Genome-Wide Identification and Analysis of Lipases in Fig Wasps (Chalcidoidea, Hymenoptera)
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Manual Annotation of the Lipase Gene Family
2.2. Phylogenetic Analysis
2.3. Gene Family Expansions and Contractions
2.4. Gene Structure Analysis
2.5. Identification of Catalytic Triads in Lipases
2.6. β9 Loop and Lid Motifs
2.7. Prediction of Signal Peptide and Subcellular Locations
2.8. Gene Expression Pattern Predicted by Codon Adaptation Index Analysis
2.9. Protein Structure
2.10. Gene Function Prediction
3. Results
3.1. Identification of Lipases in Fig Wasps
3.2. Gene Family Expansion and Contraction
3.3. Tandem Duplications of Lipase
3.4. Phylogenetic Analysis
3.5. Sequence Characterization
3.5.1. Incomplete Catalytic Triads in Predicted Lipases
3.5.2. Identification of β9 Loop and Lids of Lipases
3.5.3. Secretion Signals
3.6. Structure Analysis
3.6.1. Exon/Intron Arrangements
3.6.2. Motifs
3.6.3. Tertiary Structures
3.7. Expression Profiles and Function Prediction
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Abbreviation | Neutral | Acid | Lipase2 | Lipase3 | GDSL | HSL | Total Number | |
---|---|---|---|---|---|---|---|---|---|
Non-pollinating fig wasp | Apocrypta bakeri | Abak | 29 | 15 | 0 | 2 | 2 | 1 | 49 |
Philotrypesis tridentata | Ptri | 32 | 30 | 0 | 1 | 1 | 1 | 65 | |
Sycobia sp.2 | Sbsp | 29 | 17 | 0 | 2 | 1 | 1 | 50 | |
Sycophila sp.2 | Spsp | 26 | 30 | 0 | 1 | 2 | 1 | 60 | |
Sycophaga agraensis | Sagr | 26 | 12 | 0 | 1 | 0 | 1 | 40 | |
Pollinating fig wasp | Dolichoris vasculosae | Dvas | 18 | 12 | 0 | 1 | 1 | 1 | 33 |
Wiebesia pumilae | Wpum | 18 | 10 | 0 | 1 | 1 | 1 | 31 | |
Ceratosolen solmsi | Csol | 17 | 11 | 0 | 1 | 1 | 1 | 31 | |
Ceratosolen fusciceps | Cfus | 15 | 11 | 0 | 1 | 1 | 1 | 29 | |
Eupristina koningsbergeri | Ekon | 15 | 11 | 0 | 2 | 1 | 2 | 31 | |
Platyscapa corneri | Pcor | 19 | 11 | 0 | 1 | 1 | 1 | 33 | |
Kradibia gibbosae | Kgib | 15 | 12 | 0 | 1 | 0 | 1 | 29 | |
Total number | 259 | 182 | 0 | 15 | 12 | 13 | 481 |
Neutral | Acid | ||||||
---|---|---|---|---|---|---|---|
Clade | Number of Genes | Clade | Number of Genes | Clade | Number of Genes | Clade | Number of Genes |
I | 12 | XI | 14 | I | 13 | XI | 14 |
