Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations
Abstract
:1. Introduction
2. Materials and Methods
2.1. Virus Amplification and DNA Extraction
2.2. Sequencing, Consensus Genome Assembly and Annotation
2.3. Mutation Detection and Analyses
2.4. Detection of Large Deletions
3. Results and Discussion
3.1. AcMNPV-WP10 Genome Sequence and Annotation
WP10/C6 sequence a | Position on WP10 b | Position on C6 c | Type | WP10 gene d | C6 gene |
---|---|---|---|---|---|
-/A | 9707 | 14,226 | Indel | Ac17 | Ac17 |
G/A | 11,651 | 16,171 | SNP | Ac20/21 | Ac20 |
CG/- | 11,685 | 16,205 | Indel | Ac20/21 | Ac20 |
AC/- | 11,690 | 16,208 | Indel | Ac20/21 | Ac20 |
G/C | 11,692 | 16,208 | SNP | Ac20/21 | Ac20 |
-/G | 11,698 | 16,214 | Indel | Ac20/21 | Ac20 |
-/C | 11,788 | 16,305 | Indel | Ac20/21 | Ac21 |
-/G | 38,855 | 44,372 | Indel | Ac52 | Ac52 |
G/T | 43,197 | 47,714 | SNP | Ac58/59 | Ac58 |
A/- | 43,398 | 47,914 | Indel | Ac58/59 | Ac59 |
-/CGACGGTCGAGGG | 67,379 | 71,893 | Indel | Non-coding e | Non-coding e |
-/TATAATTTTT | 69,604 | 74,134 | Indel | Non-codinge | Ac86 |
A/- | 89,218 | 93,749 | Indel | Ac106/107 | Ac106 |
A/- | 89,288 | 93,818 | Indel | Ac106/107 | Ac106 |
C/- | 89,326 | 93,865 | Indel | Ac106/107 | Ac106 |
CA/- | 89,414 | 93,953 | Indel | Ac106/107 | Ac106 |
C/A | 89,417 | 93,954 | SNP | Ac106/107 | Ac106 |
G/- | 89,447 | 93,983 | Indel | Ac106/107 | Ac106 |
CG/- | 89,497 | 94,033 | Indel | Ac106/107 | Ac106 |
A/G | 89,573 | 94,107 | SNP | Ac106/107 | Ac107 |
ATTTGG/- | 89,576 | 94,110 | Indel | Ac106/107 | Ac107 |
A/- | 89,587 | 94,114 | Indel | Ac106/107 | Ac107 |
-/A | 92,249 | 96,777 | Indel | Ac112/113 | Ac112 |
G/A | 92,440 | 96,968 | SNP | Ac112/113 | Ac113 |
T/C | 92,635 | 97,163 | SNP | Ac112/113 | Ac113 |
C/T | 92,885 | 97,413 | SNP | Ac112/113 | Ac113 |
T/C | 92,998 | 97,526 | SNP | Ac112/113 | Ac113 |
G/A | 93,065 | 97,593 | SNP | Ac112/113 | Ac113 |
G/- | 107,127 | 111,645 | Indel | Ac131 | Ac131 |
-/T | 120,584 | 125,113 | Indel | Ac143 | Ac143 |
-/T | 120,586 | 125,116 | Indel | Ac143 | Ac143 |
-/A | 121,748 | 126,790 | Indel | Ac145 | Ac145 |
ATCTG/- | 133,286 | 3919 | Indel | Ac7 | Ac7 |
TATTT/- | 133,602 | 4229 | Indel | Ac7 | Ac7 |
AACAACGCTGCAT/- | 133,610 | 4232 | Indel | Ac7 | Ac7 |
ACATTA/- | 133,625 | 4234 | Indel | Ac7 | Ac7 |
ATTTCGGCTT/- | 133,808 | 4411 | Indel | Non-coding e | Non-coding e |
3.2. Nucleotide Variation in the AcMNPV-WP10 Genome Population
Cluster | Nucleotide | Number of loci | Mean Frequency a | # per genome b | # per OB c |
---|---|---|---|---|---|
1 | A | 903 | 0.23 | 1.39 | 137.71 |
T | 969 | 0.20 | 1.44 | ||
G | 328 | 0.44 | 0.87 | ||
C | 361 | 0.36 | 0.89 | ||
2 | A | 98 | 8.97 | 7.07 | 933.75 |
T | 104 | 8.77 | 7.41 | ||
G | 112 | 10.02 | 9.79 | ||
C | 86 | 9.43 | 6.86 | ||
3 | A | 39 | 16.75 | 5.94 | 842.56 |
T | 41 | 16.31 | 6.35 | ||
G | 46 | 23.59 | 9.72 | ||
C | 38 | 19.92 | 6.07 | ||
4 | A | 25 | 35.82 | 6.03 | 901.33 |
T | 25 | 34.86 | 5.10 | ||
G | 30 | 35.99 | 7.95 | ||
