Most soil and litter arthropods are unidentifable based on current DNA barcode reference libraries

We are far from knowing all species living on the planet.Understanding biodiversity is demanding and requires time and expertise.Most groups are understudied given problems of identifying and delimiting species.DNA barcoding emerged to overcome some of the difficulties in identi-fying species.Its limitations derive from incomplete taxonomic knowledge and the lack of comprehensive DNA barcode libraries for so many taxonomic groups.Here,we evaluate how useful barcoding is for identifying arthropods from highly diverse leaf litter communities in the south-ern Appalachian Mountains(USA).We used 3 reference databases and several automated classification methods on a data set including several arthropod groups.Acari,Araneae,Collembola,Coleoptera,Diptera,and Hymenoptera were well represented,showing different performances across methods and databases.Spiders performed the best,with correct identification rates to species and genus levels of~50%across data-bases.Springtails performed poorly,no barcodes were identified to species or genus.Other groups showed poor to mediocre performance,from around 3%(mites)to 20%(beetles)correctly identified barcodes to species,but also with some false identifications.In general,BOLD-based identification offered the best identification results but,in all cases except spiders,performance is poor,with less than a fifth of specimens correctly identified to genus or species.Our results indicate that the soil arthropod fauna is still insufficiently documented,with many species unrepresented in DNA barcode libraries.More effort toward integrative taxonomic characterization is needed to complete our reference libraries before we can rely on DNAbarcoding as a universally applicable identification method.

A NORTHWEST DATABASE MODEL OF SHORT TANDEM REPEAT LOCI IN FORENSIC MEDICINE

Objective To establish the northwest database of short tandem repeat(STR) loci in forensic medicine. Methods Bloodstains or whole blood samples were collected from the unrelated prisoners in Xi'an city. Genetic distribution for 13 STR loci and amelogenin locus were determined in prisons based on GeneScan. One primer for each locus was labeled with the fluorescent by 5 FAM, JOE, or NED. The forensic database were generated by using multiple amplification, GeneScan, genotype, and genetic distribution analysis. Results 113 alleles and 302 genotypes were observed, with the corresponding frequency between 0.0050-0.5250 and 0.0100-0.4100. The mean H was 0.7667. The accumulative DP was 0.9999999,. The accumulative EPP was 0.9999999. The scope of PIC was 0.6036- 0.8562 . PM was less than 10 -11 . The observed and expected genotype frequencies were evaluated using χ 2 test and all were in accordance with Hardy Weinberg equilibrium ( P > 0.05 ). Conclusion STR loci is an ideal genetic marker with powerful polymorphism and stable heredity. It can be used for individual identification and paternity in forensic medicine. The forensic DNA database model can be established successfully.

Development and application of perfect SSR markers in cotton

Background:This study aimed to develop a set of perfect simple sequence repeat(SSR)markers with a single copy in the cotton genome,to construct a DNA fingerprint database suitable for authentication of cotton cultivars.We optimized the polymerase chain reaction(PCR)system for multi-platform compatibility and improving detection efficiency.Based on the reference genome of upland cotton and 10×resequencing data of 48 basic cotton germplasm lines,single-copy polymorphic SSR sites were identified and developed as diploidization SSR markers.The SSR markers were detected by denaturing polyacrylamide gel electrophoresis(PAGE)for initial screening,then fluorescence capillary electrophoresis for secondary screening.The final perfect SSR markers were evaluated and verified using 210 lines from different sources among Chinese cotton regional trials.Results:Using bioinformatics techniques,1246 SSR markers were designed from 26626 single-copy SSR loci.Adopting a stepwise(primary and secondary)screening strategy,a set of 60 perfect SSR markers was selected with high amplification efficiency and stability,easy interpretation of peak type,multiple allelic variations,high polymorphism information content(PIC)value,uniform chromosome distribution,and single-copy characteristics.A multiplex PCR system was established with ten SSR markers using capillary electrophoresis detection.Conclusions:A set of perfect SSR markers of cotton was developed and a high-throughput SSR marker detection system was established.This study lays a foundation for large-scale and standardized construction of a cotton DNA fingerprint database for authentication of cotton varieties.

DNA recovery and analysis from skeletal material in modern forensic contexts

The generation of a DNA profile from skeletal remains is an important part of the identifica-tion process in both mass disaster and unidentified person cases. Since bones and teeth are often the only biological materials remaining after exposure to environmental conditions, intense heat, certain traumatic events and in cases where a significant amount of time has passed since the death of the individual, the ability to purify large quantities of informative DNA from these hard tissues would be beneficial. Since sampling the hard tissues for gen-etic analysis is a destructive process, it is important to understand those environmental and intrinsic factors that contribute to DNA preservation. This will serve as a brief introduction to these topics, since skeletal sampling strategies and molecular taphonomy have been dis-cussed in depth elsewhere. Additionally advances in skeletal DNA extraction and analysis will be discussed. Currently there is great variation in the DNA isolation methods used by laboratories to purify DNA from the hard tissues;however, a standardized set of short tan-dem repeat (STR) loci is analyzed by many US laboratories to allow for comparisons across samples and jurisdictions. Recent advances have allowed for the generation of DNA profiles from smaller quantities of template DNA and have expanded the number of loci analyzed for greater discriminatory power and predictions regarding the geographic ancestry and phenotype of the individual. Finally, utilizing databases and expanding the number of com-parison samples will be discussed in light of their role in the identification process.