clone and the genomic duplication. This is seen in BAC14, where all five transcripts are found on two supercontigs in the same order and structure. Intergenic sequences from the first two transcripts are identical to that on supercont1.140 while the remaining transcripts have intergenic sequences corresponding to that on supercont1.146. This is also seen with BAC9, where the last transcript and its intergenic sequence are found on one scaffold while the remaining transcripts and their intergenic sequnce correspond to another scaffold - even though all transcripts are found on both scaffolds.

BAC1 was the most complicated with the five transcripts, being found on four supercontigs. All transcripts were seen in supercont1.789 while the remaining usually terminated at the end of a scaffold or had gaps which did not include all transcripts. These three transcripts were also seen with different intergenic sequences on supercont1.1137. The fourth transcript had the 3' end matching up to this scaffold and the 5' end on supercont1.393. The fifth transcript was found on supercont1.1393, whereas a sixth transcript with identical intergenic sequence was not found in the genome, although transcripts matching it but with varying intergenic sequence were found. These replicated regions were usually flanked by highly repetitive DNA and/or gaps or were present at the end of a supercontig.

Orthology and synteny

When compared with the Anopheles and Drosophila gene sets (Table 3), 50 and 43 Aedes transcript annotations had orthologous transcripts in the Anopheles and Drosophila gene sets, respectively. The genes from the two other dipteran genomes that were similar to the manual annotations were almost always orthologs of each other (determined by reciprocal BLASTs) [4]. Although most Aedes annotations had a one-to-one relationship in the other genomes, some matches were to genes from multigene families. In some cases, the primary BLAST match was much better than the rest and in these cases, an ortholog was postulated. In cases where a number of transcripts matched the manual annotation with similar e-values, orthologs could not be predicted. A single manual annotation did not have any similarity in either genome, and when compared to other dipteran datasets with less stringent parameters it demonstrated similarity to an Ae. albopictus salivary protein.
Table 3

Orthology and synteny with Anopheles gambiae and Drosophila melanogaster

Aedes aegypti

Anopheles gambiae

Drosophila melanogaster

BAC number

Transcript number

Aedes transcripts

Ortholog

E-value

Chromosome

Syntenic block

Ortholog

E-value

Syntenic block

1

1

AAEL013103

ENSANGG00000021076

3.8E-133

3R-37D

Yes

CG31938

9.5E-094

--

 

2

AAEL013088

ENSANGG00000026626

5.5E-009

3R-37D

Yes

-

-

-

 

3

AAEL013092

ENSANGG00000011837

0.0E+0.0

3R-37D

Yes

CG10413

0.0E+0.0

-

 

4

AAEL013582

ENSANGG00000023798

1.1E-035

3R-37D

Yes

CG11247

1.1E-128

-

 

5

AAEL015006

ENSANGG00000011941

1E-106

3R-37D

Yes

CG3661

2.2E-104

-

 

6

AAEL013098

ENSANGG00000002369

0.0E+0.0

3R-37D

Yes

CG7961

0.0E+0.0

-

3

7

AAEL009524

ENSANGG00000015193

7.3E-281

2R-10C

NA

CG8696

7.2E-226

NA

4

8

AAEL008104

1 to many

9.4E-058

GW

-

1 to many

8.7E-040

-

 

9

AAEL008110

ENSANGG00000011807

3E-154

2R-12B

Yes

CG4832

2.5E-078

-

 

10

AAEL008114

ENSANGG00000009472

4.4E-037

GW

-

CG12752

1.6E-026

-

 

11

AAEL008115

ENSANGG00000011761

2.2E-108

2R-12B

Yes

CG11025

3.2E-037

-

 

12

AAEL008103

ENSANGG0000012462

7.90E-061

2R-12B

-

CG7808

2.8E-073

-

 

13

AAEL008100

ENSANGG00000009215

1.4E-053

2R-8B

-

CG1078

3E-040

-

5

14

AAEL014561

ENSANGG00000022738

3.0E-009

3R-32C

-

-

-

-

 

15

AAEL014559

ENSANGG00000010922/ENSANGG00000022179

3.3E-068

3R-35C

-

-

-

-

6

16

AAEL014711

ENSANGG00000005482

0.0E+0.0

3R-29B

Yes

CG8815

0.0E+0.0

-

 