II | 11 | XII | 16 | II | 12 | XII | 16 |
III | 12 | XIII | 12 | III | 12 | ||
IV | 12 | XIV | 12 | IV | 11 | ||
V | 9 | XV | 12 | V | 17 | ||
VI | 16 | XVI | 12 | VI | 18 | ||
VII | 12 | XVII | 22 | VII | 12 | ||
VIII | 12 | XVIII | 23 | VIII | 21 | ||
IX | 13 | XIX | 11 | IX | 13 | ||
X | 14 | X | 23 |
Species | Gene Name | β9 Loop | Length | Lid | Length | Number |
---|---|---|---|---|---|---|
Apocrypta bakeri | Abak_neutral_11 | HTDGSADFADGFGLLKPIGH | 20 | CKDVKNSVVVSHLNEDSLDINIAC | 24 | 11 |
Abak_neutral_12 | HTDCSPFISGGLGISQPVAH | 20 | CNEGVFNSITLEKGSFFRGIKRFLGC | 26 | ||
Abak_neutral_13 | HTDGKSIFFLGLPGYGMSQPCGH | 23 | CTDLSETTPSLPLTLIREGLEEASRVLVAC | 30 | ||
Abak_neutral_15 | HTDGGVLGFPIPLGH | 15 | CELENVFAMGVGKLINRFVTC | 21 | ||
Abak_neutral_16 | HTNGRVLSRLGLGLPNPVGH | 20 | CILSNKASLWQYLPIPISLISETIC | 25 | ||
Abak_neutral_17 | HTNGRILRKLGLGLPYPLGH | 20 | CLLTKSSIWNYLPLPIESTYRSMVCFYLFIYFVLFVEIQKTIC | 43 | ||
Abak_neutral_18 | HSNGEQLILGGLGSWQPMGD | 20 | CSNLFVGAVSDIIWSSPVEGRSLC | 24 | ||
Abak_neutral_23 | HTDGAQERNRAFGLYDAIGH | 20 | CLSRRIDSQYTYEYAVKLFGHTINTRAC | 28 | ||
Abak_neutral_24 | HTDGARRRNSAFGILEPIGH | 20 | CQSGRRSMPTWGSVINFAFEAYQHIESNGPC | 31 | ||
Abak_neutral_25 | HTNGQYLKKLGLGLPEPIGH | 20 | CALTSFSIPILSIPRETVNKAIC | 23 | ||
Abak_neutral_26 | HTNARNILLLGLGLPEQLGN | 20 | CANIDAKFWDFLLLPINIVKSAIC | 24 | ||
Philotrypesis tridentata | Ptri_neutral_10 | HTDGSVDFADGFGLLKPIGH | 20 | CNDVKNSVVVSHLNEDSLDINIAC | 24 | 15 |
Ptri_neutral_11 | HTDGKSIFFLGLPGYGMSQPCGH | 23 | CTDLSETTPSLPLTLIREGLEEASRVLVAC | 30 | ||
Ptri_neutral_12 | HTDCSPFISGGLGISQPVAH | 20 | CNEGVFNSITLEKGSFFRGIKRFLGC | 26 | ||
Ptri_neutral_13 | HTDGGVLGFPIPLGH | 15 | CNIANVFAMGVNRIINRFITC | 21 | ||
Ptri_neutral_17 | HSNGDHFLNGGLGLIEPIGH | 20 | CTEVNIPVIDVKARTEPVYKAIC | 23 | ||
Ptri_neutral_18 | HANADKFLKGGLGLVEPIGH | 20 | CTEIKVPLPLVPLRIKTDVAFRAIC | 25 | ||
Ptri_neutral_19 | HTDTDPLQKGGLGLADPIGH | 20 | CSDIQLPYYLPFPIKWLEKRIAKATC | 26 | ||
Ptri_neutral_21 | HTNGGILKKLRLGLPNPSGD | 20 | CILMKSSLWEYLPLPIEKIESTIC | 24 | ||
Ptri_neutral_22 | HTDGAQKMNSAFGIFEPIGH | 20 | CGRTKRTPAIGDVIKKIFKVADHVLNHGSC | 30 | ||
Ptri_neutral_24 | HSNGEQLILGGLGSWQPMGD | 20 | CSNLFVGAVSDIIWSSPVEGRSLC | 24 | ||
Ptri_neutral_26 | HTDADALYKGGVSLFEPIGH | 20 | CSKIQLPDDLPHPIKLLKKLIERAIC | 26 | ||
