The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success
Abstract
:1. Introduction
2. Methods
2.1. Insect Strain
2.2. Photography
2.3. Measurement of Genome Size
2.4. Extraction of Nucleic Acids, Sequencing, and Assembly
2.4.1. Genome Sequencing and Assembly
2.4.2. Transcriptome Sequencing and Gene Expression Analysis
2.5. Post Genome Analysis
2.5.1. Gene Prediction and Annotation
2.5.2. Manual Annotation
2.5.3. Phylogenetic Analysis
2.5.4. Expression Analysis
2.5.5. Repeat Structure Analysis
3. Results
3.1. Sequencing and Assembly
3.2. Manual Annotation
3.2.1. Detoxification Genes
ATP Binding Cassette Transporters
Cytochrome P450s, UDP-Glucuronosyltransferases, Glutathione S-Transferases, and Carboxylesterases
3.2.2. Chemosensory Biology
Odorant Receptors
Gustatory and Ionotropic Receptors
3.2.3. Digestive Enzymes
Carbohydrases
Peptidases
Proline-Specific Peptidases (PSPs)
Serine Peptidases
Metalloexopeptidases
3.2.4. Other Genes of Interest
Aquaporins
RdCad1, a Putative Receptor of Insecticidal Cry Toxins
Cysteine Peptidases
Phosphine Resistance Genes
3.3. Repeat Sequence/Structure
3.3.1. Transposon Elements (TE)
3.3.2. Identification and Characterization of Satellite DNAs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ABC | ATP binding cassette |
APP | aminopepdidase P |
AQP | Aquaporin |
Bib | Drosophila big-brain |
Bt | Bacillus thuringiensis |
BUSCO | Benchmarking Universal Single-Copy Orthologs |
CGAHR | Center for Grain and Animal Health Research |
COesterases | Carboxylesterases |
CYT | Cytoplasmic |
DLD | dihydrolipoamide dehydrogenase |
DPP | dipeptdidylpeptidases |
Drip | Drosophila integral protein |
EC | Ectodomain |
Eglps | entomoglyveroporins |
FAP | fibroblast activation protein |
GH | glucosyl hydrolase |
GLPs | aquaglyceroporins |
GR | gustatory receptor |
INT | internal exons |
IR | ionotropic receptor |
LINE | long interspersed nuclear element |
LTR | long terminal repeat; |
MPED | membrane proximal extracellular domain |
MRPs | multidrug resistance proteins |
NBD | nucleotide binding domain |
NPA motif | asparagine-proline-alanine motif |
NTE | N-terminal |
OR | odorant receptor |
PCWDE | plant cell wall degrading enzymes |
PSPs | proline-specific peptidases |
PER | period to eliminate multiple reporting of repeats |
POP | prolyloligopeptidase |
PRCP | prolylcarboxypeptidase |
Prip | Pyrocoelia rufa integral protein |
RdCad1 | BtR1-like cadherin gene |
RNAi | RNA interference |
RPKM | reads per kilobase per million mapped reads |
satDNA | satellite DNA |
SP | single-domain serine peptidases |
SPHs | non-catalytic SP homologs |
TBR | toxin-binding regions |
TE | transposable elements |
TIR | terminal inverted repeats |
TM/TMD | transmembrane/transmembrane domain |
TRBD | tandem repeat database |
UGTs | Uridine 5′-diphospho-glucuronosyltransferase |
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Assembly | # Scaffolds | Total Mb | N50 1 (Mb) | L50 1 | N901 (Mb) | L90 1 | Longest Scaffold | BUSCO 2 |
---|---|---|---|---|---|---|---|---|
