New Light on Historical Specimens Reveals a New Species of Ladybird (Coleoptera: Coccinellidae): Morphological, Museomic, and Phylogenetic Analyses
Abstract
:Simple Summary
Abstract
1. Introduction
2. Material and Methods
2.1. Specimens and Taxonomy
2.2. DNA Extraction
2.3. Library Preparation and DNA Sequencing
2.4. Genome Assembly, Annotation, and Reconstruction
2.5. Phylogenetic Analysis
2.6. Estimation of Evolutionary Divergence between Sequences
3. Results
Taxonomy
4. Discussion
4.1. Morphological Considerations and Geographical Distribution
4.2. Genome Organization
4.3. Phylogenetic Considerations
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Data Availability Statement
New Species Registration
References
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Family Subfamily | Species | Author | Mitogenome | Reference | ||
---|---|---|---|---|---|---|
Length (bp) | Partial—Complete + | GenBank Code | ||||
Corylophidae | ||||||
Corylophinae | Gloeosoma sp. | 12,474 | – | JX412843 | Unpublished | |
Bothrideridae | ||||||
Bothriderinae | Dastarcus helophoroides | (Fairmaire) | 15,878 | + | NC_024271 | [61] |
Coccinellidae | ||||||
Coccinellinae | Aiolocaria hexaspilota | (Hope) | 17,549 | + | MK583344 | [62] |
Anatis ocellata | (Linnaeus) | 17,092 | + | NC_036272 | Unpublished | |
Anisosticta novemdecimpunctata | (Linnaeus) | 15,289 | – | KT876880 | [63] | |
Calvia champinorum | Booth | 17,575 | – | KX132085 | Unpublished | |
Calvia decemguttata | (Linnaeus) | 16,425 | – | KX087252 | Unpublished | |
Cheilomenes sexmaculata | Fabricius | 17,192 | – | KM244706 | [64] | |
Coccinella septempunctata | Linnaeus | 18,965 | + | JQ321839 | [42] | |
Coccinella transversoguttata | Faldermann | 15,806 | – | MG584726 | [65] | |
Coleomegilla maculata | De Geer | 17,516 | – | KJ778881 | Unpublished | |
Cycloneda munda | (Say) | 14,292 | – | KJ778882 | Unpublished | |
Cycloneda sanguinea | (Linnaeus) | 15,137 | + * | KU877170 | [66] | |
Eriopis connexa | (Germar) | 17,652 | + | MG253268 | Unpublished | |
Eriopis patagonia | Salazar | 16,194 | – | MN509443 | This study | |
Halyzia sedecimguttata | (Linnaeus) | 15,766 | – | KT780652 | Unpublished | |
Harmonia axyridis | (Pallas) | 16,382 | – | KR108208 | [67] | |
Harmonia quadripunctata | (Pontoppidan) | 18,051 | + * | KX087296 | Unpublished | |
Hippodamia convergens | Guérin-Méneville | 18,419 | + | KX755331 | [66] | |
Hippodamia variegata | (Goeze) | 17,823 | + | MK334129 | [68] | |
Coelophora saucia | (Mulsant) | 14,106 | – | MK574678 | [69] | |
Propylea japonica | (Thunberg) | 15,027 | – | KM244660 | [64] | |
