Isolation and characterization of DNA barcodes from distinctive and rare terrestrial animals in China using universal COI and 16S primers
Background: Accurate taxonomic identification is the cornerstone for monitoring, conservation and management of ecological resources. China has the highest biodiversities and the richest species assemblages in the world, but is lacking in sufficient assessment to the abundant genetic variability. DNA barcoding is a proven tool employing sequence information for rapid and unambiguous species delineation. However, the ability of barcodes to distinguish species that are archaic and distinctive evolutionary lines remains largely untested.
Methods: In order to investigate the resources of terrestrial animals in China, regions from mitochondrial COI and 16S are barcoded for 395 specimens belonging to 54 selected species, many of which are indigenous representatives in danger. High success rate of PCR amplification is achieved by using universal COI and 16S primers with many numts pseudogenes co-amplified from mammalian samples.
Results: Application of barcodes to flag species is generally straightforward since no COI or 16S haplotypes are shared between closely related species. Barcoding gap, species resolution and phylogenetic relationships relying on our barcode libraries are further compared using distance and tree based approaches.
Conclusion: Results show that the discriminatory power of the two barcode markers could differentiate on a case-by-case basis, and also suggest a careful consideration of the nuclear numts for barcoding studies as they might provide a new understanding for evolution.
Liu J, Ouyang Z, Pimm SL, Raven PH, Wang X, Miao H, et al. Protecting China's Biodiversity. Science. 2003, 300:1240-1.
He J, Yan C, Marcel H, Wan X, Ren G, Hou Y, et al. Quantifying the effects of climate and anthropogenic change on regional species loss in China. PLoS One. 2018, 13(7):e0199735.
Zheng HR, Cao S. Threats to China's biodiversity by contradictions policy. Ambio. 2015, 44(1):23-33.
Daugherty CH, Cree A, Hay JM, Thompson MB. Neglected taxonomy and continuing extinctions of tuatara (Sphenodon). Nature. 1990, 347(6289):177-9.
Brisson, J. Aphid wing dimorphisms: linking environmental and genetic control of trait variation. Philos Trans R Soc Lond B Biol Sci. 2010, 365(1540):605-16.
Kreuzer M, Howard C, Adhikari B, Pendry CA, Hawkins JA. Phylogenomic approaches to DNA barcoding of herbal medicines: developing clade-specific diagnostic characters for berberis. Front Plant Sci. 2019, 10:586.
JMurugaiyan J, Roesler U. MALDI-TOF MS profiling-advances in species identification of pests, parasites, and vectors. Front Cell Infect Microbiol. 2017, 7:184.
Hebert P, Cywinska A. Biological identifications through DNA barcodes. Proc Biol Sci. 2003, 270(1512):313-21.
Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R. Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philos Trans R Soc Lond B Biol Sci. 2005, 360(1462):1805-11.
Haji Bab Aei M, Singer G, Hebert P, Hickey DA. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 2007, 23(4):167-72.
Matilainen O, Quirós P, Auwerx J. Mitochondria and epigenetics – crosstalk in homeostasis and stress. Trends Cell Biol. 2017, 27(6):453-63.
Akhmedov AT, Marín-García J. Mitochondrial DNA maintenance: an appraisal. Mol Cell Biochem. 2015, 409(1):283-305.
Vences M, Thomas M, Arie V, Chiari Y, Vieites DR. Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front Zool. 2005, 2(1):5.
Hebert PD, Ratnasingham S, deWaard JR. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci. 2003;270 Suppl 1(Suppl 1):S96-9.
Ratnasingham S, Hebert PD. bold: The Barcode of Life Data System (http://www.barcodinglife.org). Mol Ecol Notes. 2007;7(3):355-64.
Yang C, Xiao Z, Zou Y, Zhang X, Yang B, Hao Y, et al. DNA barcoding revises a misidentification on musk deer. Mitochondrial DNA. 2015;26(4):605-12.
Che J, Chen HM, Yang JX, Jin JQ, Jiang KE, Yuan ZY, et al. Universal COI primers for DNA barcoding amphibians. Mol Ecol Resour. 2012, 12(2):247-58.
Van D, Ranjit K, Morrow CD, Blanchard EE, Taylor CM, Martin DH, et al. In silico and experimental evaluation of primer sets for species-level resolution of the vaginal microbiota using 16S ribosomal RNA gene sequencing. J Infect Dis. 2019, 219(2):305-14.
