DNA Barcoding as A Tool for Taxonomic Identification of  Ladybird Beetles (Coleoptera: Coccinellidae) from Pakistan: A Review

Asif Hanif; Zia-U-Din; Abdul Manan; Fazal u Rehman; Irshad Ali

doi:10.31580/pjmls.v6i1.1970

Authors

Asif Hanif Center for Advanced Studies in Vaccinology and Biotechnology (CASVAB), UoB, Quetta, Pakistan Author
Zia-U-Din Center for Advanced Studies in Vaccinology and Biotechnology, (CASVAB), UoB, Quetta Author
Abdul Manan Center for Advanced Studies in Vaccinology and Biotechnology, (CASVAB), UoB, Quetta Author
Fazal u Rehman Department of Microbiology, University of Balochistan, Quetta, Pakistan Author
Irshad Ali Department of Chemistry, University of Balochistan, Quetta, Pakistan Author

DOI:

https://doi.org/10.31580/pjmls.v6i1.1970

Keywords:

COI gene, DNA Barcoding, Integrated Pest Management (IPM), Ladybird Beetles, Mitochondrial DNA, Predators

Abstract

Despite having a large number of species and being ecologically diversified, ladybird beetles (family Coccinellidae) have always been difficult for describing due to their poorly understood evolutionary relations. An alternative to morphological identification is molecular identification techniques like DNA barcoding. Barcoding may result in less expensive, quicker, and more precise identifications. In order to identify organisms, DNA barcoding uses a short sequence of DNA that has been adopted by the scientific community. As the "barcode" for animal life, the Folmer region of the mitochondrial cytochrome oxidase subunit 1 (COI) gene has long been recognized. COI is highly variable among animal species, providing good identification power, and it is flanked by conserved regions that make good primer sites. It is also short, only 658 bp, making it easy to sequence. The present study summarizes the current status of insect species' barcoding in Pakistan and identifies any blanks that need filling. This study reveals that very little of the known taxonomy and defined species are represented by barcoded data. In order to carry out the DNA barcoding of all known insect taxa from Pakistan, it is required to significantly speed up insect species discovery and documentation in a cooperative manner between traditional taxonomists and molecular biology researchers.

Author Biographies

Asif Hanif, Center for Advanced Studies in Vaccinology and Biotechnology (CASVAB), UoB, Quetta, Pakistan

Despite having a large number of species and being ecologically diversified, ladybird beetles (family Coccinellidae) have always been difficult for describing due to their poorly understood evolutionary relations. An alternative to morphological identification is molecular identification techniques like DNA barcoding. Barcoding may result in less expensive, quicker, and more precise identifications. In order to identify organisms, DNA barcoding uses a short sequence of DNA that has been adopted by the scientific community. As the "barcode" for animal life, the Folmer region of the mitochondrial cytochrome oxidase subunit 1 (COI) gene has long been recognized. COI is highly variable among animal species, providing good identification power, and it is flanked by conserved regions that make good primer sites. It is also short, only 658 bp, making it easy to sequence. The present study summarizes the current status of insect species' barcoding in Pakistan and identifies any blanks that need filling. This study reveals that very little of the known taxonomy and defined species are represented by barcoded data. In order to carry out the DNA barcoding of all known insect taxa from Pakistan, it is required to significantly speed up insect species discovery and documentation in a cooperative manner between traditional taxonomists and molecular biology researchers.
Zia-U-Din, Center for Advanced Studies in Vaccinology and Biotechnology, (CASVAB), UoB, Quetta

