Molecular Markers and Their Optimization: Addressing the Problems of Nonhomology Using Decapod COI Gene

Abstract

Advancements in DNA sequencing and computational technologies influenced almost all areas of biological sciences. DNA barcoding technology employed for generating nucleotide sequences (DNA barcodes) from standard gene region(s) is capable of resolving the complexities caused due to morphological characters. Thus, they complement taxonomy, population analysis, and phylogenetic and evolutionary studies. DNA barcodes are also utilized for species identification from eggs, larvae, and commercial products. Sequence similarity search using Basic Local Alignment Search Tool (BLAST) is the most reliable and widely used strategy for characterizing newly generated sequences. Similarity searches identify “homologous” gene sequence(s) for query sequence(s) by statistical calculations and provide identity scores. However, DNA barcoding relies on diverse DNA regions which differ considerably among taxa. Even, region-specific variations within barcode sequences from a single gene leading to “nonhomology” have been reported. This causes complications in specimen identification, population analysis, phylogeny, evolution, and allied studies. Hence, the selection of appropriate barcode region(s) homologous to organism of interest is inevitable. Such complications could be avoided using standardized barcode regions sequenced using optimized primers. This chapter discusses about the potential problems encountered due to the unknown/unintentional/intentional use of nonhomologous barcode regions and the need for primer optimization.