Ptri_neutral_27 | HTNVKMYLNLGIGLPDRLGH | 20 | CKKINTAFWNFLLLPIHIVEWAIC | 24 | ||
Ptri_neutral_28 | HTNADHILRLGFGLPDRLGH | 20 | CEKINATFWNFLLLPIHIVQAAIC | 24 | ||
Ptri_neutral_29 | HTNAQSILLAGLGLPDRLGH | 20 | CEKIDVKFWDFLMLPVGVIKTAIC | 24 | ||
Ptri_neutral_30 | HTNAQNILLLGLGLPEQLGD | 20 | CAKINPKIWDFLLLPVDIVKSAIC | 24 | ||
Sycobia sp.2 | Sbsp_neutral_10 | HTDGSIDFTDGFGLLKPIGH | 20 | CRDVKNSVVVSHLNEDNLDIHIAC | 24 | 7 |
Sbsp_neutral_14 | HSNGEQLILGGLGSWQPMGD | 20 | CSNLFLGAVSDIIWSSAVEGRSLC | 24 | ||
Sbsp_neutral_15 | HTNGRLLRQLGLGLPFPIGH | 20 | CVVKKSSFWKYLPLPFRKIERTLC | 24 | ||
Sbsp_neutral_21 | HTNGRGLLKLGLGLPNPLGH | 20 | CNITRSFIERVLPLPFKTIKETIC | 24 | ||
Sbsp_neutral_22 | HTDGGVLGFPIPLGH | 15 | CNIDNILAMGLNKIINRFSES | 21 | ||
Sbsp_neutral_23 | HTDCSPFISGGLGISQPVAH | 20 | CNEGVLNSITLEKGSFFRGIKRFLGC | 26 | ||
Sbsp_neutral_24 | HTDGKSIFFLGLPGYGMSQPCGH | 23 | CTDLSETTPSLPLTLIREGLEEASRVLVAC | 30 | ||
Sycophila sp.2 | Spsp_neutral_7 | HTDGSADFADGFGLLKPIGH | 20 | CNDVKNSVVVSHLNEDSLDIHIAC | 24 | 11 |
Spsp_neutral_11 | HTNGRVLSKLGLGLPNPVGR | 20 | CIESESSFWKYLPMPVKKISETIC | 24 | ||
Spsp_neutral_14 | HSNGEQLILGGLGSWQPMGD | 20 | CSNLFVGAVSDIIWSSPVEGRSLC | 24 | ||
Spsp_neutral_16 | HTDGGVLGFPVPLGH | 15 | CDLGNVIAMGIGSLLNRYVTC | 21 | ||
Spsp_neutral_18 | HTDCSPFISGGLGISQPVAH | 20 | CNEGVFNSITLEKGSFFRGIKRFLGC | 26 | ||
Spsp_neutral_19 | HTDGKSIFFLGLPGYGMSQPCGH | 23 | CTDLSETTPSLPLTLIREGLEEASRVLVAC | 30 | ||
Spsp_neutral_20 | HTNARSIMLLGFGLPEDLGH | 20 | CDDIDASSWGSLAYPKSALTSAIC | 24 | ||
Spsp_neutral_21 | HTNAKHLFFLGLGLPNQLGY | 20 | CLDIDLSLWGFLMLPKDIILESIC | 24 | ||
Spsp_neutral_22 | HTNGRIWTDLGLGLPQSIGH | 20 | CESTDFKIPVLSIPKEAIAKMIC | 23 | ||
Spsp_neutral_24 | HTDGARTKNGAFGLIKPLGH | 20 | CESTNNSRRYLNYLSLFQHALGCTNC | 26 | ||
Spsp_neutral_25 | HTNSEPEKRMKDNLGTYDPLGH | 22 | CDLNKDARSLTYLKEIVETFLADSLRFITRTILKIDATNIILKYLNNIIPGSEERFDLIC | 60 | ||
Sycophaga agraensis | Sagr_neutral_9 | HTDGSIDFADGFGLLKPIGH | 20 | CNDVKNSVVVSHLNEDSLDIHIAC | 24 | 9 |
Sagr_neutral_10 | HTDGGVLGFPIPLGH | 15 | CNIENVLAMGFSKIINRYITC | 21 | ||
Sagr_neutral_12 | HTNARILAKLGLGLPNPIGH | 20 | CTLNVPLWKFLPIPLRKISEMIC | 23 | ||
Sagr_neutral_13 | HSNGEQLILGGLGSWQPMGD | 20 | CSNLFLGAVSDIIWSSPVEGRSLC | 24 | ||
