Multilocus marker-based delimitation of Salicornia persica and its population discrimination assisted by supervised machine learning approach.

The Salicornia L. has been considered one of the most taxonomically challenging genera due to high morphological plasticity, intergradation between related species, and lack of diagnostic features in preserved herbarium specimens. In the United Arab Emirates (UAE), only one species of this genus, Salicornia europaea, has been reported, though investigating its identity at the molecular level has not yet been undertaken. Moreover, based on growth form and morphology variation between the Ras-Al-Khaimah (RAK) population and the Umm-Al-Quwain (UAQ) population, we suspect the presence of different species or morphotypes. The present study aimed to initially perform species identification using multilocus DNA barcode markers from chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA), followed by the genetic divergence between two populations (RAK and UAQ) belonging to two different coastal localities in the UAE. The analysis resulted in high-quality multilocus barcode sequences subjected to species discrimination through the unsupervised OTU picking and supervised learning methods. The ETS sequence data from our study sites had high identity with the previously reported sequences of Salicornia persica using NCBI blast and was further confirmed using OTU picking methods viz., TaxonDNAs Species identifier and Assemble Species by Automatic Partitioning (ASAP). Moreover, matK sequence data showed a non-monophyletic relationship, and significant discrimination between the two populations through alignment-based unsupervised OTU picking, alignment-free Co-Phylog, and alignment & alignment-free supervised learning approaches. Other markers viz., rbcL, trnH-psbA, ITS2, and ETS could not distinguish the two populations individually, though their combination with matK (cpDNA & cpDNA+nrDNA) showed enough population discrimination. However, the ITS2+ETS (nrDNA) exhibited much higher genetic divergence, further splitting both the populations into four haplotypes. Based on the observed morphology, genetic divergence, and the number of haplotypes predicted using the matK marker, it can be suggested that two distinct populations (RAK and UAQ) do exist. Further extensive morpho-taxonomic studies are required to determine the inter-population variability of Salicornia in the UAE. Altogether, our results suggest that S. persica is the species that grow in the present study area in UAE, and do not support previous treatments as S. europaea.

Evaluating germinability of eight desert halophytes under long-term seed storage: Implications for conservation.

Ex situ conservation in seed banks is a potential complementary conservation strategy for native plant species. It is well established that ex situ seed banking of native wild plants prolongs seed viability and thereby preserves genetic and species diversity for future use. We evaluated ex situ storage potential of eight halophytic species from deserts in the United Arab Emirates (UAE) by studying seed germination. Specifically, we examined the germinability of freshly collected seeds and seeds stored for three years in a seed bank. We also examined the effect of light conditions on fresh and stored seed germination. Fresh seeds of seven of the eight species tested had a higher germination rates under 12/12 h light/dark fluctuations than did those exposed to total darkness. Storage reduced light sensitivity in Halocnemum strobilaceum, Suaeda aegyptiaca, Salsola drummondii and Salsola imbricata, but increased the requirement for light in Arthrocnemum macrostachyum. In Anabasis setifera, storage decreased germination percentage when there was a 12-hour light/dark fluctuation, but increased germination rate when exposed to the dark treatment. Storage significantly reduced germination in both the light/dark and dark treatments in Suaeda vermiculata and S. aegyptiaca. Germination speed also responded differently to storage; whereas Timson's index significantly increased in A. macrostachyum and H. strobilaceum, it significantly decreased for S. drummondii, S. aegyptiaca and S. vermiculata. Germination of these species at a range of temperatures requires further testing; additionally, we strongly suggest that these laboratory findings be complemented by field studies.

Correction to: Effect of maturation time on dormancy and germination of Citrullus colocynthis (Cucurbitaceae) seeds from the Arabian hyper-arid deserts.

Following publication of the original article [1] author Hatem Shabana wrote to say that one of her affiliations was missing. The affiliation is as follows: Departmento de Biología Vegetal, Universidad de Málaga, P. O. Box 59, 29080 Málaga, Spain.

The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora.

The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.

Effect of maturation time on dormancy and germination of Citrullus colocynthis (Cucurbitaceae) seeds from the Arabian hyper-arid deserts.

BACKGROUND: Light and temperatures of germination greatly affect germination of several Cucurbitaceae species. Environmental conditions prevailing at seed maturation time can affect dormancy and germination requirements. Citrullus colocynthis seeds have a deep dormancy. This perennial prostrate shrub grows all over the year in the arid Arabian deserts. We explored if seed dormancy and germination requirements of C. colocynthis depend on time of fruit collection. Matured seeds were collected at five different times during 2014/2015 year from a population around Dubai city. Fresh seeds were germinated at three temperature regimes in both continuous darkness and alternating 12 h light/12 h darkness. Impacts of seed storage and other treatments on germination were applied on seeds collected in March and exhibited deep dormancy. RESULTS: March collected seeds almost did not germinate in both light and dark at the three temperatures, but those of the other collections responded differently to both light and temperatures. At the lowest temperatures, seeds of all collections did not germinate in light, but those of June, October and December collections germinated in dark. There were negative correlations between final germination and seed length, width, mass and coat thickness. Physical scarification, water soaking and seed storage did not break dormancy of March collection. CONCLUSIONS: Germination of C. colocynthis is very sensitive to light and incubation temperature as well as to the environmental conditions associated with the time of seed maturation. It is important to investigate the effects of environmental factors prevailing during seed maturation under controlled conditions to understand exact reasons for unusual seed dormancy and germination requirements of C. colocynthis, which seems to be very sensitive to maternal environment.