CANU | 1861 3 | 493 | 0.87 | 158 | 0.15 | 627 | 5,205,710 | 99.3 |
Chicago/HiRise | 948 | 493 | 7.32 | 20 | 1.11 | 84 | 27,933,969 | 99.4 |
Hybrid 4 | 336 | 479 | 7.44 | 19 | 1.48 | 74 | 27,934,817 | 97.6 |
Hi-C/HiRise | 139 | 479 | 53.6 | 4 | 15.9 | 9 | 82,855,609 | 98.5 |
Species | Subfamily | Total | Reference | |||||||
---|---|---|---|---|---|---|---|---|---|---|
A | B | C | D | E | F | G | H | |||
Rhyzopertha dominica | 3 | 6 | 14 | 2 | 1 | 3 | 13 | 3 | 45 | This study |
Diabrotica v. virgifera | 4 | 7 | 32 | 2 | 1 | 3 | 12 | 4 | 65 | [89] * |
Aethina tumida | 4 | 6 | 24 | 2 | 1 | 3 | 13 | 3 | 56 | [90] |
Tribolium castaneum | 10 | 6 | 35 | 2 | 1 | 3 | 14 | 3 | 74 | [61] |
Altica viridicyanea | 8 | 9 | 37 | 2 | 1 | 3 | 8 | 1 | 69 | [91] |
Chrysomela populi | 5 | 8 | 29 | 2 | 1 | 3 | 14 | 3 | 65 | [92] * |
Drosophila melanogaster | 10 | 8 | 14 | 2 | 1 | 3 | 15 | 3 | 56 | [93] |
Type | MEROPS | Peptidase * | R. dominica Sequence ID | Active Site Residues | RNA Expression (RPKM) | Signal Peptide (Amino Acid) | ||
---|---|---|---|---|---|---|---|---|
Gut | Carcass | Head | ||||||
Serine | S9 | POP | RDOM022815 | SDH | 40.0 | 66.0 | 179 | n/a |
DPP 4 | RDOM016604 | SDH | 29.0 | 15.0 | 6.00 | 13 | ||
RDOM017825 | SDH | 13.0 | 10.0 | 9.00 | n/a | |||
DPP 9 | RDOM002099 | SDH | 4.40 | 4.30 | 6.00 | n/a | ||
DPP 10 | RDOM007500 | GDH | 0.60 | 1.30 | 1.30 | n/a | ||
RDOM016697 | GDH | 0.04 | 11.0 | 26.0 | n/a | |||
RDOM007053 | SDH | 0.50 | 1.00 | 1.00 | n/a | |||
S28 | PRCP | RDOM021888 | SDH | 25.0 | 47.0 | 60.0 | 18 | |
RDOM004644 | SDH | 56.0 | 105 | 79.0 | 18 | |||
Metal-dependent | M24 | APP1 | RDOM014136 | DDHEE | 0.50 | 1.40 | 0.60 | n/a |
RDOM016283 | DDHEE | 50.0 | 29.0 | 29.0 | n/a | |||
APP3 | RDOM000819 | DDHEE | 246 | 222 | 88.0 | n/a | ||
Prolidase | RDOM021565 | DDHEE | 182 | 74.0 | 71.0 | n/a |
Name | Position | Intron # | CDS (bp) | Residues |
---|---|---|---|---|
RDO_Drip | Scaffold_97:54496632–54558762 − strand | 4 | 681 | 227 |
RDO_Prip | Scaffold_97:54640277–54649322 + strand | 3 | 819 | 272 |
RDO_Bigbrain | Scaffold_5:3510369–3521423 − strand | 3 | 1161 | 386 |
RDO_AQP12L | Scaffold_2:13423224–13433006 − strand | 4 | 924 | 307 |
RDO_Eglp1 | Scaffold_1:3563523–3572656 + strand | 5 | 942 | 313 |
RDO_Eglp2 | Scaffold_1:34240108–34250443 + strand | 4 | 660 | 219 |
RDO_Eglp3 | Scaffold_1:3546737–3555431 + strand | 6 | 888 | 295 |
RDO_Eglp4 | Scaffold_1:26416818–26424599 − strand | 4 | 831 | 276 |
Gene names | Annotation | Gene Coordinates | Expression (RPKM) | Active Site Residues | |||
---|---|---|---|---|---|---|---|
Adult | Gut 1 | Carcass 1 | Head 1 | ||||
RdL_97 | Cathepsin L | Scaffold_97:41752520–41759245 + strand | 305 | 202 | 272 | 359 | QCHN |
RdLc1_97 | Cathepsin Lc1 | Scaffold_97:41485991–41504771 − strand | 5.79 | 0 | 2.17 | 0.49 | QCHN |
RdLc2_97 | Cathepsin Lc2 | Scaffold_97:41733271–41745109 + strand | 115 | 14.8 | 903 | 335 | QCHN |
RdLl_3 | Cathepsin L1 | Scaffold_3:61931842–61935045 + strand | 114 | 160 | 145 | 108 | QCHN |