Sagr_neutral_15 | HTDGKSIFFLGYGMSQPCGH | 20 | CTDLSETTPSLPLTLIREGLEEASRVLVAC | 30 | ||
Sagr_neutral_16 | HTDCSPFISGGLGISQPVAH | 20 | CNEGVFNSITLEKGSFFRGIKRFLGC | 26 | ||
Sagr_neutral_17 | HTNGRHLLQIGLGLPESIGH | 20 | CQLKNSLYIPGINLPREAIHKAVC | 24 | ||
Sagr_neutral_18 | HTNANNLLLLGLGLSEQLGN | 20 | CERIDASIWSFLLLPVNIIKEAIC | 24 | ||
Sagr_neutral_19 | NTNIQNSNELKSLGH | 15 | CDDSNFILPQGMGLAKLIEKASC | 23 | ||
Dolichoris vasculosae | Dvas_neutral_7 | HSDGSIDFADGFGLLKPIGH | 20 | CNDVKNSVVVSHLNEDSLDIHIAC | 24 | 7 |
Dvas_neutral_11 | HTDGGVLGFPIPLGH | 15 | CNLENVLAMGISKIINRYITC | 21 | ||
Dvas_neutral_12 | HSNGEQLILGGLGSWQPMGH | 20 | CSNLFVGAVSDIIWASPVEGRSLC | 24 | ||
Dvas_neutral_13 | HTDCSPFISGGLGISQPVAH | 20 | CNEGVFNSITLEKGSLFRGIKRFLGC | 26 | ||
Dvas_neutral_14 | HTDGKSIFFLGLPGYGMSQPCGH | 23 | CTDLSETTPSLPLTLIREGLEEASRVLVAC | 30 | ||
Dvas_neutral_16 | HTNARNILLLGLGLPDQLGK | 20 | CTNINTSFWNFLLLPANIIKEAIC | 24 | ||
Dvas_neutral_18 | HTDGAISENEAFGLFDSIGH | 20 | CGSFLSKRSVPSLLKLLLHAVKNGVC | 26 | ||
Wiebesia pumilae | Wpum_neutral_6 | HSDGSIDFADGFGLLKPIGH | 20 | CNDVKNSVVVSHLNEDSLDIHIAC | 24 | 6 |
Wpum_neutral_10 | HTDGGVLGFPIPLGH | 15 | CNLENVLAMGISKIINRYITC | 21 | ||
Wpum_neutral_11 | HTNARNILLLGLGLPDQLGQ | 20 | CTNINPSFWSFLLLPAKIIKEIIC | 24 | ||
Wpum_neutral_12 | HTDCSPFISGGLGINQPVAH | 20 | CNEGVFNSITLEKGSLFRGIKRFLGC | 26 | ||
Wpum_neutral_13 | HTDGKSIFFLGYGMSQPCGH | 20 | CTDLSETTPSLPLTLIREGLEEASRVLVAC | 30 | ||
Wpum_neutral_14 | HSNGEQLILGGLGSWQPMGH | 20 | CSNLFVGAVSDIIWSNPVEGRSLC | 24 | ||
Ceratosolen solmsi | Csol_neutral_7 | HSDGSIDFADGFGLLKPIGH | 20 | CNDVKNSVVVSHLNEDSLDIHIAC | 24 | |
Csol_neutral_9 | HSNGEQLILGGLGSWQPMGD | 20 | CSNLFVGAVSDIIWSSPVEGRSLC | 24 | 6 | |
Csol_neutral_11 | HTDGKSIFFLGLPGYGMSQPCGH | 23 | CTDLSETTPSLPLTLIREGLEEASRVLVAC | 30 | ||
Csol_neutral_12 | HTDCSPFISGGLGISQPVAH | 20 | CNEGVFNSITLEKGSLFRGIKRFLGC | 26 | ||
Csol_neutral_13 | HTDGGVLGFPIPLGH | 15 | CNLENRESTICSSHVSVTC | 19 | ||
Csol_neutral_15 | HTDGALSQNEAFGLYDPIGH | 20 | CGFLASQKSVPSLLKLLVHAMENGIC | 26 | ||
Ceratosolen fusciceps | Cfus_neutral_6 | HTDGSVDFADGFGLLKPIGH | 20 | CKDVKNSVVVSHLNEDSLDIEIAC | 24 | 5 |
Cfus_neutral_8 | HTDCSPFISGGLGINQPVAH | 20 | CNEGVFNSITLEKGSLFRGIKRFLGC | 26 | ||
Cfus_neutral_9 | HTDGKSIFFLGLPGYGMSQPCGH | 23 | CTDLSETTPSLPLTLIREGLEEASRVLVAC | 30 | ||
