Species discrimination in Sisyrinchium (Iridaceae): assessment of DNA barcodes in a taxonomically challenging genus

Abstract

DNA barcoding aims to develop an efficient tool for species identification based on short and standardized DNA sequences. In this study, the DNA barcode paradigm was tested among the genera of the tribe Sisyrinchieae (Iridoideae). Sisyrinchium, with more than 77% of the species richness in the tribe, is a taxonomically complex genus. A total of 185 samples belonging to 98 species of Sisyrinchium, Olsynium, Orthrosanthus and Solenomelus were tested using matK, trnH-psbA and internal transcribed spacer (ITS). Candidate DNA barcodes were analysed either as single markers or in combination. Detection of a barcoding gap, similarity-based methods and tree-based analyses were used to assess the discrimination efficiency of DNA barcodes. The levels of species identification obtained from plastid barcodes were low and ranged from 17.35% to 20.41% for matK and 5.11% to 7.14% for trnH-psbA. The ITS provided better results with 30.61-38.78% of species identified. The analyses of the combined data sets did not result in a significant improvement in the discrimination rate. Among the tree-based methods, the best taxonomic resolution was obtained with Bayesian inference, particularly when the three data sets were combined. The study illustrates the difficulties for DNA barcoding to identify species in evolutionary complex lineages. Plastid markers are not recommended for barcoding Sisyrinchium due to the low discrimination power observed. ITS gave better results and may be used as a starting point for species identification.

Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)

“…However, ITS region has proved to be a suitable marker in authentication of Cassia species in the commercial herbal market (Seethapathy et al, 2014). The strong identification ability of nuclear region ITS have been verified in many complex groups (Baldwin et al, 1995; Alves et al, 2014; Wang et al, 2014; Giudicelli, Mäder & De, 2015). Therefore, we suggest that ITS1 itself could be the first option for DNA barcoding in subtribe Cassiinae, though ITS2 should not be discarded.…”

Nuclear simple sequence repeat markers are superior to DNA barcodes for identification of closely related Rhododendron species on the same mountain

“…However, these suggested DNA barcodes, matK , rbcL , psbA‐trnH , and ITS, are not effective enough to discriminate closely related or recently diverged species (Newmaster et al, ; Newmaster & Subramanyam, ), especially in certain species‐rich genera (Yan et al, ). For example, Alves et al () used three DNA barcodes (ITS, matK , and psbA ‐ trnH ) to identify the previously named species in the genus Sisyrinchium L. (Iridaceae). They found that only 20% or 39% of sampled species could be identified by two plastid barcodes or ITS, respectively.…”

Isolation and characterization of microsatellite loci in Sisyrinchium (Iridaceae) and cross amplification in other genera

“…Within the past century, species of this genus have undergone additional fragmentation due to human activities, which has resulted in isolated subpopulations. The study of the genus Sisyrinchium is highly complex owing to the lack of reliable morphological apomorphies (Henderson, 1976), unresolved phylogenetic relationships at the species level (Chauveau et al, 2011;Karst and Wilson, 2012), reticulate evolution driven by polyploidy (Tacuatiá et al, 2012a,b;Alves et al, 2014), and hybridization (Henderson, 1976;Cholewa and Henderson, 1984;Yamaguchi and Hirai, 1987). The most complete phylogenetic study of Sisyrinchium performed by Chauveau et al (2011) strongly suggests that species classified in section Hydastylus and section Viperella belong to a single group of plants that has undergone a recent adaptive radiation (Clade IV).…”

“…In addition, the putative occurrence of incomplete lineage sorting within this clade may be partly explained by the low level of discrimination observed between species. Furthermore, Alves et al (2014) also had difficulties assigning species identifications in this taxonomic group using plant barcode markers (ITS, matK, and trnH-psbA). The authors suggest natural hybridization as one possible explanation because it can reduce the efficiency of DNA barcoding since it generally fails to identify species undergoing extensive reticulation.…”

“…The authors suggest natural hybridization as one possible explanation because it can reduce the efficiency of DNA barcoding since it generally fails to identify species undergoing extensive reticulation. Sisyrinchium palmifolium L. and S. marchioides Spreng have great morphological similarity in flowers traits which may be attributable to a recent adaptive radiation of Sisyrinchium species (Alves et al, 2014). In earlier taxonomical studies, S. palmifolium was classified in the section Hydastylus and S. marchioides in the section Viperella (Ravenna, 2002).…”