Species boundaries in the Astragalus cusickii complex delimited using molecular phylogenetic techniques.

Understanding the source of phenotypic variability is a challenge in the biological sciences. Variation in phenotypes is the result of variation in the genetics and environment the organism experiences, but elucidating the relative contribution of these two parameters can pose problems, especially in the field of systematics. Systematists are challenged to classify biological diversity into groups that share common ancestry. Phenotypic variation can be useful to demonstrate common ancestry, but only when the primary contributor to the variation is under strong genetic control, and thus heritable. Cusick's milkvetch (Astragalus cusickii) is a perennial forb endemic to the northwestern intermountain region of the United States. The species currently comprises four varieties based on subtle morphological dissimilarities, such as leaf size and density, and the size and shape of the seed pods. The taxonomic organization of the varieties of A. cusickii and related species of Astragalus were reexamined through phylogenetic analysis of low copy nuclear, nuclear-ribosomal, and chloroplast gene regions. Maximum parsimony, maximum likelihood, Bayesian inference, the genealogical sorting index, and an approximately unbiased test were used to determine appropriate species boundaries under the phylogenetic species concept. The results support reclassification of A. cusickii var. packardiae and A. cusickii var. sterilis as separate species. Additionally, evidence suggests a chloroplast capture event may have occurred in one population of A. cusickii var. packardiae.

A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency.

BACKGROUND: Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation. RESULTS: Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N50 size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production. CONCLUSIONS: Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species.

Collagen duplicate genes of bone and cartilage participate during regeneration of zebrafish fin skeleton.

The zebrafish fin is widely used as a model for skeleton regeneration. For years, the nature of the fin skeleton has been controversial as its extracellular matrix shows hybrid characteristics of both bone and cartilage. The presence of co-orthologs genes also increases the complexity of these tissues. In this article, we have identified and described the expression of fibrillar collagens in zebrafish fin skeleton. We found that genes coding for types I, II, V, XI and XXVII collagens are duplicated, showing in several cases, different expression domains. We also identified specific genomic features, such as the presence of type XXIV collagen and the absence of type III collagen in the zebrafish genome. Our study showed that actinotrichia-forming cells and osteoblasts synthesize a wide variety of these fibrillar collagens during fin regeneration. An intertrichial domain expressing most of the collagens was located in the transition between the mesenchyme condensations of actinotrichia and lepidotrichia and may determine an important niche associated with fin skeleton morphogenesis. We also confirmed the hybrid nature of the fin exoskeleton and provided a complete description of those fibrillar collagens expressed during the formation of the fin skeleton.