Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus

The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA “universal” barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed

A qualitative study of women and partners from Lebanon and Quebec regarding an expanded scope of noninvasive prenatal testing

Background: In the near future, developments in non-invasive prenatal testing (NIPT) may offer couples the opportunity to expand the range of genetic conditions tested with this technology. This possibility raises a host of ethical and social concerns, such as the type of information (medical vs. non-medical information) that couples might be exposed to and how this might complicate their informed decision-making. Currently, only limited research, mainly carried out in western countries, was conducted on women's and partners' views regarding the potential expansion of NIPT. Methods: This study used semi-structured interviews with pregnant women and their partners to explore their views on future potential NIPT applications such as non-medical sex selection and non-medical traits, paternity testing, and NIPT use for fetal whole genome sequencing (FWGS). It was conducted in Lebanon and Quebec, as case studies to explore the impact of cultural differences on these views. Results: We found no differences and many similarities when comparing the perceptions of participants in both contexts. While couples in both settings disapproved of the use of NIPT for non-medical sex selection and non-medical traits such as physical characteristics, they were near-unanimous about their support for its use for paternity testing in specific cases, such as legal doubts or conflicts related to the identity of the father. Participants were more ambivalent about NIPT for Fetal Whole Genome Sequencing. They supported this use to detect conditions that would express at birth or early childhood, while objecting to testing for adult-onset conditions. Conclusions: These results can further inform the debate on the future uses of NIPT and future policy related its implementation

The value of non-invasive prenatal testing: preferences of Canadian pregnant women, their partners, and health professionals regarding NIPT use and access

Abstract Background Canadian policies regarding the implementation and public coverage of non-invasive prenatal testing (NIPT) are heterogeneous and shifting, with NIPT being publicly covered for high-risk pregnancies in some provinces, but not others. Such a diverse and evolving policy landscape provides fertile ground for examining the preferences of pregnant women, their partners, and health professionals regarding the implementation and coverage of NIPT by the public healthcare system, as well as the factors influencing their preferences, which is what the present study does. Methods In this paper, we report the results of three-large scale Canadian surveys, in which 882 pregnant women, 395 partners of pregnant women, and 184 healthcare professionals participated. Results The paper focuses on preferences regarding how and when NIPT should be used, as well as the factors influencing these preferences, and how coverage for NIPT should be provided. These are correlated with respondents’ levels of knowledge about Down syndrome and testing technologies and with their stated intended use of NIPT results. Conclusion Salient is the marked difference between the preferences of prospective parents and those of healthcare professionals, which has potential implications for Canadian policy regarding NIPT implementation and insurance coverage

DNA barcoding for conservation, seed banking and ecological restoration of Acacia in the Midwest of Western Australia

We used DNA barcoding to address an important conservation issue in the Midwest of Western Australia, working on Australia's largest genus of flowering plant. We tested whether or not currently recommended plant DNA barcoding regions (matK and rbcL) were able to discriminate Acacia taxa of varying phylogenetic distances, and ultimately identify an ambiguously labelled seed collection from a mine-site restoration project. Although matK successfully identified the unknown seed as the rare and conservation priority listed A. karina, and was able to resolve six of the eleven study species, this region was difficult to amplify and sequence. In contrast, rbcL was straightforward to recover and align, but could not determine the origin of the seed and only resolved 3 of the 11 species. Other chloroplast regions (rpl32-trnL, psbA-trnH, trnL-F and trnK) had mixed success resolving the studied taxa. In general, species were better resolved in multilocus data sets compared to single-locus data sets. We recommend using the formal barcoding regions supplemented with data from other plastid regions, particularly rpl32-trnL, for barcoding in Acacia. Our study demonstrates the novel use of DNA barcoding for seed identification and illustrates the practical potential of DNA barcoding for the growing discipline of restoration ecology