Despite having a large number of species and being ecologically diversified, ladybird beetles (family Coccinellidae) have always been difficult for describing due to their poorly understood evolutionary relations. An alternative to morphological identification is molecular identification techniques like DNA barcoding. Barcoding may result in less expensive, quicker, and more precise identifications. In order to identify organisms, DNA barcoding uses a short sequence of DNA that has been adopted by the scientific community. As the "barcode" for animal life, the Folmer region of the mitochondrial cytochrome oxidase subunit 1 (COI) gene has long been recognized. COI is highly variable among animal species, providing good identification power, and it is flanked by conserved regions that make good primer sites. It is also short, only 658 bp, making it easy to sequence. The present study summarizes the current status of insect species' barcoding in Pakistan and identifies any blanks that need filling. This study reveals that very little of the known taxonomy and defined species are represented by barcoded data. In order to carry out the DNA barcoding of all known insect taxa from Pakistan, it is required to significantly speed up insect species discovery and documentation in a cooperative manner between traditional taxonomists and molecular biology researchers.
Abdul Manan, Center for Advanced Studies in Vaccinology and Biotechnology, (CASVAB), UoB, Quetta

Despite having a large number of species and being ecologically diversified, ladybird beetles (family Coccinellidae) have always been difficult for describing due to their poorly understood evolutionary relations. An alternative to morphological identification is molecular identification techniques like DNA barcoding. Barcoding may result in less expensive, quicker, and more precise identifications. In order to identify organisms, DNA barcoding uses a short sequence of DNA that has been adopted by the scientific community. As the "barcode" for animal life, the Folmer region of the mitochondrial cytochrome oxidase subunit 1 (COI) gene has long been recognized. COI is highly variable among animal species, providing good identification power, and it is flanked by conserved regions that make good primer sites. It is also short, only 658 bp, making it easy to sequence. The present study summarizes the current status of insect species' barcoding in Pakistan and identifies any blanks that need filling. This study reveals that very little of the known taxonomy and defined species are represented by barcoded data. In order to carry out the DNA barcoding of all known insect taxa from Pakistan, it is required to significantly speed up insect species discovery and documentation in a cooperative manner between traditional taxonomists and molecular biology researchers.
Fazal u Rehman, Department of Microbiology, University of Balochistan, Quetta, Pakistan

Despite having a large number of species and being ecologically diversified, ladybird beetles (family Coccinellidae) have always been difficult for describing due to their poorly understood evolutionary relations. An alternative to morphological identification is molecular identification techniques like DNA barcoding. Barcoding may result in less expensive, quicker, and more precise identifications. In order to identify organisms, DNA barcoding uses a short sequence of DNA that has been adopted by the scientific community. As the "barcode" for animal life, the Folmer region of the mitochondrial cytochrome oxidase subunit 1 (COI) gene has long been recognized. COI is highly variable among animal species, providing good identification power, and it is flanked by conserved regions that make good primer sites. It is also short, only 658 bp, making it easy to sequence. The present study summarizes the current status of insect species' barcoding in Pakistan and identifies any blanks that need filling. This study reveals that very little of the known taxonomy and defined species are represented by barcoded data. In order to carry out the DNA barcoding of all known insect taxa from Pakistan, it is required to significantly speed up insect species discovery and documentation in a cooperative manner between traditional taxonomists and molecular biology researchers.
Irshad Ali, Department of Chemistry, University of Balochistan, Quetta, Pakistan

Despite having a large number of species and being ecologically diversified, ladybird beetles (family Coccinellidae) have always been difficult for describing due to their poorly understood evolutionary relations. An alternative to morphological identification is molecular identification techniques like DNA barcoding. Barcoding may result in less expensive, quicker, and more precise identifications. In order to identify organisms, DNA barcoding uses a short sequence of DNA that has been adopted by the scientific community. As the "barcode" for animal life, the Folmer region of the mitochondrial cytochrome oxidase subunit 1 (COI) gene has long been recognized. COI is highly variable among animal species, providing good identification power, and it is flanked by conserved regions that make good primer sites. It is also short, only 658 bp, making it easy to sequence. The present study summarizes the current status of insect species' barcoding in Pakistan and identifies any blanks that need filling. This study reveals that very little of the known taxonomy and defined species are represented by barcoded data. In order to carry out the DNA barcoding of all known insect taxa from Pakistan, it is required to significantly speed up insect species discovery and documentation in a cooperative manner between traditional taxonomists and molecular biology researchers.

