Large-scale general collection of wild-plant DNA in Mustang, Nepal

Rapid Pomegranate Juice Authentication Using a Simple Sample-to-Answer Hybrid Paper/Polymer-Based Lab-on-a-Chip Device

As a super fruit, pomegranate and its juice have attracted increased consumer demands during the past decades. Given the high production cost and market price, adulteration of pomegranate juice is highly likely to occur. To authenticate pomegranate juice and avoid the addition of cheaper fruit juices, such as apple and grape, an analytical method based on loop-mediated isothermal amplification (LAMP) was developed. This LAMP-based authentication method achieved highly sensitive (i.e., 10 pg for pomegranate DNA and 100 pg for grape and apple DNA) and specific detection of pomegranate, apple, and grape DNA present in fresh fruit juice. To further simplify the overall analysis, a hybrid paper/polymer-based lab-on-a-chip (LOC) platform was designed to integrate DNA extraction, LAMP reaction, and LAMP result visualization onto a single device. This LOC device was able to detect 2 μL of fresh pomegranate juice and 5 μL of fresh apple and grape juice. Using a homemade portable heating device, the overall analysis could be completed in ∼1 h in an almost instrument-free setting. The cost for each authentication test is estimated to be ∼4 USD and the reusable homemade portable heating device is ∼15 USD. This LAMP-based simple sample-to-answer hybrid paper/polymer-based LOC device has high potential to be adopted by government laboratories and the food industry to rapidly and routinely authenticate pomegranate juice even in a resource-limited environment.

Arundina graminifolia var. revoluta (Arethuseae, Orchidaceae) has fern-type rheophyte characteristics in the leaves

Morphological and molecular variation between Arundina graminifolia var. graminifolia and the dwarf variety, A. graminifolia var. revoluta, was examined to assess the validity of their taxonomic characteristics and genetic background for identification. Morphological analysis in combination with field observations indicated that A. graminifolia var. revoluta is a rheophyte form of A. graminifolia characterized by narrow leaves, whereas the other morphological characteristics described for A. graminifolia var. revoluta, such as smaller flowers and short stems, were not always accompanied by the narrower leaf phenotype. Molecular analysis based on matK sequences indicated that only partial differentiation has occurred between A. graminifolia var. graminifolia and A. graminifolia var. revoluta. Therefore, we should consider the rheophyte form an ecotype rather than a variety. Anatomical observations of the leaves revealed that the rheophyte form of A. graminifolia possessed characteristics of the rheophytes of both ferns and angiosperms, such as narrower palisade tissue cells and thinner spongy tissue cells, as well as fewer cells in the leaf-width direction and fewer mesophyll cell layers.

A hypothesis on the origin of genetic heterozygosity in diploids and triploids in Japanese Cayratia japonica species complex (Vitaceae)

We previously reported the occurrence of triploid strains in Japanese populations of Cayratia japonica (Thunb.) Gagnep. Interestingly, the triploid and most diploid strains had variably reduced pollen fertility. Two questions emerged from this earlier work: (1) How do triploids arise, and are they allotriploids or autotriploids? and (2) Why is there low pollen fertility in some diploid plants? We used a molecular genetic approach to determine the phylogenetic origins of triploids in C. japonica and the closely related species Cayratia tenuifolia (Wight & Arn.) Gagnep. In our analysis, we compared the sequences of the nuclear single-copy genes LEAFY and ASYMMETRIC LEAVES1. As a result, most triploids and diploids were heterozygous for the loci examined; the triploid genome shared an allele with the diploid genome, but other alleles differed between the ploidies. Therefore, Japanese populations of C. japonica and C. tenuifolia almost certainly arose from repeated hybridization events among genetically differentiated strains. Using our sequence data, we discuss possible scenarios accounting for the occurrence of triploids in the two species of Cayratia.

Field testing of collection cards for Cannabis sativa samples with a single hexanucleotide DNA marker

The validity and feasibility of using DNA collection cards in the field for preservation and analysis of Cannabis sativa genotypes were investigated using a highly specific hexanucleotide marker. Collection cards were submitted to the National Marijuana Initiative, which selectively trained and managed the collection of specific types of samples from a variety of participating agencies. Samples collected at seizure sites included fresh marijuana leaf samples, dried "dispensary" samples, U.S. border seizures, and hashish. Using a standardized PCR kit with custom-labeled oligonucleotide primers specific to marijuana, collection cards produced eight genotypes and 13 different alleles, extremely low baselines, and no cross-reactivity with control plant species. Results were produced from all sample types with the exception of hashish. Plant DNA collection cards represent an easily implementable method for the genetic identification and relatedness of C. sativa street and grow site-seized samples with applications for databasing and market disruption.