17

AAEL014712

ENSANGG00000022484

8.9E-199

3R-29B

Yes

CG15084

8.3E-170

-

 

18

AAEL014709

ENSANGG00000007515

0.0E+0.0

3R-29B

Yes

CG15100

0.0E+0.0

-

7

19

AAEL006423

ENSANGG00000020489

1.1E-006

2L-20C

-

CG40120

6.1E-006

-

 

20

No transcript

ENSANGG00000011708

3.5E-026

GW

-

CG33803

6.9E-028

-

 

21

AAEL006424

ENSANGG00000027449

3.0E-062

3R-30C

Yes

-

-

-

 

22

AAEL006417

ENSANGG00000020969

2.6E-056

3R-30C

Yes

-

-

-

8

23

AAEL006019

ENSANGG00000025048

8.0E-073

2L-20C

NA

CG9907

8.9E-174

NA

9

24

AAEL010573

ENSANGG00000015129

3.6E-060

2R-19B

Yes

CG6684

2E-050

-

 

25

AAEL010594

ENSANGG00000014580

3.7E-107

2R-19B

Yes

CG32418

2E-032

-

 

26

AAEL010587

ENSANGG00000014498

2E-192

2R-19B

Yes

CG9590

1E-083

-

 

27

AAEL010575

ENSANGG00000014455

2E-192

2R-19B

Yes

CG11837

3.6E-196

-

 

28

AAEL000054

ENSANGG00000002208

0.0E+0.0

2R-12E

-

CG8651

0.0E+0.0

-

 

29

AAEL010595

ENSANGG00000010690

0.0E+0.0

2L-26A

-

CG16982

1.7E-240

-

10

30

AAEL007897

ENSANGG0000016631

5.1E-194

3R-29B

Yes

CG14928

6E-164

-

 

31

AAEL007893

ENSANGG00000018850

1.3E-175

2R-12C

-

CG31548

2.3E-137

-

 

32

AAEL007907

ENSANGG00000015978

1.7E-200

3R-29B

Yes

CG4629

1.3E-144

-

11

33

AAEL002503

ENSANGG00000015084

3.8E-092

X-1B

Yes

CG1989

3E-082

Yes

 

34

AAEL002532

ENSANGG00000015036

4.4E-250

X-1B

Yes

CG3707

6.3E-285

-

 

35

AAEL002534

ENSANGG00000012432

6.5E-186

X-5C

-

CG17521

1.9E-167

Yes

 

36

AAEL002523

ENSANGG00000015081

7.3E-065

X-1B

Yes

CG1660

6.8E-051

-

12

37

AAEL001205

ENSANGP00000016497

0.0E+0.0

3R-33B

-

CG4244

0.0E+0.0

-

 

38

AAEL001215

SNAP_00000004435

9.9E-123

3R-33B

Yes

CG4230

2E-055

-

 

39

AAEL001215

ENSANGP00000023803

0.0E+0.0

3R-33B

Yes

CG7269

1.2E-299

-

 

40

AAEL001198

ENSANGP00000023805

0.0E+0.0

3R-29B

-

CG8451

4E-236

-

 

41

AAEL001201

ENSANGP00000016633

9.8E-041

3R-33B

Yes

-

-

-

 

42

AAEL001210

ENSANGP00000016606

1.9E-060

3R-33B

Yes

CG8680

2.3E-052

-

13

43

AAEL008780

ENSANGP00000021694

1.9E-079

2L-21C

Yes

CG2071/CG1304

3.1E-058

-

 

44

AAEL008781

ENSANGP00000021694

4.6E-071

2L-21C

Yes

CG2071/CG1304

3.5E-048

-

 

45

AAEL008769

ENSANGP00000021694

1.9E-088

2L-21C

Yes

CG2071/CG1304

1.1E-064

-

 

46

AAEL008778

ENSANGP00000021867

1.6E-103

2L-21C

Yes

-

-

-

14

47

AAEL005065

ENSANGP00000018910

6E-159

2R-16C

Yes

CG6746

3.7E-134

-

 

48

AAEL005085

ENSANGP00000018909

6.3E-084

2R-16C

Yes

CG10652

2.5E-078

-

 

49

AEL005237

ENSANGP00000018845

4.9E-130

2R-16C

Yes

CG1298

2.4E-095

-

 

50

AAEL005229

ENSANGP00000019493

3.7E-122

2R-16C

Yes

CG6746

8.3E-090

-

 

51

AAEL005218

ENSANGG00000016433

7.7E-151

2R-16B

Yes

CG10624

1.9E-121

-

Orthology was determined for each transcript from all 14 BACs. The presence of synteny was also determined for orthologous blocks of transcripts when more than one transcript was present on the BAC clone.

