Methods Comparison for Microsatellite Marker Development： Different Isolation Methods, Different Yield Efficiency

Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology, quantitative genetics and genomics. Therefore, it is extremely necessary to select several versatile, low-cost, efficient and time- and labor-saving methods to develop a large panel of microsatellite markers. In this study, we used Zhikong scallop (Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency, while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time- and cost-saving, it is difficult to obtain a large number of microsatellite markers, mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study, we recommend two methods, microsatellite-enriched library construction method and FIASCO-colony hybridization method, for large-scale microsatellite marker development. Both methods were derived from the mi-crosatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes.     

Formation and evolution of sand deserts in Xinjiang,Northwest China：Ⅰ. Provenances of desert sands

Sandy desert landscape is a geological product of arid climate and abundant sand materials supply in natural conditions, therefore the formation of sandy desert is an ideal studying object for understanding the interaction between various stratigraphic/epigenetic spheres of the earth system. However, until now, the knowledge about the provenance and formation of these deserts in Xinjiang, Central Asia is diverse and inconsistent, a systematic review is necessary. Ancient aeolian sand sediments in the internal areas of these deserts and their twin dust deposits in the Cenozoic strata surrounding the Xinjiang deserts are direct and indirect clues reflecting the provenance of sand materials and the formation and evolution of deserts. Based on the geochemical, mineralogical and isotopic evidences of desert sands and relevant deposits in the peripheral regions, this paper reviews the research progress on the development of the sandy deserts in Xinjiang, Northwest China. Many proofs proposed that desert sands in Xinjiang were mainly sourced from the ancient pluvial, alluvial and fluvial sediments and were eventually achieved because of the local sand supply. It pointed out that the settings of tectonic structure in Xinjiang had made sediments both in the Tarim Basin and the Junggar Basin being influenced greatly by regional hydrological system and aeolian processes originated from the planetary wind system of westerly, the East Asian winter monsoon and the topographical mountain-valley winds. However, the directions of transportation paths are different between the hydrological dynamics and the aeolian dynamics, which are decided by the slantwise structures of the basins tectonics and the regional atmospheric circulation routes, respectively, and have determined anisotropies of the transport pathway of these sediments delivered by different agents. This results in a geological cycle of detrital sediment transportation in the two large basins and thus largely increases the degree of sediment mixing, alternation and recycle between younger and older sediment sources, as well as the complexity and diversity of sand provenances.     

AFLP analysis revealed differences in genetic diversity of four natural populations of Manila clam(Ruditapes philippinarum) in China

1 IntroductionManila clam (Ruditapes philippinarum) is aworldwide distributed species. In China, it is foundfrom the northern to southern seashores (Wang etal., 1993; Zhuang, 2001). This species is eura-line with the salinity tolerance ranging from 20 to4…     

皱纹盘鲍(Haliotis discus hannai)精子的超微结构

皱纹盘鲍（Ｈａｌｉｏｔｉｓｄｉｓｃｕｓｈａｎｎａｉ）的精子属于“原始型”,由顶体（２．２μｍ×１．０μｍ）、细胞核（３．１μｍ×０．８３μｍ）、中段（０．７４μｍ×１．４μｍ）和鞭毛（５２μｍ×０．２２μｍ）组成。顶体弹头状,由两部分组成：（１）顶体的前端是一呈卵形的高电子密度的部分;（２）顶体的后端为一呈翼状的低电子密度的部分。细胞核呈长柱状。在顶体凹陷和细胞核凹陷之间为顶体下腔,内有微丝束结构。中段包括５或６个线粒体,一对中心粒及一些泡状结构。鞭毛为典型的“９＋２”结构。     

Molecular identification of scallop planktonic larvae using species-specific microsatellites

The identification of scallop larvae is essential to understand the population structure and community dynamics and to assess the potential environmental impacts caused by scallop larvae released or escaped. However, the larvae identification by morphological characteristics is notoriously difficult, mainly due to the small size （usually being less than 150 μm） and vague morphological characteristics among different scallop species. A simple and accurate molecular method was developed to identify four economically farmed scallop species, the Zhikong scallop Chlamys farreri, the noble scallop C. nobilis, the bay scallop Argopecten irradians and the Yesso scallop Mizuhopecten yessoensis. The tests used the high degree of species-specific microsatellite markers, which was specified by transferability analyses, assessed by reference individuals and evaluated by BLAST searches. The sensitivity test indicated that the species-specific microsatellites were sensitive enough for the detection of 1% -2% larvae in mixed plankton samples. Larvae collected from scallop hatcheries and their effluents and from the artificially controlled crosses were well identified to the species/hybrid level. The results demonstrated that the one-step PCR-based assay was technically simple, inexpensive and robust in identification analyses, and also less sensitive to initial quality of template DNA extracted from the ethanol-preserved samples for several years.     

