Evaluating DNA barcoding using five loci (matK, ITS, trnH- psbA, rpoB, and rbcL) for species identification and phylogenetic analysis of Capsicum frutescens

Abstract

Solanum lycopersicum, and Solanum melongena which are a few of them [4]. The genus Capsicum comprises the five most domestically cultivated species out of the overall 37 known species. These includes C. annuum L., C. frutescens L., C. chinense Jacq., C. pubescens., and C. baccatum L [5]. The identification of all these species is usually made on the basis of the differences in their morphological characteristics, such as the shape of the fruit, color of the corolla, length of pedicel, and the number of growth at each pedicel [5,6]. Unfortunately, the Capsicum species annuum, frutescens, and chinense appear similar in their physical characters, making it difficult to distinguish between them morphologically. As most of the plants, physical characteristics depend on various environmental factors. The three species are commonly known as the "annuum-chinense-frutescens" group due to their close association [1,5]. Various attempts have been made to characterize different Capsicum species utilizing their morphological traits, enzyme loci, restriction fragment length polymorphism, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism, direct or directed amplification of minisatellite region DNA amplified using the polymerase chain reaction (DAMD-PCR), cleaved amplified polymorphic sequence, simple sequence repeat length polymorphism, and inter-simple sequence repeats to determine genetic variations between and within different Capsicum species [7]. An effort was also made to distinguish C. frutescens from C. chinense using RAPD markers, where it was suggested C. frutescens and C. chinense to be