Elbrecht V, Taberlet P, Dejean T, Valentini A, Usseglio-Polatera P, Beisel JN, et al. Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects. PeerJ. 2016, 4:e1966.
Astrin JJ, Huber B, Misof B, Klütsch CFC. Molecular taxonomy in pholcid spiders (Pholcidae, Araneae): evaluation of species identification methods using CO1 and 16S rRNA. Zool Scr. 2006;35(5).
Schmitteckert EM, Prokop CM, Hedrich HJJLA. DNA detection in hair of transgenic mice-a simple technique minimizing the distress on the animals. Lab Anim. 1999, 33(4):385.
Berner DK, Cavin C, Erper I, Tunali B. First report of anthracnose of mile-a-minute (Persicaria perfoliata) caused by colletotrichum cf. gloeosporioides in Turkey. Plant Dis. 2012, 96(10):1578.
Srivathsan A, Meier R. On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics. 2012, 28:190-194.
Clare EL, Kerr K, KönigslöW T, Wilson JJ, Hebert PDN. Diagnosing mitochondrial DNA diversity: applications of a sentinel gene approach. J Mol Evol. 2008, 66(4):362-7.
Min XJ, Hickey DA. DNA barcodes provide a quick preview of mitochondrial genome composition. PLoS One. 2007;2(3):e325.
Zhang AB, Feng J, Ward RD, Wan P, Gao Q, Wu J, et al. A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods. PLoS One. 2012;7(2):e30986.
Austerlitz F, David O, Schaef Fe R B, Bleakley K, Olteanu M, Leblois R, et al. DNA barcode analysis: a comparison of phylogenetic and statistical classification methods. BMC Bioinformatics. 2009, 10 Suppl 14(Suppl 14):S10.
Meyer CP, Paulay G. DNA barcoding: error rates based on comprehensive sampling. PLoS Biol. 2005, 3(12):e422.
Fišer Pečnikar Ž, Buzan EV. 20 years since the introduction of DNA barcoding: from theory to application. J Appl Genet. 2013;55(1):43-52.
Song H, Buhay JE, Whiting MF, Crandall KA. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Natl Acad Sci U S A. 2008, 105(36):13486-91.
Thalmann O, Hebler J, Poinar HN, Pääbo S, Vigilant L. Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol Ecol. 2004, 13(2):321-35.
Turvey ST, Marr MM, Barnes I, Brace S, Tapley B, Murphy RW, et al. Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians. Ecol Evol. 2019, 9(18):10070-84.
Kress WJ, Erickson DL. DNA barcodes: methods and protocols. Methods Mol Biol. 2012, 858:3-8.
Varadharajan B, Parani M. DMSO and betaine significantly enhance the PCR amplification of ITS2 DNA barcodes from plants. Genome. 2021;64(3):165-71.
Moritz C, Dowling TE, Brown WM. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu Rev Ecol Syst. 1987, 18(1):269-92.
White DJ, Wolff JN, Pierson M, Gemmell NJ. Revealing the hidden complexities of mtDNA inheritance. Mol Ecol. 2008, 17(23):4925-42.
Lightowlers RN, Chinnery PF, Turnbull DM, Howell N. Mammalian mitochondrial genetics: heredity, heteroplasmy and disease. Trends Genet. 1997, 13(11):450-5.
Jenuth JP, Peterson AC, Shoubridge EA. Tissue-specific selection for different mtDNA genotypes in heteroplasmic mice. Nat Genet. 1997, 16(1):93-5.
Li M, SchröDer R, Ni S, Madea B, Stoneking M. Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations. Proc Natl Acad Sci U S A. 2015, 112(8):2491-6.
Berg OG, Kurland CG. Why mitochondrial genes are most often found in nuclei. Mol Biol Evol. 2000;17(6):951-61.
Bensasson D, Zhang DX, Hartl DL, Hewitt GM. Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol Evol. 2001, 16(6):314-21.
Ricardo PC, Franoso E, Arias MC. Mitochondrial DNA intra-individual variation in a bumblebee species: A challenge for evolutionary studies and molecular identification. Mitochondrion. 2020, 53:243-54.
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