Propylea sp. | 15,915 | – | KX132084 | Unpublished | ||
Henosepilachna pusillanima | (Mulsant) | 16,216 | + | NC_023469 | [70] | |
Henosepilacna vigintioctopunctata | (Fabricius) | 17,057 | + | NC_041172 | Unpublished | |
Epilachna admirabilis | Crotch | 17,445 | + * | MN053053 | [71] | |
Subcoccinella vigintiquatuorpunctata | (Linnaeus) | 14,645 | – | KT780695 | Unpublished | |
Coccidula rufa | Herbst | 10,589 | – | JX412767 | Unpublished | |
Cryptolaemus montrouzieri | Mulsant | 17,010 | + | KT874575 | [72] | |
Microweiseinae | Coccidophilus cariba | Gordon | 15,343 | + | MN447521 | [73] |
Gene | Location | Length (bp) | Codon | Anticodon | Strand Reverse – Forward + | ||
---|---|---|---|---|---|---|---|
Start | Stop | Sequence | Location | ||||
tRNA-Ile | ? | ? | ? | ||||
tRNA-Gln | 1–70 | 70 | TTG | 37–39 | – | ||
tRNA-Met | 68–136 | 69 | CAT | 98–100 | + | ||
NAD2 | 133–1143 | 1011 | ATA | TAA | + | ||
tRNA-Trp | 1141–1204 | 64 | TCA | 1172–1174 | + | ||
tRNA-Cys | 1197–1258 | 62 | GCA | 1227–1229 | – | ||
tRNA-Tyr | 1261–1323 | 63 | GTA | 1291–1293 | – | ||
COX1 | <1326–2864 | >1539 | AAT | TAA | + | ||
tRNA-Leu2 | 2862–2921 | 60 | TAA | 2889–2891 | + | ||
COX2 | 2923–3601 | 679 | ATA | TAA1 | + | ||
tRNA-Lys | 3602–3670 | 69 | CTT | 3632–3634 | + | ||
tRNA-Asp | 3671–3734 | 64 | GTC | 3702–3704 | + | ||
ATP8 | 3735–3896 | 162 | ATA | TAA | + | ||
ATP6 | 3890–4546 | 657 | ATG | TAA | + | ||
COX3 | 4549–5329 | 781 | ATG | TAA1 | + | ||
tRNA-Gly | 5330–5392 | 63 | TCC | 5360–5362 | + | ||
NAD3 | 5390–5746 | 357 | ATA | TAG | + | ||
tRNA-Ala | 5743–5807 | 65 | TGC | 5773–5775 | + | ||
tRNA-Arg | 5806–5869 | 64 | TCG | 5835–5837 | + | ||
tRNA-Asn | 5866–5930 | 65 | GTT | 5898–5900 | + | ||
tRNA-Ser1 | 5931–5986 | 56 | TCT | 5951–5953 | + | ||
tRNA-Glu | 5986–6049 | 64 | TTC | 6017–6019 | + | ||
tRNA-Phe | 6048–6111 | 64 | GAA | 6079–6081 | – | ||
NAD5 | 6111–7828 | 1718 | TAT | – | – | ||
tRNA-His | 7826–7889 | 64 | GTG | 7856–7858 | – | ||
NAD4 | 7889–9205 | 1317 | TAT | TTA | – | ||
NAD4L | 9205–9480 | 276 | TAT | TTA | – | ||
tRNA-Thr | 9482–9545 | 64 | TGT | 9512–9514 | + | ||
tRNA-Pro | 9546–9607 | 62 | TGG | 9573–9575 | – | ||
NAD6 | 9637–10,079 | 443 | ATA | – | + | ||
CYT B | 10,079–11,221 | 1143 | ATG | TAA | + | ||
tRNA-Ser2 | 11,220–11,283 | 64 | TGA | 11,247–11,249 | + | ||
NAD1 | 11,301–12,245 | 945 | TAT | CTA | – | ||
tRNA-Leu1 | 12,243–12,304 | 62 | TAG | 12,273–12,275 | – | ||
Large subunit rRNA | 12,305–13,580 | 1284 | – | ||||
tRNA-Val | 13,590–13,652 | 63 | TAC | 13,621–13,623 | – | ||
Small subunit rRNA | 13,651–14,426 | 776 | – | ||||