To compare gene sizes between the two mosquitoes, the amount of sequence covered by the orthologous genes in Aedes and Anopheles were compared. Single-exon genes were usually the same size; however, the size of multiexon genes was directly proportionate to the number of introns in Aedes. On average, Aedes genes were about 3.9 times the size of their Anopheles orthologs. Only one Aedes BAC sequence demonstrated any degree of synteny with Drosophila. BAC11 had two adjacent transcripts that were found to be next to each other in the Drosophila genome. Of the 11 BACs with more than one annotated transcript, nine sequences demonstrated synteny with the Anopheles genome. Overall, 38 of the 50 transcripts included in these BACs demonstrated synteny in 10 blocks.

For a summary of each BAC clone assembly and analysis please see Additional data file 1.

Discussion

Fourteen BAC clones encompassing 1.57 Mb were sequenced, assembled and analyzed for repeat and gene content. Manual gene annotations were compared to the Ae. aegypti, A. gambiae and D. melanogaster gene sets. A subset of these annotations had their expression and sequence confirmed with reverse transcription-PCR (RT-PCR) and sequencing. This benchmark analysis of the Aedes genome has yielded a set of manually annotated transcripts that has been validated with molecular and comparative data. In addition, we have presented data that may clarify the origin of duplicated transcripts in the genome assembly.

BAC assembly

The quality of these BAC assemblies is critical for a valid assessment of the genome assembly and the automatic gene-annotation pipeline. To enable this assessment, each BAC clone was individually assembled using two assembly algorithms and the resulting duplicated assemblies were compared to make sure that contigs were identical. In addition, all BAC sequences were assembled together to ensure that they sorted independently into the contigs corresponding to individual BAC clones. These stringent assemblies revealed that the sequence of BAC9 (GenBank: AC149799), which was submitted to GenBank before this analysis, had contigs in it that were from BAC8 (GenBank: AC149798). A stringent analysis of these BACs in particular enabled their correct assembly. It was interesting to note that gaps present in the final BAC scaffolds were identical to those present in the genome assembly. We believe that the high repeat content of the sequence in the remaining gaps produces tertiary structures that are not conducive to sequencing. A high G+C content may also contribute to this phenomenon. As a result, we were unable to close several gaps. The 14 final assemblies were confirmed both with PCR, sequencing and a comparison to the genome assembly.

Repeat content

Assembled and oriented BAC scaffolds were masked for repeat sequence to characterize the transposon content as well as to enable a more efficient in silico gene model prediction. Gene-prediction algorithms cannot distinguish transposon ORFs, resulting in their being annotated along with species-specific ORFs. Resulting gene models may not be indicative of real genes, as genes could be split, merged or have extra exons. Initial repeat identification demonstrated that the Aedes genome has an unusually high repeat content [15]. Repeat masking [16, 17] was performed using multiple repeat datasets to maximize the number of repeats identified. An initial analysis of in silico gene annotations derived from the masked sequences revealed that a number of transposons were not identified as a result of the incomplete cataloging of the Aedes transposon dataset. This is seen with BAC2, where there were no transcripts annotated on the assembled sequence but gene prediction on repeat-masked sequence suggested the presence of up to 18 transcripts that are derived from unmasked transposon ORFs. The high repeat content of this genome is particularly interesting and impacted on the sequencing, assembly, in silico and manual annotation presented in this study. The proper identification of a genome's repeat content is vital as it impacts on these analyses that form the basis of genomic studies.

Manual annotation and RT-PCR

Manually curated genes are generally considered to be the highest tier of gene models for genome annotation and training datasets. Annotations were based on several sets of data that include manual inspection of species-specific ESTs and comparative data. A portion of the ESTs mapped to transposons, complicating the manual annotation. These transposon-related ESTs can be attributed either to active transposition or to genome-related transposition silencing. As a result, in silico gene prediction on unmasked sequence resulted in a higher number of predicted genes (around 4 times more), while the presence of unidentified repeat sequences on masked sequence resulted in over-prediction as well. Although most of the ORFs from the 51 final manually annotated gene models were present in these predictions, transposons present in intergenic sequences led to the splitting and merging of exons along with transposon ORFs. Though the resulting gene predictions from the two ab initio gene-prediction programs were not alike, they did capture similar exons. These in silico predicted exons were helpful in determining splice sites, along with EST and comparative evidence during manual annotation. The large repeat content in this genome highlights the importance of proper repeat identification and masking before gene prediction in annotation pipelines.

