Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. Results: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. Conclusion: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experiencedsub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.

Complete genomic sequences for hepatitis C virus subtypes 6e and 6g isolated from Chinese patients with injection drug use and HIV-1 co-infection

In one of our recent studies, two HCV genotype 6 variants were identified in patients from Hong Kong and Guangxi in southern China, with injection drug use and HIV-1 co-infection. We report the complete genomic sequences for these two variants: GX004 and

Foraging habitats and utilization distributions of Black-necked Cranes wintering at the Napahai Wetland, China

One of the most endangered populations of Black-necked Cranes (Grus nigricollis), the central population, is declining due to habitat loss and degradation, but little is known about their space use patterns and habitat preferences. We examined the space use and habitat preferences of Black-necked Cranes during the winter of 2007-2008 at the Napahai wetland in northwest Yunnan, China, where approximately 300 Black-necked Cranes (>90% of the total central population) spent the winter. Euclidean distance analysis was employed to determine the habitat preferences of Black-necked Cranes, and a local nearest-neighbor, convex-hull construction method was used to examine space use. Our results indicate that Black-necked Cranes preferred shallow marsh and wet meadow habitats and avoided farmland and dry grassland. Core-use areas (50% isopleths) and total-use areas (100% isopleths) accounted for only 1.2% and 28.2% of the study area, respectively. We recommend that habitat protection efforts focus on shallow marsh and wet meadow habitats to maintain preferred foraging sites. Core-use areas, such as the primary foraging areas of Black-necked Cranes, should be designated as part of the core zone of the nature reserve. Monthly shifts in the core-use areas of the cranes also indicate that the reserve should be large enough to permit changes in space use. In addition to preserving habitat, government officials should also take measures to decrease human activity in areas used by foraging Black-necked Cranes.