Genome-Wide Identification and Characterization of Carboxypeptidase Genes in Silkworm (Bombyx mori)
Abstract
:1. Introduction
2. Results
2.1. Identification and Characterization of the Carboxypeptidase Family
2.2. Phylogenetic Analysis
2.3. Expression Profiles
2.4. Carboxypeptidase Expression Profile after Starvation
3. Discussion
4. Materials and Methods
4.1. Biological Materials
4.2. Identification of the Carboxypeptidase Family in Silkworm
4.3. Bioinformatics and Phylogeny Analysis of the Silkworm Carboxypeptidase Family
4.4. Expression Profiles of Silkworm Carboxypeptidase Genes via Whole-Genome Microarrays
4.5. Silkworm Starvation Experiment
4.6. RNA Extraction
4.7. qRT-PCR
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Gene | Name in SilkDB | Chromosome | Scaffold | Position | Strand | Domain | Size (AA) | Probe | MW/Da | pI | Signal Peptide |
---|---|---|---|---|---|---|---|---|---|---|---|
BmMCP1 | BGIBMGA002530-TA | 9 | nscaf2511 | 5048133–5052368 | + | Peptidase_M2 | 73 | sw03136 | 8984.4 | 9.3 | no |
BmMCP2 | BGIBMGA006234-TA | 6 | nscaf2851 | 1576285–1581353 | − | Peptidase_M2 | 409 | sw03231 | 46,754.2 | 4.89 | no |
BmMCP3 | BGIBMGA002527-TA | 9 | nscaf2511 | 4990965–5002524 | + | Peptidase_M2 | 649 | sw14172 | 74,229.8 | 5.11 | yes |
BmMCP4 | BGIBMGA006539-TA | 6 | nscaf2853 | 6801913–6813068 | + | Peptidase_M2 | 647 | sw11710 | 74,185.1 | 5.39 | no |
BmMCP5 | BGIBMGA002529-TA | 9 | nscaf2511 | 5030694–5035485 | + | Peptidase_M2 | 173 | sw20193 | – | – | no |
BmMCP6 | BGIBMGA002531-TA | 9 | nscaf2511 | 5192136–5202359 | + | Peptidase_M2 | 153 | sw11006 | 17,724 | 7.01 | no |
BmMCP7 | BGIBMGA003228-TA | 2 | nscaf2623 | 1029259–1049209 | − | Peptidase_M2 | 711 | sw17925 | 82,533.6 | 9.06 | no |
BmMCP8 | BGIBMGA002526-TA | 9 | nscaf2511 | 4965783–4980141 | + | Peptidase_M2 | 648 | sw00643 | 74,913.1 | 5.34 | yes |
BmMCP9 | BGIBMGA009693-TA | 2 | nscaf2964 | 820517–835616 | − | Peptidase_M2 | 535 | sw19815 | 62,129.8 | 7.32 | no |
BmMCP10 | BGIBMGA009487-TA | 14 | nscaf2953 | 517470–526524 | + | Peptidase_M14 | 428 | – | 48,175.4 | 6.06 | yes |
BmMCP11 | BGIBMGA004799-TA | 25 | nscaf2818 | 2043455–2064130 | − | Peptidase_M14 | 468 | sw03973 | 53,767.3 | 9.18 | no |
BmMCP12 | BGIBMGA004800-TA | 25 | nscaf2818 | 2024210–2029825 | − | Peptidase_M14 | 344 | sw20598 | 38,598.6 | 6.55 | no |
BmMCP13 | BGIBMGA013275-TA | 16 | nscaf3063 | 3241878–3245274 | + | Peptidase_M14 | 346 | sw18892 | 39,898 | 5.24 | yes |