Gene models (see Table 2) were predicted only if they had supporting EST and comparative evidence and did not overlap with sequence that was homologous to transposons. We do not believe we have eliminated any 'domesticated' transposons, although this remains a possibility.

PCR performed on a cDNA library confirmed expression of a subset of transcripts, enabled a sequence comparison of the expressed transcripts with the manual annotations and also introduced an annotation quality-control step. To enable the most thorough expression analysis, the cDNA library was derived from RNA extracted from all stages of mosquito development (see Materials and methods). This molecular verification points to the importance of manual annotations in a genome-annotation pipeline that can not only verify the quality of the auto-annotation but also provide a set of high-quality transcripts that can be used to develop and improve it.

Comparison of gene models to the Aedesgene build

All manual annotations were compared to the Aedes genome assembly and Genebuild - AaegL1.1 (see Table 2). Almost all manually annotated transcripts were found in the Aedes gene build. Differences between the manually annotated models and the transcripts from the gene build included a transcript missing, extra transcripts in the gene build and differences in annotation (see Table 3). When looking at nucleotide similarity (BLASTN), only one transcript on BAC7 (number 20, see Tables 2, 3) did not have a match in the gene build, even though it had perfect nucleotide match in the genome. This annotation belonged to a multigene family (histone H3) and had several almost identical annotated transcripts elsewhere in the Aedes genome. The sequence flanking this gene model consisted of transposon sequence, and the entire region was labeled as repetitive in the genome assembly [4]. This transcript, present in multiple copies in the genome as well as being flanked by transposon sequence, was masked before mapping of ESTs to the assembled genome and consequent gene annotation. This points to the importance of differentiating multicopy gene sequences versus those that are homologous to transposons and to the necessity of a comprehensive catalog of the Aedes transposon dataset.

This set of manually annotated transcripts enables a quality check of the Aedes genome auto-annotation. Approximately 12% of the manually annotated transcripts possessed minor differences from their auto-annotation counterparts, indicating a high-quality genome annotation effort. These differences, as well as the identification of a rhabdovirus nucleocapsid incorporation, highlights the importance of manual annotation and points to a few issues an auto-annotation pipeline may have.

Replicated BAC transcripts in genome assembly

The 14 BACs were identified from single-locus genetic markers [9]. However, eight of these blocks of genomic sequence possessed transcripts (including the single-copy markers) that were replicated in the genome assembly, along with flanking transcripts, in the same order and structure (see Table 2). A further analysis of the single-copy genetic markers in Severson et al. [9], reveals that 26 of the 146 single-copy genetic markers used are present more than once in the genome assembly (data not shown). The high percentage of repeated single-copy markers from a well-known study presents the possibility that these duplicated assembly regions may have resulted from actual segmental duplications, haplotype polymorphisms or misassemblies.

If these regions represented segmental duplications, they would have to be physically close to each other - as the genetic markers have been extensively used and the genetic positions calculated have been well characterized and fall out as one genetic locus [9]. However, the genome assembly has these repeated single-copy markers sometimes localizing to different supercontigs (suggesting a greater distance between them). These different supercontigs sometimes also have markers on them that localize to different linkage groups. This suggests that even though there may be a number of repeated markers present close to each other, a certain degree of misassembly would explain how a single-copy genetic marker would be duplicated on another supercontig or present along with a genetic marker from another linkage group. These events can be explained by the high repeat content of this genome and the presence of repeats flanking these regions, further complicating their proper assembly. It was interesting to note that shotgun sequences from identical repeats were some of the only discrepancies in our assemblies in this study. However, the relatively small size of these assemblies enabled us to completely assemble the BACs correctly.