C | 38 | 32.91 | 10.96 |
Nt a | Gene function b | Position c | Perc. d | Cluster | Gene e | Codon Change | AA change | AA class change f |
---|---|---|---|---|---|---|---|---|
C | Accessory | 101,605 | 37.55 | 4 | Ac126/chitinase | TCA->GCA | S->A | NP->No polarity |
C | Accessory | 101,638 | 38.05 | 4 | Ac126/chitinase | AAA->GAA | K->E | BP->AP |
T | Accessory | 101,647 | 38.08 | 4 | Ac126/chitinase | CCC->ACC | P->T | No polarity->NP |
G | Accessory | 101,716 | 40.18 | 4 | Ac126/chitinase | GGT->CGT | G->R | No polarity->BP |
G | Accessory | 101,793 | 36.25 | 4 | Ac126/chitinase | AGA->AGC | R->S | BP->NP |
A | Accessory | 101,851 | 35.62 | 4 | Ac126/chitinase | GGC->TGC | G->C | No polarity->NP |
C | Accessory | 101,884 | 37.25 | 4 | Ac126/chitinase | TCA->GCA | S->A | NP->No polarity |
T | Host interaction | 110,347 | 15.71 | 3 | Ac134/p94 | CGC->AGC | R->S | BP->NP |
G | BV specific | 14,832 | 19.28 | 3 | Ac23/f-protein | ACA->GCA | T->A | NP->No polarity |
T | BV specific | 14,833 | 18.27 | 3 | Ac23/f-protein | ACA->ATA | T->I | NP->No polarity |
A | BV specific | 103,990 | 21.18 | 3 | Ac128/gp64 | TCG->TTG | S->L | NP->No polarity |
A | ODV specific | 2 | 36.71 | 4 | Ac8/polyhedrin | ATG->AAG | M->K | No polarity->BP |
A | ODV specific | 4 | 38.94 | 4 | Ac8/polyhedrin | CCG->ACG | P->T | No polarity->NP |
T | ODV specific | 4 | 32.48 | 4 | Ac8/polyhedrin | CCG->TCG | P->S | No polarity->NP |
A | ODV specific | 5 | 12.99 | 3 | Ac8/polyhedrin | CCG->CAG | P->Q | No polarity->NP |
A | ODV specific | 13,917 | 14.02 | 3 | Ac22/pif-2 | GGG->AGG | G->R | No polarity->BP |
A | ODV specific | 33,571 | 30.25 | 4 | Ac46/odv-e66 | GCC->ACC | A->T | No polarity->NP |
G | ODV specific | 64,772 | 22.98 | 3 | Ac83/vp91 | ACC->GCC | T->A | NP->No polarity |
A | ODV specific | 70,144 | 13.09 | 3 | Ac88/cg30 | CAA->AAA | Q->K | NP->BP |
A | ODV specific | 70,234 | 13.58 | 3 | Ac88/cg30 | GCC->TCC | A->S | No polarity->NP |
A | ODV specific | 70,268 | 13.58 | 3 | Ac88/cg30 | ACA->ATA | T->I | NP->No polarity |
A | ODV specific | 70,381 | 13.68 | 3 | Ac88/cg30 | GAC->TAC | D->Y | AP->NP |
T | ODV specific | 70,399 | 13.78 | 3 | Ac88/cg30 | GCG->ACG | A->T | No polarity->NP |
G | ODV specific | 94,932 | 23.84 | 3 | Ac115/pif-3 | GGT->CGT | G->R | No polarity->BP |
C | ODV specific | 97,271 | 40.46 | 4 | Ac119/pif-1 | TCG->CCG | S->P | NP->No polarity |
T | PA | 71,103 | 14.86 | 3 | Ac89/vp39 | CGC->AGC | R->S | BP->NP |
C | PA | 74,220 | 21.51 | 3 | Ac92/p33 | AAA->GAA | K->E | BP->AP |
C | PA | 74,391 | 17.50 | 3 | Ac92/p33 | AAA->GAA | K->E | BP->AP |
A | PA | 74,421 | 32.40 | 4 | Ac92/p33 | CAC->TAC | H->Y | BP->NP |
G | PA | 84,226 | 30.75 | 4 | Ac103/p45 | ACT->CCT | T->P | NP->No polarity |
T | PA | 91,064 | 13.25 | 3 | Ac109/odv-ec43 | GAG->AAG | E->K | AP->BP |
A | Replication | 29,534 | 13.78 | 3 | Ac42/gta | GCG->ACG | A->T | No polarity->NP |
A | Transcription | 28,878 | 30.16 | 4 | Ac41/lef-12 | GAC->AAC | D->N | AP->NP |