BmMCP14 | BGIBMGA013276-TA | 16 | nscaf3063 | 3256098–3269527 | + | Peptidase_M14 | 445 | sw05014 | 50,709.9 | 5.41 | yes |
BmMCP15 | BGIBMGA004801-TA | 25 | nscaf2818 | 1996486–2007642 | − | Peptidase_M14 | 427 | sw18974 | 48,293.5 | 5.78 | no |
BmMCP16 | BGIBMGA008973-TA | 3 | nscaf2930 | 2150368–2156343 | + | Peptidase_M14 | 365 | – | 41,363.1 | 9.22 | no |
BmMCP17 | BGIBMGA001892-TA | 19 | nscaf2204 | 1727896–1729970 | − | Peptidase_M14 | 298 | sw09352 | 33,757.5 | 6.37 | no |
BmMCP18 | BGIBMGA001891-TA | 19 | nscaf2204 | 1730646–1734010 | − | Peptidase_M14 | 418 | sw14852 | 48,425.2 | 9.24 | no |
BmMCP19 | BGIBMGA008975-TA | 3 | nscaf2930 | 2171627–2175156 | + | Peptidase_M14 | 267 | sw07649 | 30,547.4 | 5.31 | no |
BmMCP20 | BGIBMGA009477-TA | 14 | nscaf2953 | 493144–498033 | − | Peptidase_M14 | 429 | sw02069 | 48,772.3 | 6.08 | yes |
BmMCP21 | BGIBMGA004797-TA | 25 | nscaf2818 | 2109792–2113829 | − | Peptidase_M14 | 383 | sw11839 | 43,402.5 | 5.51 | no |
BmMCP22 | BGIBMGA009478-TA | 14 | nscaf2953 | 480242–485505 | − | Peptidase_M14 | 394 | sw00546 | 44,578.6 | 5.39 | no |
BmMCP23 | BGIBMGA004798-TA | 25 | nscaf2818 | 2099617–2105069 | − | Peptidase_M14 | 395 | sw03321 | 44,319.1 | 4.8 | no |
BmMCP24 | BGIBMGA006871-TA | 10 | nscaf2859 | 1283815–1295739 | + | Peptidase_M14 | 604 | sw12842 | 68,595.4 | 6.45 | yes |
BmMCP25 | BGIBMGA008976-TA | 3 | nscaf2930 | 2176287–2190645 | + | Peptidase_M14 | 365 | sw03831 | 41,702.1 | 6.15 | no |
BmMCP26 | BGIBMGA008910-TA | 3 | nscaf2930 | 1816975–1823616 | − | Peptidase_M14 | 479 | sw07559 | 53,979.4 | 5.75 | yes |
BmMCP27 | BGIBMGA004830-TA | 25 | nscaf2818 | 155397–165470 | − | Peptidase_M14 | 670 | sw03365 | 75,788.8 | 8.55 | no |
BmMCP28 | BGIBMGA006715-TA | 10 | nscaf2855 | 3350086–3361536 | + | Peptidase_M14 | 371 | sw20772 | 42,903 | 5.3 | no |
BmMCP29 | BGIBMGA001890-TA | 19 | nscaf2204 | 1746161–1749490 | − | Peptidase_M14 | 353 | sw20818 | 40,328.8 | 6.09 | no |
BmMCP30 | BGIBMGA009486-TA | 14 | nscaf2953 | 512395–515181 | + | Peptidase_M14 | 409 | sw10048 | 46,594.4 | 5.81 | no |
BmMCP31 | BGIBMGA009476-TA | 14 | nscaf2953 | 546619–551421 | − | Peptidase_M14 | 397 | sw12317 | 45,444.3 | 6.06 | no |
BmMCP32 | BGIBMGA000307-TA | 22 | nscaf1681 | 1661872–1673460 | − | Peptidase_M14 | 483 | sw11693 | 54,330.3 | 5.73 | yes |
BmMCP33 | BGIBMGA012807-TA | 16 | nscaf3058 | 6657227–6684446 | − | Peptidase_M14 | 996 | sw17444 | 11,1592 | 5.73 | no |
BmMCP34 | BGIBMGA012806-TA | 16 | nscaf3058 | 6684947–6690407 | − | Peptidase_M14 | 294 | – | 33,318.1 | 5.55 | yes |