Taxonomic status of Monotropastrum humile, with special reference to M. humile var. glaberrimum (Ericaceae, Monotropoideae)

Taxonomic treatment of the achlorophyllous monotropoid plant Monotropastrum humile is still unclear and confusing because of the lack of detailed morphological analyses and molecular phylogeny. In particular, the taxonomic status of a glabrous variety, M. humile var. glaberrimum, is under debate. Our detailed examination of the morphological characteristics of living plants revealed that M. humile var. glaberrimum can be easily distinguished from the putative conspecific taxon M. humile var. humile by characteristics not previously recognized, namely the shape and color of the floral disc. Most morphological features characterizing Cheilotheca were also found in M. humile var. glaberrimum. Moreover, there was considerable nucleotide differentiation in the internal transcribed spacer (ITS)2 sequences of M. humile var. humile and var. glaberrimum. Molecular analysis of the phylogenetic relationship of M. humile var. humile, var. glaberrimum, and other monotropoids using ITS2 sequences showed that two varieties of M. humile formed a monophyletic clade with a member of a different genus, Monotropa L., but obvious phylogenetic relationships among these three taxa were not obtained. Thus we conclude that Monotropastrum humile var. glaberrimum should be treated as a distinct species. However, the generic affiliation of M. humile var. glaberrimum could not be determined because of its intermediate character state combination and the insufficient characterization of related species. We strongly suggest that Monotropastrum as a whole needs re-evaluation.

DNA banking for plant breeding, biotechnology and biodiversity evaluation

The manipulation of DNA is routine practice in botanical research and has made a huge impact on plant breeding, biotechnology and biodiversity evaluation. DNA is easy to extract from most plant tissues and can be stored for long periods in DNA banks. Curation methods are well developed for other botanical resources such as herbaria, seed banks and botanic gardens, but procedures for the establishment and maintenance of DNA banks have not been well documented. This paper reviews the curation of DNA banks for the characterisation and utilisation of biodiversity and provides guidelines for DNA bank management. It surveys existing DNA banks and outlines their operation. It includes a review of plant DNA collection, preservation, isolation, storage, database management and exchange procedures. We stress that DNA banks require full integration with existing collections such as botanic gardens, herbaria and seed banks, and information retrieval systems that link such facilities, bioinformatic resources and other DNA banks. They also require efficient and well-regulated sample exchange procedures. Only with appropriate curation will maximum utilisation of DNA collections be achieved.

Ultra-rapid preparation of total genomic DNA from isolates of yeast and mould using Whatman FTA filter paper technology – a reusable DNA archiving system

Conventional methods for purifying PCR-grade fungal genomic DNA typically require cell disruption (either physical or enzymatic) coupled with laborious organic extraction and precipitation stages, or expensive column-based technologies. Here we present an easy and extremely rapid method of preparing yeast and mould genomic DNAs from living cultures using Whatman FTA filter matrix technology. Aqueous suspensions of yeast cells or hyphal fragments and conidia (in the case of moulds) are applied directly (or after freeze-thawing) to dry FTA filters. Inoculated filters are then subjected to brief microwave treatment, to dry the filters and inactivate the organisms. Filter punches are removed, washed rapidly, dried and placed directly into PCR reactions. We show that this procedure inactivated all of the 38 yeast and 75 mould species tested, and generated PCR-grade DNA preparations in around 15 minutes. A total of 218 out of 226 fungal isolates tested liberated amplifiable DNA after application to FTA filters. Detection limits with yeast cultures were approximately 10 colony-forming units per punch. Moreover, we demonstrate that filter punches can be recovered after PCR, washed and used in fresh PCR reactions without detectable cross-contamination. Whatman FTA technology thus represents a cheap, ultra-rapid method of fungal genomic DNA preparation, and also potentially represents a powerful fungal DNA archiving and storage system.