A + T rich region | 14,427– >16,194 | >1768 |
Feature | Proportion (%) | Skews | N° of Nucleotides (bp) | ||||||
---|---|---|---|---|---|---|---|---|---|
A | T | A+T | G | C | G+C | AT | GC | ||
Whole genome | 41.0 | 38.9 | 79.9 | 8.5 | 11.6 | 20.0 | 0.03 | −0.15 | 16,194 |
PCGs | 40.4 | 38.8 | 79.2 | 8.9 | 11.9 | 20.8 | 0.02 | −0.14 | 11,028 |
NAD2 | 37.6 | 46.2 | 83.8 | 6.9 | 9.3 | 16.2 | −0.10 | −0.15 | |
COX1 | 32.9 | 39.6 | 72.5 | 13.6 | 13.9 | 27.5 | −0.09 | −0.01 | |
COX2 | 33.7 | 40.2 | 73.9 | 11.8 | 14.3 | 26.1 | −0.09 | −0.1 | |
ATP8 | 46.9 | 43.8 | 90.7 | 3.1 | 6.2 | 9.3 | 0.03 | −0.33 | |
ATP6 | 34.4 | 43.4 | 77.8 | 8.2 | 14.0 | 22.2 | −0.12 | −0.26 | |
COX3 | 33.5 | 41.9 | 75.4 | 12.0 | 12.5 | 24.5 | −0.11 | −0.02 | |
NAD3 | 34.5 | 46.2 | 80.7 | 7.0 | 12.3 | 19.3 | −0.14 | −0.27 | |
NAD5 | 48.5 | 33.2 | 81.7 | 7.0 | 11.2 | 18.2 | 0.19 | −0.23 | |
NAD4 | 49.4 | 32.8 | 82.2 | 6.9 | 10.9 | 17.8 | 0.20 | −0.22 | |
NAD4L | 51.8 | 33.7 | 85.5 | 4.7 | 9.8 | 14.5 | 0.21 | −0.35 | |
NAD6 | 37.7 | 49.0 | 86.7 | 6.3 | 7.0 | 13.3 | −0.13 | −0.05 | |
CYT B | 33.6 | 42.9 | 76.5 | 10.5 | 13.0 | 23.5 | −0.12 | −0.11 | |
NAD1 | 49.8 | 29.9 | 79.7 | 7.6 | 12.6 | 20.2 | 0.25 | −0.25 | |
Large subunit rRNA | 44.2 | 39.1 | 83.3 | 6.0 | 10.7 | 16.7 | 0.06 | −0.28 | |
Small subunit rRNA | 43.9 | 37.1 | 81.0 | 6.4 | 12.5 | 18.9 | 0.08 | −0.32 | |
A+T rich region | 41.3 | 40.8 | 82.1 | 7.8 | 10.1 | 17.9 | 0.01 | −0.13 | |
tRNAs | 41.4 | 38.4 | 79.8 | 8.9 | 11.3 | 20.2 | 0.04 | −0.12 | 1341 |
rRNAs | 44.1 | 38.3 | 82.4 | 6.2 | 11.4 | 17.6 | 0.07 | −0.3 | 2060 |
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Salazar, K.; Nattier, R. New Light on Historical Specimens Reveals a New Species of Ladybird (Coleoptera: Coccinellidae): Morphological, Museomic, and Phylogenetic Analyses. Insects 2020, 11, 766. https://doi.org/10.3390/insects11110766
Salazar K, Nattier R. New Light on Historical Specimens Reveals a New Species of Ladybird (Coleoptera: Coccinellidae): Morphological, Museomic, and Phylogenetic Analyses. Insects. 2020; 11(11):766. https://doi.org/10.3390/insects11110766
Chicago/Turabian StyleSalazar, Karen, and Romain Nattier. 2020. "New Light on Historical Specimens Reveals a New Species of Ladybird (Coleoptera: Coccinellidae): Morphological, Museomic, and Phylogenetic Analyses" Insects 11, no. 11: 766. https://doi.org/10.3390/insects11110766
APA StyleSalazar, K., & Nattier, R. (2020). New Light on Historical Specimens Reveals a New Species of Ladybird (Coleoptera: Coccinellidae): Morphological, Museomic, and Phylogenetic Analyses. Insects, 11(11), 766. https://doi.org/10.3390/insects11110766