In Vivo Epigenomic Profiling of Germ Cells Reveals Germ Cell Molecular Signatures

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Highlights? Modified small-scale ChIP-seq method applicable to small number of cells ? Genome-wide maps of H3K4me3, H3K27me3, H3K27ac, and H2BK20ac of germ cells in vivo ? Identification of active and inactive regulatory elements in germ cells in vivo ? Germ cell H3K27me3 regions are enriched for retrotransposon repeats     

Deep Whole-Genome Sequencing of 100 Southeast Asian Malays

Whole-genome sequencing across multiple samples in a population provides an unprecedented opportunity for comprehensively characterizing the polymorphic variants in the population. Although the 1000 Genomes Project (1KGP) has offered brief insights into the value of population-level sequencing, the low coverage has compromised the ability to confidently detect rare and low-frequency variants. In addition, the composition of populations in the 1KGP is not complete, despite the fact that the study design has been extended to more than 2,500 samples from more than 20 population groups. The Malays are one of the Austronesian groups predominantly present in Southeast Asia and Oceania, and the Singapore Sequencing Malay Project (SSMP) aims to perform deep whole-genome sequencing of 100 healthy Malays. By sequencing at a minimum of 30× coverage, we have illustrated the higher sensitivity at detecting low-frequency and rare variants and the ability to investigate the presence of hotspots of functional mutations. Compared to the low-pass sequencing in the 1KGP, the deeper coverage allows more functional variants to be identified for each person. A comparison of the fidelity of genotype imputation of Malays indicated that a population-specific reference panel, such as the SSMP, outperforms a cosmopolitan panel with larger number of individuals for common SNPs. For lower-frequency (<5%) markers, a larger number of individuals might have to be whole-genome sequenced so that the accuracy currently afforded by the 1KGP can be achieved. The SSMP data are expected to be the benchmark for evaluating the value of deep population-level sequencing versus low-pass sequencing, especially in populations that are poorly represented in population-genetics studies.     

中国石斛属一新种

Dendrobium fanjingshanense Z. H. Tsi ex X. H. Jin et Y. W. Zhang, sp. nov. Fig. 1 Habitu D. wilsonii Rolfe simile, a quo tepalis revolutis fulvis, lobo labelli intermedii infra medium macula una flabellata purpurea ornato. Epiphyticum; caulis teres, 20～40 cm altus, 2～3 mm crassus, caespitosus, superne 5～6-foliatus, internodiis 1～1.5 cm longis. Folia oblongo-lanceolata, subcoriacea, 2～5 cm longa, 5～15 mm lata, apice obtusa et plus minusve hamata, basi vaginis tubulatis membranaceis obtecta. Inflorescentiae e lateribus partium superarum caulium annotinorum defoliatorum nascentes, versus apicem caulis laterales, 1～2-florae; pedunculi 2～3 mm longi, ca. 1 mm crassi, basi vaginis 3～4 membranaceis 3～4 mm longis instructi; bracteae ovato-triangulatae, 3～5 mm longae, apice acutae, macula atro-fusca ornatae. Flores patentes; pedicelli cum ovario ca. 2～3 cm longi; tepala revoluta, fulva, apice obtusa; sepalum intermedium oblongum 2 cm longum, medio 6～7 mm latum, apice fere obtusum; sepala lateralia paulo oblique ovato-lanceolata, sepalo intermedio aequilonga sed medio paulo angustiora, apice obtusa, basi cum pede columnae mentum obconoideum ca. 8 mm longum 6 mm latum apice obtusum formantia; petala subelliptica, ca. 2 cm longa, medio 6 mm lata, apice subobtusa; labellum fulvum, basi purpureum et dense velutinum, obscure trilobatum, lobis lateralibus semiorbiculatis erectis, basi (inter lobos laterales) callo uno purpureo praeditis, lobo intermedio ovato, ca. 1 cm longo, 7 mm lato, apice subacuto et recurvo, supra medio carinato, glabro; columna alba, ca. 3 mm longa, basi in pedem ca. 9 mm longum producta, pede medio purpurato, glabro; operculum antherae album, ambitu rhombicum, glabrum; pollinia 4.     

China's Century: Fast Forward with Historical Baggage

Private Life under Socialism: Love, Intimacy, and Family Change in. Chinese Village 1949–1999 . Yan Yunxiang. Stanford: Stanford University Press, 2003. 289 pp.
Only Hope: Coming of Age under China's One-Child Policy . Vanessa Fong. Stanford: Stanford University Press, 2004. 242 pp.
On the Move: Women in Rural-to-Urban Migration in Contemporary China . Arianne M. Gaetano and Tamara Jacka, eds. New York: Columbia University Press, 2004. 355 pp.     

Evaluating the Coverage and Potential of Imputing the Exome Microarray with Next-Generation Imputation Using the 1000 Genomes Project

Next-generation genotyping microarrays have been designed with insights from large-scale sequencing of exomes and whole genomes. The exome genotyping arrays promise to query the functional regions of the human genome at a fraction of the sequencing cost, thus allowing large number of samples to be genotyped. However, two pertinent questions exist: firstly, how representative is the content of the exome chip for populations not involved in the design of the chip; secondly, can the content of the exome chip be imputed with the reference data from the 1000 Genomes Project (1KGP). By deep whole-genome sequencing two Asian populations that are not part of the 1KGP, comprising 96 Southeast Asian Malays and 36 South Asian Indians for which the same samples have also been genotyped on both the Illumina 2.5 M and exome microarrays, we discovered the exome chip is a poor representation of exonic content in our two populations. However, up to 94.1% of the variants on the exome chip that are polymorphic in our populations can be confidently imputed with existing non-exome-centric microarrays using the 1KGP panel. The coverage further increases if there exists population-specific reference data from whole-genome sequencing. There is thus limited gain in using the exome chip for populations not involved in the microarray design. Instead, for the same cost of genotyping 2,000 samples on the exome chip, performing whole-genome sequencing of at least 35 samples in that population to complement the 1KGP may yield a higher coverage of the exonic content from imputation instead.     

广西兰科植物增补

报道了广西兰科植物区系 2个新记录属和 5个新记录种。