Bidens identification using the noncoding regions of chloroplast genome and nuclear ribosomal DNA

Tsai, Li Chin; Wang, Jenn Che; Hsieh, Hsing Mei; Liu, Kuo Lan; Linacre, Adrian; Lee, James Chun-I

doi:10.1016/j.fsigen.2007.07.005

Cited by 21 publications

(11 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…3 (both reared from an unidentified species of Celastraceae). This intraspecific variation for the locus is not unprecedented and has been reported previously (Taberlet et al , 2007; Tsai et al , 2008). However, it does mean that in examples of 1‐ or 2‐bp differences in trnL sequences we do not know whether this is associated with intraspecific or interspecific variation without being able to identify the plants in another way.…”

Section: Discussionsupporting

confidence: 81%

DNA profiling of host–herbivore interactions in tropical forests

Navarro

Jurado‐Rivera

Gómez‐Zurita

et al. 2010

Ecological Entomology

View full text Add to dashboard Cite

Abstract. 1. The diversity of insects in tropical forests remains poorly known, in particular regarding the critical feeding associations of herbivores, which are thought to drive species richness in these ecosystems.2. Host records remain elusive and traditionally require labour-intensive feeding trials. A recent approach analyses plant DNA ingested by herbivorous insects; direct PCR amplification from DNA extracts from weevils (Curculionoidea) using chloroplast (trnL intron) primers was successful in 41 of 115 cases, resulting in 40 different sequences.3. The resulting trnL intron sequences were identified against public databases to various hierarchical levels based on their position in phylogenetic trees and shown to be members of 26 plant families from different major groups of angiosperms.4. Among the trnL intron sequences, seven pairs or triplets of close relatives (0-2 bp difference) were found which may represent intraspecific variation in the respective host plants.5. Molecular clock calibrations of mitochondrial cox1 sequences of weevils established great distances of lineages obtained (all splits estimated >20 Mya). Distant taxa were found to feed on the same or similar hosts in some cases, showing low evolutionary conservation of host associations among deeper levels.6. The technique provides a new means of studying species diversity and plant-herbivore interactions in tropical forests, and removes the constraints of the need for actual observations of feeding in ecological and evolutionary studies.

show abstract

Section: Discussionsupporting

confidence: 81%

DNA profiling of host–herbivore interactions in tropical forests

Navarro

Jurado‐Rivera

Gómez‐Zurita

et al. 2010

Ecological Entomology

View full text Add to dashboard Cite

show abstract

“…Assessment of the potential of DNA barcoding to distinguish between plant varieties of agri-food interest would be valuable for both breeders and farmers. Whereas the utility of DNA barcoding in species identification has been widely investigated, the intraspecific discrimination of single varietal genotypes, such as clones, pure lines, and hybrids, has been poorly investigated, and few studies have focused on the use of DNA barcoding as a sufficiently informative technique to be exploited for the genetic identification of closely related crop varieties (Tsai et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Biodiversity studies inPhaseolusspecies by DNA barcoding

NicolèSilvia

EricksonDavid

AmbrosiDaria

et al. 2011

Genome

View full text Add to dashboard Cite

The potential of DNA barcoding was tested as a system for studying genetic diversity and genetic traceability in bean germplasm. This technique was applied to several pure lines of Phaseolus vulgaris L. belonging to wild, domesticated, and cultivated common beans, along with some accessions of Phaseolus coccineus L., Phaseolus lunatus L., and Vigna unguiculata (L.) Walp. A multilocus approach was exploited using three chloroplast genic regions (rbcL, trnL, and matK), four intergenic spacers (rpoB-trnC, atpBrbcL, trnT-trnL, and psbA-trnH), and nuclear ITS1 and ITS2 rDNA sequences. Our main goals were to identify the markers and SNPs that show the best discriminant power at the variety level in common bean germplasm, to examine two methods (tree based versus character based) for biodiversity analysis and traceability assays, and to evaluate the overall utility of chloroplast DNA barcodes for reconstructing the origins of modern Italian varieties. Our results indicate that the neighbor-joining method is a powerful approach for comparing genetic diversity within plant species, but it is relatively uninformative for the genetic traceability of plant varieties. In contrast, the character-based method was able to identify several distinct haplotypes over all target regions corresponding to Mesoamerican or Andean accessions; Italian accessions originated from both gene pools. On the whole, our findings raise some concerns about the use of DNA barcoding for intraspecific genetic diversity studies in common beans and highlights its limitations for resolving genetic relationships between landraces and varieties.

show abstract

“…Analysis of trace botanical evidence is a developing forensic discipline and techniques based on molecular biology should support and complement traditional forensic botany in the identification of evidence. The problem of reproducibility and standardization, especially from degraded specimens, prevents the use of classical methods in routine forensic investigations [9][10][11][12][13][14][15] but the use of genetic markers could have the potential to overcome shortcomings associated with traditional forensic botany, and it has been recently proposed in forensic applications [16][17][18].…”

Section: Introductionmentioning

confidence: 99%

Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach

et al. 2009

View full text Add to dashboard Cite

Forensic botany can provide significant supporting evidence during criminal investigations. However, it is still an underutilized field of investigation with its most common application limited to identifying specific as well as suspected illegal plants. The ubiquitous presence of plant species can be useful in forensics, but the absence of an accurate identification system remains the major obstacle to the present inability to routinely and correctly identify trace botanical evidence. Many plant materials cannot be identified and differentiated to the species level by traditional morphological characteristics when botanical specimens are degraded and lack physical features. By taking advantage of a universal barcode system, DNA sequencing, and other biomolecular techniques used routinely in forensic investigations, two chloroplast DNA regions were evaluated for their use as "barcoding" markers for plant identification in the field of forensics. We therefore investigated the forensic use of two non-coding plastid regions, psbA-trnH and trnL-trnF, to create a multimarker system for species identification that could be useful throughout the plant kingdom. The sequences from 63 plants belonging to our local flora were submitted and registered on the GenBank database. Sequence comparison to set up the level of identification (species, genus, or family) through Blast algorithms allowed us to assess the suitability of this method. The results confirmed the effectiveness of our botanic universal multimarker assay in forensic investigations.

show abstract

Bidens identification using the noncoding regions of chloroplast genome and nuclear ribosomal DNA

Cited by 21 publications

References 15 publications

DNA profiling of host–herbivore interactions in tropical forests

DNA profiling of host–herbivore interactions in tropical forests

Biodiversity studies inPhaseolusspecies by DNA barcoding

Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach

Contact Info

Product

Resources

About