Cfus_neutral_12 | HTDGGVLGFPIPLGH | 15 | CNLENVLAMGIGKIINRYITC | 21 | ||
Cfus_neutral_13 | HTNGEQLILGGLGSWQPMGD | 20 | CSNLFVGAVSDIIWSSPVEGRSLC | 24 | ||
Eupristina koningsbergeri | Ekon_neutral_5 | HSDGSVDFSDGFGLLKPMGH | 20 | CNDVKNSVVVSHLNENSLDIHIAC | 24 | 5 |
Ekon_neutral_9 | HSNGEQLILGGLGSWQPMGH | 20 | CSNLFVGAVSDIIWSNPVEGRSLC | 24 | ||
Ekon_neutral_10 | HTDGGVLGFPIPLGH | 15 | CDFENVLSMGISKIINRYITC | 21 | ||
Ekon_neutral_11 | HTDGKSIFFLGLPGYGMSQPCGH | 23 | CTDLSETTPSLPLTLIREGLEEASRVLVAC | 30 | ||
Ekon_neutral_12 | HTDCSPFISGGLGISQAVAH | 20 | CNEGVFNSITLEKGSFFRGIKRFLGC | 26 | ||
Platyscapa corneri | Pcor_neutral_5 | HSDGSIDFADGFGLLKPIGH | 20 | CNDVKNSVVVSHLNEDSLDIQIAC | 24 | 7 |
Pcor_neutral_10 | HTDCSPFISGGLGISQPVAH | 20 | CNEGVFNSITLEKGSLFRGIKRFLGC | 26 | ||
Pcor_neutral_11 | HTDGKSIFFLGLPGYGMSQPCGH | 23 | CTDLSETTPSLPLTLIREGLEEASRVLVAC | 30 | ||
Pcor_neutral_12 | HSNGEQLILGGLGSWQPMGH | 20 | CSNLFVGAVSDIIWSSPVEGRSLC | 24 | ||
Pcor_neutral_13 | HTNARNILLLGLGLPEKLGM | 20 | CKNIDVSFWNFLLLPAKIIKEIIC | 24 | ||
Pcor_neutral_14 | HTDGGVLGFPIPLGH | 15 | CNFENVLAMGISKIINRYITC | 21 | ||
Pcor_neutral_18 | HTDGAISEDEAFGLLEPIGH | 20 | CSLLRRRKRSAESLLKLLVHAIENGAC | 27 | ||
Kradibia gibbosae | Kgib_neutral_8 | HSDGSVDFADGFGLLKPIGH | 20 | CNDVKNSVVVSHLNEDSLDIHIAC | 24 | 4 |
Kgib_neutral_9 | HTDGKSIFFLGLPGYGMSQPCGH | 23 | CTDFGEATPLTLIREGLEEASRVLVAC | 27 | ||
Kgib_neutral_10 | HTDCSPFISGGLGISQPVAH | 20 | CNEGVFNSITLEKGSLFRGIKRFLGC | 26 | ||
Kgib_neutral_13 | HSNGEQLILGGLGSWQQMGD | 20 | CSNLFLGAVSDIIWSSSVEGRSLC | 24 |
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Wei, X.; Li, J.; Wang, T.; Xiao, J.; Huang, D. Genome-Wide Identification and Analysis of Lipases in Fig Wasps (Chalcidoidea, Hymenoptera). Insects 2022, 13, 407. https://doi.org/10.3390/insects13050407
Wei X, Li J, Wang T, Xiao J, Huang D. Genome-Wide Identification and Analysis of Lipases in Fig Wasps (Chalcidoidea, Hymenoptera). Insects. 2022; 13(5):407. https://doi.org/10.3390/insects13050407
Chicago/Turabian StyleWei, Xianqin, Jiaxing Li, Tao Wang, Jinhua Xiao, and Dawei Huang. 2022. "Genome-Wide Identification and Analysis of Lipases in Fig Wasps (Chalcidoidea, Hymenoptera)" Insects 13, no. 5: 407. https://doi.org/10.3390/insects13050407