G | Transcription | 29,337 | 18.47 | 3 | Ac41/lef-12 | ACA->GCA | T->A | NP->No polarity |
T | Transcription | 29,346 | 18.55 | 3 | Ac41/lef-12 | CCA->TCA | P->S | No polarity->NP |
A | Transcription | 36,848 | 17.11 | 3 | Ac50/lef-8 | CAC->TAC | H->Y | BP->NP |
G | Transcription | 45,913 | 26.33 | 3 | Ac62/lef-9 | AAA->GAA | K->E | BP->AP |
C | Transcription | 68,643 | 24.53 | 3 | Ac86/pnk/pnl | ACA->GCA | T->A | NP->No polarity |
T | Transcription | 73,303 | 16.73 | 3 | Ac90/lef-4 | TCG->TTG | S->L | NP->No polarity |
T | Transcription | 73,356 | 16.95 | 3 | Ac90/lef-4 | CCG->TCG | P->S | No polarity->NP |
G | Unknown | 23,830 | 24.44 | 3 | Ac34 | AAT->CAT | N->H | NP->BP |
G | Unknown | 23,932 | 22.47 | 3 | Ac34 | TAT->CAT | Y->H | NP->BP |
T | Unknown | 23,938 | 22.88 | 3 | Ac34 | GAG->AAG | E->K | AP->BP |
C | Unknown | 24,013 | 22.45 | 3 | Ac34 | CGC->GGC | R->G | BP->No polarity |
G | Unknown | 24,025 | 22.20 | 3 | Ac34 | AAT->CAT | N->H | NP->BP |
G | Unknown | 24,112 | 24.62 | 3 | Ac34 | TAT->CAT | Y->H | NP->BP |
G | Unknown | 24,205 | 24.73 | 3 | Ac34 | GGG->CGG | G->R | No polarity->BP |
G | Unknown | 24,226 | 24.57 | 3 | Ac34 | GGG->CGG | G->R | No polarity->BP |
G | Unknown | 24,263 | 24.26 | 3 | Ac34 | GAT->GCT | D->A | AP->No polarity |
C | Unknown | 24,267 | 24.15 | 3 | Ac34 | AAT->AAG | N->K | NP->BP |
T | Unknown | 24,277 | 24.28 | 3 | Ac34 | CAG->AAG | Q->K | NP->BP |
C | Unknown | 41,973 | 34.83 | 4 | Ac55 | TTG->TCG | L->S | No polarity->NP |
A | Unknown | 73,784 | 25.98 | 3 | Ac91 | CCA->TCA | P->S | No polarity->NP |
T | Unknown | 74,061 | 15.53 | 3 | Ac91 | TTA->TAA | L-> * | No polarity->None |
A | Unknown | 89,718 | 14.28 | 3 | Ac106/107 | CCA->ACA | P->T | No polarity->NP |
G | Unknown | 93,822 | 20.30 | 3 | Ac114 | AAT->CAT | N->H | NP->BP |
C | Unknown | 133,289 | 37.26 | 4 | Ac7/orf603 | CTG->CGG | L->R | No Polarity->BP |
T | Unknown | 133,648 | 37.68 | 4 | Ac7/orf603 | CCA->ACA | P->T | No polarity->NP |
G | Unknown | 133,708 | 26.94 | 3 | Ac7/orf603 | AAC->CAC | N->H | NP->BP |
C | Unknown | 133,738 | 27.70 | 4 | Ac7/orf603 | AAG->GAG | K->E | BP->AP |
3.3. Characterization of Large Deletions
4. Conclusions
Supplementary Files
Supplementary File 1Acknowledgments
Author Contributions
Data Deposition
Conflicts of Interest
References and Notes
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Chateigner, A.; Bézier, A.; Labrousse, C.; Jiolle, D.; Barbe, V.; Herniou, E.A. Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations. Viruses 2015, 7, 3625-3646. https://doi.org/10.3390/v7072788
Chateigner A, Bézier A, Labrousse C, Jiolle D, Barbe V, Herniou EA. Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations. Viruses. 2015; 7(7):3625-3646. https://doi.org/10.3390/v7072788
Chicago/Turabian StyleChateigner, Aurélien, Annie Bézier, Carole Labrousse, Davy Jiolle, Valérie Barbe, and Elisabeth A. Herniou. 2015. "Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations" Viruses 7, no. 7: 3625-3646. https://doi.org/10.3390/v7072788