If these regions represent haplotype polymorphic regions, they should demonstrate genetic drift and therefore a certain amount of sequence variation. These differences would result in the haplotype regions assembling into two scaffolds and therefore complicating the assembly. This phenomenon is seen in polymorphic regions of the A. gambiae genome (demonstrating 95-99% similarity) that assembled independently of each other ([4, 8] and R. Bruggner and M. Hammond, personal communication). Strains used for sequencing are usually inbred to eliminate usual genomic variation to enable an easier assembly and analysis (the strain of Ae. aegypti used for genome sequencing (LVPib12) was inbred for 12 generations from an already inbred strain). However, this cannot eliminate the presence of balanced polymorphisms where homozygous regions result in lethality - a phenomenon extensively used in Drosophila genetics. Haplotype polymorphic regions are expected in genome assemblies; however, their negative effects on assembly and analysis can be minimized by proper strain selection and inbreeding. The replicated regions seen here were not precise duplications, as a comparison of the entire nucleotide sequence revealed intergenic differences between the replicated blocks. A comparative analysis revealed that 23 of the 28 transcripts encompassed by these 'replicated' BACs were single copy in both the A. gambiae and D. melanogaster genomes, again suggesting a single-copy nature. The variation seen between replicated regions, the 'hybrid' nature seen between the BAC sequence and the genomic replicates, the characterization of the markers and encompassed genes as being single copy in Aedes [9], as well as in Anopheles and Drosophila, lead us to believe that these replicated regions in the genome assembly represent polymorphic haplotypes coupled with some misassembly resulting from flanking repeat sequence. There remains the possibility that some of these regions are actually duplicated in the genome and are present close to each other.

The replication of an unusually high percentage of genomic blocks experimentally shown to contain single-copy sequences (57% (8 of 14)), indicates the presence of an assembly issue which affects the number of gene predictions in the gene build and the relation of various scaffolds to each other. This phenomenon also emphasizes the importance of strain selection and proper inbreeding to enable an easier genome assembly. The proper characterization of these probable haplotype regions would enable a better genome assembly and mapping of scaffolds to linkage groups.

Similarity to Drosophila and Anopheles

All manually annotated transcripts were compared to the Drosophila and Anopheles gene sets (see Table 3). Only one annotation (number 19) did not show homology to Anopheles or Drosophila proteins with the search parameters used. This transcript did demonstrate similarity to an Aedes salivary protein (D7cclu23-like salivary protein). When the search parameters were relaxed, the primary hit to Anopheles is an odorant-binding protein (OBP49). A salivary- or odorant-related gene would be expected to have significantly diverged from Anopheles and even further diverged from Drosophila homologs and would not show a high degree or any similarity in the stringent comparative searches used.

Of the remaining 50 transcripts, 50 and 43 demonstrated similarity to the Anopheles and Drosophila gene sets, respectively. Seven manual annotations that did not have any similarity to the Drosophila genome (but did to the Anopheles genome) may have either been lost in the lineage that gave rise to the higher dipterans or have significantly diverged from their homologs. Most transcripts had a one-to-one relationship with a gene in the other dipteran genomes. In general, most manually annotated transcripts were similar in length and amino-acid identity to the other dipteran transcripts. The transcripts that had similarity to Anopheles transcripts had an average of 72% identity to the manually annotated transcripts with a range 32-100% identity. The 49 Drosophila transcripts had an average of around 60% identity with a range 31-97%.

The 51 transcripts represent a gene density of one gene every 30.8 kb, which is considerably lower than in A. gambiae [7] or D. melanogaster [6]. Aedes genes possessed larger intergenic sequences, resulting in multi-exon genes being about four times as large as their Anopheles counterparts. This lower gene density seen in Aedes can be related to its larger genome size, with a much higher repeat/transposon content.

Synteny

To look for syntenic relationships, the 11 blocks of transcripts (those with more than one annotation) were compared with the Anopheles and Drosophila genome (see Table 3). Ten of the blocks had transcripts in them that were similarly clustered in the Anopheles genome, whereas only one cluster of two adjacent transcripts was found in Drosophila. Overall, 38 transcripts in 10 blocks demonstrated the closer relationship and shorter divergence times between the two mosquitoes [18].

Syntenic studies between genomes can have important applications, including the verification of transcripts and gene annotations. Transcript 38 did not have similarity to any anopheline annotation but possessed significant similarity to a Drosophila transcript. This BAC sequence demonstrated synteny to the Anopheles genome and was the only transcript missing, although the nucleotide sequence corresponding to this sequence was present. Further investigation revealed that the transcript corresponding to it was removed in the last Anopheles gene build. The presence of this transcript in both the Drosophila and Anopheles genome, as well as the corresponding nucleotide sequence in the Anopheles genome, suggests that this anopheline transcript needs to be reinstated.