References

Siddall ME, Fontanella FM, Watson SC, Kvist S, Erséus C. Barcoding Bamboozled by Bacteria: Convergence to Metazoan Mitochondrial Primer Targets by Marine Microbes. Syst Biol. 2009;58(4):445–51.

Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R. Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philos Trans R Soc B Biol Sci. 2005;360(1462):1805–11.

Hebert PDN, Ratnasingham S, de Waard JR. Barcoding animal life: cytochrome c oxidase subunit 1 divergence among closely related species. Proc R Soc London Ser B Biol Sci. 2003;270(suppl_1).

Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 2007;23(4):167–72.

Bergsten J, Bilton DT, Fujisawa T, Elliott M, Monaghan MT, Balke M. The Effect of Geographical Scale of Sampling on DNA Barcoding. Syst Biol. 2012;61(5):851–69.

Lambert DM, Baker A, Huynen L, Haddrath O, Hebert PDN, Millar CD. Is a Large-Scale DNA-Based Inventory of Ancient Life Possible? J Hered. 2005;96(3):279–84.

Ball SL, Armstrong KF. DNA barcodes for insect pest identification: a test case with tussock moths (Lepidoptera: Lymantriidae). Can J For Res. 2006;36(2):337–50.

Pires AC, Marinoni L. DNA barcoding and traditional taxonomy unified through Integrative Taxonomy: a view that challenges the debate questioning both methodologies. Biota Neotrop. 2010;10(2):339–46.

Jalali SK, Ojha R, Venkatesan T. DNA Barcoding for Identification of Agriculturally Important Insects. In: New Horizons in Insect Science: Towards Sustainable Pest Management. New Delhi: Springer India; 2015:13–23.

Lentz DL, Hockaday B. Tikal timbers and temples: ancient Maya agroforestry and the end of time. J Archaeol Sci. 2009;36(7):1342–53.

Goetz DW. Seasonal inhalant insect allergy: Harmonia axyridis ladybug. Curr Opin Allergy Clin Immunol. 2009;9(4):329–33.

Michaud JP. Numerical Response of Olla v-nigrum (Coleoptera: Coccinellidae) to Infestations of Asian Citrus Psyllid, (Hemiptera: Psyllidae) in Florida. Florida Entomol. 2001;84(4):608.

Mäser P, Thomine S, Schroeder JI, Ward JM, Hirschi K, Sze H. Phylogenetic Relationships within Cation Transporter Families of Arabidopsis. Plant Physiol. 2001;126(4):1646–67.

Yang Z, Rannala B. Molecular phylogenetics: principles and practice. Nat Rev Genet. 2012;13(5):303–14.

Hughes LC, Ortí G, Huang Y, Sun Y, Baldwin CC, Thompson AW. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proc Natl Acad Sci. 2018;115(24):6249–54.

Hopkins GW, Freckleton RP. Declines in the numbers of amateur and professional taxonomists: implications for conservation. Anim Conserv. 2002;5(3):245–9.

Rubinoff D. Essays: Utility of Mitochondrial DNA Barcodes in Species Conservation. Conserv Biol. 2006;20(4):1026–33.

Packer L, Gibbs J, Sheffield C, Hanner R. DNA barcoding and the mediocrity of morphology. Mol Ecol Resour. 2009;9:42–50.

Ball SL, Hebert PDN, Burian SK, Webb JM. Biological identifications of mayflies (Ephemeroptera) using DNA barcodes. J North Am Benthol Soc. 2005;24(3):508–24.

Meyer M, Briggs AW, Maricic T, Höber B, Höffner B, Krause J, et al. From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Res. 2008;36(1):e5–e5.