RdO_135 | Cathepsin O | Scaffold_135:6970795–6971976 − strand | 12.0 | 7.41 | 8.53 | 7.30 | QCHN |
RdF_3 | Cathepsin F | Scaffold_3:45747905–45769454 − strand | 94.8 | 57.2 | 176 | 213 | QCHN |
RdI_5 | Cathepsin I | Scaffold_5:4129386–4130669 + strand | 9.99 | 0.21 | 0.58 | 0.31 | QCHN |
RdB_100 | Cathepsin B | Scaffold_100:30781674–30791599 + strand | 272 | 729 | 571 | 164 | QCHN HH |
RdTINAL-like_3 | Cathepsin B TINAL-like | Scaffold_3:13137364-13151656 − strand | 32.3 | 27.4 | 35.3 | 43.9 | QSHN |
Repeat Name | Consensus Monomer Length (bp) | Number of Arrays in a Cluster | Total Number of Monomers | Maximum Number of Monomers in an Array | Average Number of Monomers in an Array | AT Content of Consensus Sequence (%) | Average Monomer Similarity (%) | Genome Occupancy (bp) | % of the Assembled Genome |
---|---|---|---|---|---|---|---|---|---|
RD rep1 | 147 | 320 | 1836.8 | 37.1 | 5.7 | 52.4 | 93.6 | 270,614 | 0.0565 |
RD rep2 | 123 | 308 | 3765.4 | 230.0 | 12.2 | 61.0 | 78.4 | 462,627 | 0.0965 |
RD rep3 | 126 | 266 | 3389.4 | 190.7 | 12.7 | 63.5 | 85.2 | 418,239 | 0.0873 |
RD rep4 | 126 | 182 | 2390.3 | 173.5 | 13.1 | 65.1 | 91.1 | 298,197 | 0.0622 |
RD rep5 | 127 | 107 | 429.3 | 11.3 | 4.0 | 55.1 | 91.9 | 54,080 | 0.0113 |
RD rep6 | 272 | 98 | 751.1 | 58.3 | 7.6 | 61.4 | 89.0 | 203,159 | 0.0424 |
RD rep7 | 294 | 97 | 1350.2 | 59.7 | 13.9 | 59.5 | 86.6 | 397,984 | 0.0831 |
RD rep8 | 110 | 97 | 260.2 | 7.0 | 2.7 | 63.6 | 96.4 | 28,933 | 0.0060 |
RD rep9 | 135 | 95 | 734.4 | 23.7 | 7.7 | 65.2 | 89.4 | 95,988 | 0.0200 |
RD rep10 | 153 | 89 | 898.4 | 31.7 | 10.1 | 54.9 | 93.6 | 137,075 | 0.0286 |
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Oppert, B.; Muszewska, A.; Steczkiewicz, K.; Šatović-Vukšić, E.; Plohl, M.; Fabrick, J.A.; Vinokurov, K.S.; Koloniuk, I.; Johnston, J.S.; Smith, T.P.L.; et al. The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success. Genes 2022, 13, 446. https://doi.org/10.3390/genes13030446
Oppert B, Muszewska A, Steczkiewicz K, Šatović-Vukšić E, Plohl M, Fabrick JA, Vinokurov KS, Koloniuk I, Johnston JS, Smith TPL, et al. The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success. Genes. 2022; 13(3):446. https://doi.org/10.3390/genes13030446
Chicago/Turabian StyleOppert, Brenda, Anna Muszewska, Kamil Steczkiewicz, Eva Šatović-Vukšić, Miroslav Plohl, Jeffrey A. Fabrick, Konstantin S. Vinokurov, Igor Koloniuk, J. Spencer Johnston, Timothy P. L. Smith, and et al. 2022. "The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success" Genes 13, no. 3: 446. https://doi.org/10.3390/genes13030446
APA StyleOppert, B., Muszewska, A., Steczkiewicz, K., Šatović-Vukšić, E., Plohl, M., Fabrick, J. A., Vinokurov, K. S., Koloniuk, I., Johnston, J. S., Smith, T. P. L., Guedes, R. N. C., Terra, W. R., Ferreira, C., Dias, R. O., Chaply, K. A., Elpidina, E. N., Tereshchenkova, V. F., Mitchell, R. F., Jenson, A. J., ... Campbell, J. F. (2022). The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success. Genes, 13(3), 446. https://doi.org/10.3390/genes13030446