Conclusion

This study has resulted in the description of the repeat content, gene content and relationship to other dipteran genomes of 14 Ae. aegypti BACs. The high repeat content of this genome adversely affected the assembly and complicated in silico annotation. The verification of the haplotype nature of some scaffolds will enable an enhanced assembly and mapping of scaffolds to linkage groups. A well-defined set of Aedes transcripts (such as those in this study) combined with Aedes ESTs, and the demonstrated similarity to the A. gambiae and D. melanogaster genome are necessary for a high-quality genome annotation. This study allows us to get an overall view of the genome-assembly quality of this important disease vector and presents a benchmark set of manually annotated and validated transcripts in addition to validating the whole genome auto-annotation.

Materials and methods

The Ae. aegypti BAC library [19] was screened with primers specific to known single-locus genetic markers [9] to isolate BAC clones for further analysis. Fourteen BAC clones were shotgun sequenced and assembled using both the TIGR assembler [2] and Seqman [10]. All shotgun sequences were assembled together to ensure that they sorted independently into the contigs corresponding to individual BAC clones. Primers were designed to single-copy sequence flanking gaps in an effort to close them through PCR and sequencing of the BAC clone. Assembled sequences were analyzed for repetitive/transposon content using Repeatmasker [16] and CENSOR [17], using the arthropod, D. melanogaster and A. gambiae repeat datasets.

GENESCAN 1.0 [12] and FGENESH 1.0 [13] were used with default parameters and the vertebrate, D. melanogaster and A. gambiae training datasets to predict genes in silico. To identify expressed transcripts, BLAST was performed with these assembled scaffolds to the Ae. aegypti, D. melanogaster and A. gambiae EST databases [2, 4, 20]. The cutoff used to limit the number of ESTs was e < -100 for Ae. aegypti and e < -50 for Anopheles and Drosophila ESTs.

Evidence used for the manual annotation of the BAC sequences included ab initio gene prediction and ESTs from the Aedes, Anopheles and Drosophila genomes. Predicted exons and ESTs that were similar to transposons were not used. BLAST to the Drosophila and Anopheles peptide datasets was used to capture exons and genes that were not included in Aedes ESTs or predicted gene models. Manual annotation was performed using Apollo [14]. Predictions were made conservatively with evidence needed from non-transposon-related Aedes ESTs and/or similarity to other dipteran genes/ESTs.

PCR primers were designed to manually annotated transcripts for PCR and sequencing validation. Total RNA was isolated with Trizol Reagent (Invitrogen, Carlsbad, CA) from Ae. aegypti LVPib12 mosquitoes (one to three instar larvae (11.5%); fourth instar larvae and pupae (11.5%); 1-2-day adults (22%); 5-7-day adults (15%); 2-day post-bloodfed female (41%)). cDNA was prepared from the above RNA using the SuperScriptII (Invitrogen) system. Primers were designed across introns when possible. Control primers were designed to the Ae. aegypti gene for ribosomal protein 17A (AY064121). PCR was conducted with Platinum Taq using 35 cycles. PCR products were gel-purified (QIAquick Gel Extraction Kit, Qiagen, Valencia, CA) and sequenced using primers from the PCR reactions. Sequencing was performed on ABI3730XL (Applied Biosystems, Foster City, CA). Sequence obtained was used to confirm or correct manual annotations and splice sites. Manually annotated transcripts were compared to the Anopheles and Drosophila genomes (BLASTX, BLOSUM90 [4]) for evaluation of similarity and synteny.

Additional data files

The following additional data are available with the online version of this paper. Additional data file 1 contains detailed descriptions of the assembly and annotation of each BAC clone, the presence of replicated regions, and orthologous and syntenic relationships.

Notes

Declarations

Acknowledgements

The authors would like to thank R. Bruggner and E.O. Stinson for bioinformatic support. This study was supported by NIH NIAID contract HHSN266200400039C (FHC) and grant U01-AI50936 (DWS).

Authors’ Affiliations

(1)
Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame
(2)
Harvard University
(3)
TIGR

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Copyright

© Lobo et al.; licensee BioMed Central Ltd. 2007

This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.