Diptera-Specific Polymerase Chain Reaction Amplification Primers of use in Molecular Phylogenetic Research

Abstract

DNA sequence data from a variety of mitochondrial and nuclear gene regions are significant components of phylogenetic research in entomology. Polymerase chain reaction (PCR) amplification primers for many gene regions have been developed that are specific to a range of dipteran groups. Here, we review the existing Diptera-specific PCR amplification primers that have been published for 11 mitochondrial and nuclear gene regions: 12S small ribosomal subunit, cytochrome b, cytochrome oxidase c subunit I, 28S ribosomal RNA, alanyl-tRNA synthetase, the carbamoyl phosphate synthase region of CAD, elongation factor-1α, 6-phosphogluconate dehydrogenase, triose phosphate isomerase, white, and wingless. We also have designed in total 94 new PCR amplification primers for use in these same gene regions. Our new primers have been developed and tested using our DNA sequence database of > 1,600 specimens representing 40 families of Diptera. All of the past and newly developed primer sequences are presented in tables, and their locations are shown on gene maps. This combined data will facilitate future molecular phylogenetic research within Diptera.

Bryophyte-Feeders in a Basal Brachyceran Lineage (Diptera: Rhagionidae: Spaniinae): Adult Oviposition Behavior and Changes in the Larval Mouthpart Morphology Accompanied with the Diet Shifts

“…Primer sets for the PCR and cycle sequencing (CS) reactions were completed using rc28C [31] and 28S-Dipt-7176R [32] for PCR and CS, and internal primers (rc28C, rc28P, rc28D, rc28Q, rc28H, 28C, 28E, 28H, 28K, 28P, 28Z)[31] for CS. PCR and DNA sequencing were performed using a modified method described in [18].…”

A phylogenetic assessment of the polyphyletic nature and intraspecific color polymorphism in the Bactrocera dorsalis complex (Diptera, Tephritidae)

“…Three different gene regions were amplified: the mitochondrial gene cytochrome c oxidase I ( COI , 780 bp) and the nuclear genes, elongation factor-1α ( EF-1α , 759 bp) and period ( PER , 450 bp). These three genes were selected because each has been demonstrated to be informative in distinguishing populations, species complexes, species, or genera in Diptera (Folmer et al 1994, Simon et al 1994, Cho et al 1995, Bauzer et al 2002, Moulton and Wiegmann 2004, Barr et al 2005, Foley et al 2007, Virgilio et al 2009, Gibson et al 2011, San Jose et al 2013). Gene amplification followed San Jose et al (2013).…”

Molecular phylogeny of bark and ambrosia beetles (Curculionidae: Scolytinae) based on 18 molecular markers

“…Certainly, a large amount of works on mitochondrial genes (Weirauch and Munro, 2009, Maekawa et al, 2001, Liu and Beckenbach, 1992, Howland and Hewitt, 1995, Scheffer and Wiegmann, 2000 and ribosomal structural RNAs (Weller et al, 1992, Shull et al, 2001, Whiting et al, 1997, Carmean et al, 1992 paved the way of insect phylogenetics, but more recent studies which included nuclear protein coding genes provided further advancements in the field (Gibson et al, 2011, Winkler et al, 2015, Sahoo et al, 2016, Wahlberg and Wheat, 2008, Regier et al, 2013, Wahlberg et al, 2016.…”