Phylogenetic analysis of Pectinidae(Bivalvia) based on the ribosomal DNA internal transcribed spacer region

The ribosomal DNA internal transcribed spacer (ITS) region is a useful genomic region for understanding evolutionary and genetic relationships. In the current study, the molecular phylogenetic analysis of Pectinidae (Mollusca: Bivalvia) was performed using the nucleotide sequences of the nuclear ITS region in nine species of this family. The sequences were obtained from the scallop species Argopecten irradians, Mizuhopecten yessoensis, Amusium pleuronectes and Mimachlamys nobilis, and compared with the published sequences of Aequipecten opercularis, Chlamys farreri, C. distorta, M. varia, Pecten maximus, and an outgroup species Perna viridis. The molecular phylogenetic tree was constructed by the neighbor-joining and maximum parsimony methods. Phylogenetic analysis based on ITS1, ITS2, or their combination always yielded trees of similar topology. The results support the morphological classifications of bivalve and are nearly consistent with classification of two subfamilies (Chlamydinae and Pectininae) formulated by Waller. However, A. irradians, together with A. opercularis made up of genera Amusium, evidences that they may belong to the subfamily Pectinidae. The data are incompatible with the conclusion of Waller who placed them in Chlamydinae by morphological characteristics. These results provide new insights into the evolutionary relationships among scallop species and contribute to the improvement of existing classification systems.     

岩层倾斜对体应变受气压影响研究

台站实测资料反映地表倾斜时,体应变气压干扰系数明显变大.通过理论计算,求出了地表倾斜度与体应变气压系数的关系,去除气压干扰后,体应变观测的固体潮汐明显改善.     

钻孔应变仪体应力灵敏系数的影响因素研究

分别计算了水泥弹性模量、水泥层厚度、钢筒厚度、岩石弹性模量等对钻孔应变仪体应力灵敏系数的影响,得出:1)在水泥弹性模量小于某个固定值时,体应力灵敏系数随水泥弹性模量的增大而增大,大于这个值时,体应力灵敏系数又随水泥的弹性模量增大而变小;2)当水泥层厚度比N<2时,体应力灵敏系数变化剧烈,受水泥层厚度影响较大;3)体应力灵敏系数随钢筒厚度及岩石弹性模量的增大而变小。     

Tracing infiltration and recharge using stable isotope in Taihang Mt., North China

The groundwater in headwater region is an important recharge source for the adjacent mountain-front plain. In order to reveal the relationship among precipitation, soil water and groundwater, from June to September in 2004, stable isotopes (deuterium and oxygen-18) in precipitation and soil waters at the depths of 10, 20, 30, 50, 70, 90, and 110 cm were analyzed at two sites covered by black locust (Robinia Pseudoacia L.) (Site A) and grass predominated by Themeda triandra (T. japonica (Willd.) Tanaka) and Bothriochloa ischaemum (B. ischaemum (L.) Keng) (Site B) in an experimental catchment at Taihang Mt., North China, respectively. The δ¹⁸O of precipitation in daily rain events shows large variations (−13.3 to −4.3‰) with a mean of 8.1‰. The δ¹⁸O and δ D of soil waters along profiles in two sites suggest that the influence of canopy cover was just up to 10 cm in top soil water. The soil water moved over the zero flux plane at 70 cm in-depth is expected to escape the evaporative effect at the end of September in both sites. The results show that the stable isotope, instead of tritium as tradition, can be used to trace the soil water behaviors based on the movement of isotopic peak along the vertical profiles in this semi-arid and semi-humid mountainous region. The infiltration depths of soil water in Taihang Mt. are 12 and 10 mm/day from June to September in 2004 in Site A and Site B, respectively. Tracing by stable isotope, recharge fluxes of soil water to local groundwater are of 3.8 and 3.2 mm/day in Site A and Site B, respectively. The results provide desirable information for assessment of local groundwater resources. An erratum to this article can be found at     

The spatial variability of streambed vertical hydraulic conductivity in an intermittent river, northwestern China

Streambed vertical hydraulic conductivity (K) plays an important role in river water and groundwater interaction. The K at the ten transects (Ts1–Ts10) at the Donghe River (an intermittent river) in the Ejina Basin, northwestern China, was measured to investigate its spatial variation. Based on the sediment characteristics and vertical hydraulic conductivity of the riverbed, the entire riverbed of the Donghe River could be divided arbitrarily into two parts: an upper part (starting at Ts1 and ending at Ts9, without an obvious and continuous clogging layer) and a lower part (the remaining riverbed, with an obvious and continuous clogging layer). In the upper part, although the K varied with depth within the 0–30 cm layer, the variability with depth could be ignored in practice. The arithmetic mean K of the upper part ranged from 12 to 27.6 m/day, three orders of magnitude larger than that of the lower part (0.06 m/day). The change of K along the river cross section was significant, and larger values of K often occurred in the parts of the channels with greater water depth. However, there were no consistent patterns of the variability of K at transects across the river, which was influenced by the variation in streambed characteristics. The results could be useful for the estimation of groundwater recharge from river and groundwater resources evaluation in the Ejina Basin.