Blaxter M, Elsworth B, Daub J. DNA taxonomy of a neglected animal phylum: an unexpected diversity of tardigrades. Proc R Soc London Ser B Biol Sci. 2004;271(suppl_4).

Derycke S, Remerie T, Vierstraete A, Backeljau T, Vanfleteren J, Vincx M. Mitochondrial DNA variation and cryptic speciation within the free-living marine nematode Pellioditis marina. Mar Ecol Prog Ser. 2005;300:91–103.

Leasi F, Todaro MA. Meiofaunal cryptic species revealed by confocal microscopy: the case of Xenotrichula intermedia (Gastrotricha). Mar Biol. 2009;156(6):1335–46.

. MI. Distribution, Hosts, Ecology and Biotic Potentials of Coccinellids of Pakistan. Pakistan J Biol Sci. 2001;4(10):1259–63.

Ahmad R. A new species ofPseudoscymnus Chapin [Col., Coccinellidae] predaceous on Scale Insects in West Pakistan. Entomophaga. 1968;13(4):377–9.

Ahmad R. A new tribe of the family Coccinellidae (Coleoptera). Bull Entomol Res. 1973;62(3):449–52.

Chapin EA, Ahmad R. A new species of coccinellid feeding on scale insects in West Pakistan. Entomophaga. 1966;11(2):213–5.

Hussain M, Malik MF, Siddique S, Umar M, Zainab T, Zafar F. Diversity and Distribution of Coccinellid Beetles in Irrigated and Rainfed Fields of Gujrat, Punjab, Pakistan. Punjab Univ J Zool. 2018;33(1).

Rahat Ullah. Morphological characteristics of ladybird beetles collected from District Dir Lower, Pakistan. AFRICAN J Biotechnol. 2012;11(37).

Saeed K, Khan Khattak MN, Naz F. Genus Coccinella (Coccinellidae: Coleoptera) from District Buner Khyber Pakhtunkhwa Pakistan. Entomol Ornithol Herpetol Curr Res. 2016;05(04).

Coccinellidae beetles (Coleoptera) fauna of district Layyah (Punjab), Pakistan. Asian J Agric Biol. 2021;2021(1).

Hausmann A, Haszprunar G, Hebert PDN. DNA Barcoding the Geometrid Fauna of Bavaria (Lepidoptera): Successes, Surprises, and Questions. PLoS One. 2011;6(2):e17134.

Ashfaq M, Khan AM, Rasool A, Akhtar S, Nazir N, Ahmed N, et al. A DNA barcode survey of insect biodiversity in Pakistan. PeerJ. 2022;10:e13267.

Ashfaq M, Akhtar S, Khan AM, Adamowicz SJ, Hebert PDN. DNA barcode analysis of butterfly species from P akistan points towards regional endemism. Mol Ecol Resour. 2013;13(5):832–43.

Iftikhar R, Ashfaq M, Rasool A, Hebert PDN. DNA Barcode Analysis of Thrips (Thysanoptera) Diversity in Pakistan Reveals Cryptic Species Complexes. PLoS One. 2016;11(1):e0146014.

Ashfaq M, Blagoev G, Tahir HM, Khan AM, Mukhtar MK, Akhtar S, et al. Assembling a DNA barcode reference library for the spiders (Arachnida: Araneae) of Pakistan. PLoS One. 2019;14(5):e0217086.

Hussain K, Rashid K, Hafeez F, Amad I, Ashraf M. Molecular identification of sugarcane black bug (Cavelarius excavates) from Pakistan using cytochrome C oxidase I (COI) gene as DNA barcode. Int J Trop Insect Sci. 2020;40(4):1119–24.

Hickerson MJ, Meyer CP, Moritz C. DNA Barcoding Will Often Fail to Discover New Animal Species over Broad Parameter Space. Syst Biol. 2006;55(5):729–39.

Check E. Cowrie study strikes a blow for traditional taxonomy. Nature. 2005;438(7069):722–3.