Database on Demand – An online tool for the custom generation of FASTA‐formatted sequence databases

In mass spectrometry‐based proteomics, most conventional search engines match spectral data to sequence databases. These search databases thus play a crucial role in the identification process. While search engines can derive peptides in silico from protein sequences, this is usually limited to standard digestion algorithms. Customized search databases that provide detailed control over the search space can vastly outperform such standard strategies, especially in gel‐free proteomics experiments. Here we present Database on Demand, an easy‐to‐use web tool that can quickly produce a wide variety of customized search databases.     

Species versus genotypic diversity of a nitrogen-fixing plant functional group in a metacommunity

Exploring species and genetic diversity interactions provides new opportunities for furthering our understanding of the ecology and evolution of population and community dynamics, and for predicting responses of ecosystems to environmental change. Theory predicts that species diversity within communities and genetic diversity within populations will covary positively, because either species and genetic diversity interact synergistically or they respond in parallel fashion to common habitat conditions. We tested the hypothesis of positive covariation between species and genotypic diversity in a metacommunity of the species-rich southwest Australian flora. We hypothesised that the connection between genotypic diversity and species diversity is strong within functional groups, but weak or non-existent if the species considered extend beyond the functional group. We show that allelic richness of Daviesia triflora, an ant-dispersed pea, covaries positively with the species richness of six co-occurring nitrogen-fixing legume species. No pattern can be detected between allelic richness of D. triflora and species richness of ant-dispersed species when four non-legumes are added. We also show that genetic diversity of D. triflora is not governed by the same environmental factors that determine the presence of a group of large-shrub/small-tree species in the same metacommunity. This study shows that species and genetic diversity covariation are more likely to be confined to within, rather than between, plant functional groups.     

Floristic Geography of Piper (Piperaceae) in China

Piper is the largest genus and important Pantropical components of the Piperaceae family with approximately 1000-2000 species in the world. China is in the northern verge of its natural distribution. In this study, floristic geography of the Piper genus in China was analyzed to reveal its botanical characteristic, origins of speciation and its dispersal channels. The study results showed Yunnan province is one of the very important distribution regions for Piper species, served as the center of the Piper species dispersal toward to the eastern and northern regions of China with gradually reduced species numbers. The similarity level appeared to be low for its species among different provinces, and the Piper distribution regions could be approximately clustered into three clades: tropical clade, subtropical clade and Taiwan clade. Cladistically, Piper species found in China have the highest proportions which were endemic to China, and then followed by Piper species distributed in Tropical Asia, only few species belonged to Pantropical and East Asia areal types. The floristic geography of Piper genus in China is related to that of Indo Chinese Peninsula, Java Islands and Indian Peninsula in some degrees, but not closely related. This study revealed Yunnan province is one of the central of origins for the Piper species, and or one of the central of regions for its species diversification, and the Piper species of Taiwan mainly came from Philippine islands and further diversified into Taiwan clade. Our study results presented a useful method for the systematic studying of Piper genus taxonomy and the evolution of Piper speciation.     

The Flora of Siahrud e Rudbar Protected Area,Northern Iran

The vascular flora of the Siahrud e Rudbar protected area was investigated in the years 2007 and 2008. It is a sylvatic area in the Guilan province with a total area of approximately 28289 hectares. A total of 711 plant specimens were collected and 616 species, subspecies, and varieties, belonging to 373 genera and 101 families were identified. Of these, 14 species (23%) are endemic to Iran. The documented flora exhibited many typically Hyrcanian species, including Hyrcanian endemics. The global phytogeographical affinities of the species were as follows: Euro Siberian 212%, Iran Turanian & Euro Siberian 168%, Pluriregional 117%, Iran Turanian 106%, and Cosmopolite 55%.     