BmSCP1 | BGIBMGA012452-TA | 9 | nscaf3045 | 2246700–2252046 | − | Peptidase_S28 | 352 | sw12542 | 40,622 | 4.69 | yes |
BmSCP2 | BGIBMGA003579-TA | 5 | nscaf2674 | 1284051–1285310 | − | Peptidase_S28 | 419 | sw13803 | 48,709.9 | 4.96 | no |
BmSCP3 | BGIBMGA008167-TA | 24 | nscaf2891 | 256973–274367 | + | Peptidase_S28 | 282 | sw14786 | 31,433.3 | 4.83 | no |
BmSCP4 | BGIBMGA000549-TA | 1 | nscaf1690 | 3748863–3757879 | − | Peptidase_S28 | 439 | sw20204 | 49,930.5 | 6.08 | yes |
BmSCP5 | BGIBMGA013534-TA | 5 | nscaf3075 | 927568–931683 | + | Peptidase_S28 | 383 | sw14860 | 42,863.6 | 6 | no |
BmSCP6 | BGIBMGA003110-TA | 4 | nscaf2589 | 2567114–2581357 | + | Peptidase_S10 | 374 | sw00555 | 43,079.3 | 6.05 | no |
BmSCP7 | BGIBMGA012773-TA | 16 | nscaf3058 | 8186538–8187953 | − | Peptidase_S10 | 471 | sw04192 | 53,120.8 | 5.56 | yes |
BmSCP8 | BGIBMGA003111-TA | 4 | nscaf2589 | 2593763–2602101 | + | Peptidase_S10 | 402 | sw17614 | 45,191.6 | 5.11 | no |
BmSCP9 | BGIBMGA003109-TA | 4 | nscaf2589 | 2546587–2560291 | + | Peptidase_S10 | 285 | – | 32,834.9 | 5.7 | no |
BmSCP10 | BGIBMGA013085-TA | 16 | nscaf3058 | 8193345–8194772 | + | Peptidase_S10 | 475 | sw14878 | 54,378 | 8.46 | yes |
BmSCP11 | BGIBMGA003112-TA | 4 | nscaf2589 | 2615158–2633253 | + | Peptidase_S10 | 1051 | sw01972 | 11,9508 | 5.66 | no |
BmSCP12 | BGIBMGA010348-TA | 12 | nscaf2990 | 809983–812392 | + | Peptidase_S10 | 403 | sw06212 | 46,108.2 | 4.99 | no |
BmSCP13 | BGIBMGA006502-TA | 6 | nscaf2853 | 4266715–4273371 | + | Peptidase_S10 | 376 | sw15928 | 42,942.2 | 8.8 | no |
BmSCP14 | BGIBMGA010349-TA | 12 | nscaf2990 | 814696–818250 | + | Peptidase_S10 | 365 | sw06213 | 40,585.3 | 4.95 | no |
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Ye, J.; Li, Y.; Liu, H.-W.; Li, J.; Dong, Z.; Xia, Q.; Zhao, P. Genome-Wide Identification and Characterization of Carboxypeptidase Genes in Silkworm (Bombyx mori). Int. J. Mol. Sci. 2016, 17, 1203. https://doi.org/10.3390/ijms17081203
Ye J, Li Y, Liu H-W, Li J, Dong Z, Xia Q, Zhao P. Genome-Wide Identification and Characterization of Carboxypeptidase Genes in Silkworm (Bombyx mori). International Journal of Molecular Sciences. 2016; 17(8):1203. https://doi.org/10.3390/ijms17081203
Chicago/Turabian StyleYe, Junhong, Yi Li, Hua-Wei Liu, Jifu Li, Zhaoming Dong, Qingyou Xia, and Ping Zhao. 2016. "Genome-Wide Identification and Characterization of Carboxypeptidase Genes in Silkworm (Bombyx mori)" International Journal of Molecular Sciences 17, no. 8: 1203. https://doi.org/10.3390/ijms17081203