Computational resources and tools for antimicrobial peptides

Antimicrobial peptides (AMPs), as evolutionarily conserved components of innate immune system, protect against pathogens including bacteria, fungi, viruses, and parasites. In general, AMPs are relatively small peptides (<10 kDa) with cationic nature and amphipathic structure and have modes of action different from traditional antibiotics. Up to now, there are more than 19 000 AMPs that have been reported, including those isolated from nature sources or by synthesis. They have been considered to be promising substitutes of conventional antibiotics in the quest to address the increasing occurrence of antibiotic resistance. However, most AMPs have modest direct antimicrobial activity, and their mechanisms of action, as well as their structure–activity relationships, are still poorly understood. Computational strategies are invaluable assets to provide insight into the activity of AMPs and thus exploit their potential as a new generation of antimicrobials. This article reviews the advances of AMP databases and computational tools for the prediction and design of new active AMPs. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.     

Ecotypes of wild rooibos (Aspalathus linearis (Burm. F) Dahlg., Fabaceae) are ecologically distinct

Aspalathus linearis (Burm. F) Dahlg., Fabaceae is cultivated by small- and large-scale commercial farmers of the Cederberg and Bokkeveld Plateau in the Cape Floristic Region of South Africa, for the production of an herbal beverage called ‘rooibos’ or ‘rooibos tea’. Small-scale farmers also harvest A. linearis from the wild and market the tea as an organic and fair-trade certified product. However, little is known about the apparent ecotypes of wild A. linearis. We hypothesized that 1) rooibos ecotypes are ecologically distinct (occurring in different plant communities defined by environmental variables); 2) rooibos ecotypes are functionally distinct due to variance in water use efficiency; and 3) rooibos ecotypes are associated with threatened vegetation types/species, making populations of wild rooibos ecotypes worthy of conservation. Ecotypes of wild rooibos were identified based on plant habit and local knowledge. Plant communities were classified using Twinspan, environmental factors were tested as predictors of ecotype distribution and water use efficiency of ecotypes growing across a rainfall gradient was determined from foliar natural abundance of ¹³C. Wild rooibos was not generally associated with endangered vegetation types but was associated with plant species having endangered status. Wild rooibos occurred in four plant communities and comprised five wild rooibos ecotypes: shrub, tree, upright, salignus and prostrate types. Although some ecotypes clearly co-occurred, evidence is provided for habitat preference between the ecotypes: Prostrate and upright ecotypes occurred at higher elevations (> 400-600 m). Shrub ecotypes occurred at lower rainfall sites (< 200 mm p.a.) and the salignus ecotype occurred at higher rainfall sites (> 500 mm p.a.). Foliar ¹³C indicated greater water use efficiencies by ecotypes in relatively drier areas. The extent to which this is a plastic or inherent response requires further investigation. Considering that wild rooibos ecotypes differ both ecologically and possibly also functionally and genetically, it is concluded that populations of wild rooibos ecotypes should be considered as distinct and worthy of conservation. This distinctness should be considered when farmers apply for both harvesting and ploughing rights on land with wild rooibos ecotypes.     

More than meets the eye: a morphological and phylogenetic comparison of long‐spurred,white‐flowered Satyrium species (Orchidaceae) in South Africa

Superficial similarities among unrelated species are often a result of convergent evolution and can cause considerable taxonomic confusion. A case in point is Satyrium eurycalcaratum , described here as a new species, which has been confused with several other Satyrium spp. with similar long‐spurred, white flowers. A phylogenetic analysis, based on molecular data, indicated that S. eurycalcaratum is not closely related to any of the species with which it has been previously confused. A comparative analysis of morphological characters in the seven South African Satyrium spp. with long‐spurred, white flowers showed that each of these, including S. eurycalcaratum , is characterized by a unique combination of traits. Despite the similarity in pollination syndrome characters, such as spur length and flower colour, variation in rostellum structure was particularly pronounced and four distinctive forms were present. There was no phylogenetic signal in patterns of interspecific rostellum variation, as some closely related species had different rostella, whereas some distantly related species shared similar rostellum structures. We therefore conclude that the use of rostellum traits in conjunction with phylogenetic evidence can resolve species delimitations among orchid species that share the same pollination syndrome. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 166 , 417–430.