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Your search keyword '"Zhaoling Xuan"' showing total 6 results
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6 results on '"Zhaoling Xuan"'

1. Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm ( Bombyx )

Author

Huisong Zheng, Chang Yu, Ruiqiang Li, Chen Ye, Juan Wang, Xingfu Zha, Cheng Lu, Chun Liu, Chunfeng Li, Zhonghuai Xiang, Fangyin Dai, Daojun Cheng, Wei Fan, Dawei Li, Yan Zhou, Ningjia He, Haojing Shao, Ines Hellmann, Lan Jiang, Tao Jiang, Hanfu Xu, Songgang Li, Dong Li, Qingyou Xia, Zhaoling Xuan, Wei Zeng, Xuyang Yin, Yiran Guo, Guoqing Pan, Yihong Shen, Jingjing Li, Hui Liu, Guojie Zhang, Jun Wang, Celine Becquet, Zeyang Zhou, Huanming Yang, Wen Wang, Zhouhe Du, Ping Zhao, Jun Li, Ze Zhang, Ying Lin, Zhuo Li, Jianjun Cao, Xiuqing Zhang, Tingcai Cheng, Minhui Pan, Yingrui Li, Xun Xu, Shiping Liu, Si Tang, Jing Wang, Ping Wu, Jeffrey D. Jensen, Aichun Zhao, Rasmus Nielsen, and Jing Zhao

Subjects
Male, Candidate gene, Genome, Insect, Gene Expression, Genes, Insect, Polymorphism, Single Nucleotide, Genome, Linkage Disequilibrium, Article, Exocrine Glands, INDEL Mutation, Molecular evolution, Bombyx mori, Testis, Genetic variation, Animals, Genetic variability, Selection, Genetic, Domestication, Bombyx mandarina, Phylogeny, Genetics, Principal Component Analysis, Multidisciplinary, biology, fungi, Genetic Variation, Sequence Analysis, DNA, Bombyx, biology.organism_classification, Female, Digestive System
Abstract

The Taming of the Silkworm Silkworms, Bombyx mori , represent one of the few domesticated insects, having been domesticated over 10,000 years ago. Xia et al. (p. 433 , published online 27 August) sequenced 29 domestic and 11 wild silkworm lines and identified genes that were most likely to be selected during domestication. These genes represent those that enhance silk production, reproduction, and growth. Furthermore, silkworms were probably only domesticated once from a large progenitor population, rather than on multiple occasions, as has been observed for other domesticated animals.

Published
2009
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2. Prenatal Detection of Aneuploidy and Imbalanced Chromosomal Arrangements by Massively Parallel Sequencing

Author

Kwong Wai Choy, Yue Su, Tak Yeung Leung, Xiuqing Zhang, Fuman Jiang, Jingrong Lin, Shengpei Chen, Shan Dan, Weiyuan Zhang, Tze Kin Lau, Zhaoling Xuan, Wei Wang, Hui Jiang, Xuchao Li, and Fang Chen

Subjects
Male, Numerical Chromosomal Abnormality, lcsh:Medicine, Aneuploidy, Chorionic villus sampling, Prenatal diagnosis, Chromosome Disorders, Biology, DNA sequencing, Chromosomal Disorders, Pregnancy, Prenatal Diagnosis, medicine, Genetics, Humans, Copy-number variation, lcsh:Science, Whole genome sequencing, Clinical Genetics, Multidisciplinary, Massive parallel sequencing, medicine.diagnostic_test, lcsh:R, Computational Biology, High-Throughput Nucleotide Sequencing, Human Genetics, Genomics, medicine.disease, Karyotyping, Medicine, lcsh:Q, Female, Research Article
Abstract

Fetal chromosomal abnormalities are the most common reasons for invasive prenatal testing. Currently, G-band karyotyping and several molecular genetic methods have been established for diagnosis of chromosomal abnormalities. Although these testing methods are highly reliable, the major limitation remains restricted resolutions or can only achieve limited coverage on the human genome at one time. The massively parallel sequencing (MPS) technologies which can reach single base pair resolution allows detection of genome-wide intragenic deletions and duplication challenging karyotyping and microarrays as the tool for prenatal diagnosis. Here we reported a novel and robust MPS-based method to detect aneuploidy and imbalanced chromosomal arrangements in amniotic fluid (AF) samples. We sequenced 62 AF samples on Illumina GAIIx platform and with averagely 0.01× whole genome sequencing data we detected 13 samples with numerical chromosomal abnormalities by z-test. With up to 2× whole genome sequencing data we were able to detect microdeletion/microduplication (ranged from 1.4 Mb to 37.3 Mb of 5 samples from chorionic villus sampling (CVS) using SeqSeq algorithm. Our work demonstrated MPS is a robust and accurate approach to detect aneuploidy and imbalanced chromosomal arrangements in prenatal samples.

Published
2012

3. Noninvasive Fetal Trisomy (NIFTY) test: an advanced noninvasive prenatal diagnosis methodology for fetal autosomal and sex chromosomal aneuploidies

Author

Shengpei Chen, Hongyun Zhang, Jiansheng Xie, Baomin Yin, Hui Guo, Jun-Jun Wang, Hui-Hui Jiang, Yue Su, Wei-wei Wang, Xianghua Chai, Huakun Zhang, Zhongming Tian, Wei-Mou Zheng, Jianhong Xie, Songgang Li, Lifu Liu, Qiyun Li, Yuying Yuan, Shan Dan, Huifei Chen, Xiuqing Zhang, Wen Su, Yihan Li, Linhua Lin, Yuqiu Zhou, Jian Wang, Fang-Fang Chen, Fuman Jiang, Zhaoling Xuan, Yingrui Li, Chunlei Zhang, Xiaoyu Pan, Jinghui Ren, Lijian Zhao, Zhengyu Zhang, and Peipei Li

Subjects
Adult, Quality Control, Autosomal aneuploidies, medicine.medical_specialty, Down syndrome, lcsh:Internal medicine, Massively parallel sequencing, lcsh:QH426-470, Ultrasound scan, Aneuploidy, Prenatal diagnosis, Chromosome Disorders, Sex chromosomal aneuploidies, Biology, Young Adult, Fetus, Bias, Pregnancy, Prenatal Diagnosis, medicine, Genetics, Humans, Genetics(clinical), lcsh:RC31-1245, Genetics (clinical), Base Composition, Sex Chromosomes, Obstetrics, Noninvasive Fetal Trisomy (NIFTY) test, Computational Biology, DNA, Sequence Analysis, DNA, Middle Aged, medicine.disease, lcsh:Genetics, Cell-free fetal DNA, Technical Advance, Female, Down Syndrome, Trisomy
Abstract

Background Conventional prenatal screening tests, such as maternal serum tests and ultrasound scan, have limited resolution and accuracy. Methods We developed an advanced noninvasive prenatal diagnosis method based on massively parallel sequencing. The Noninvasive Fetal Trisomy (NIFTY) test, combines an optimized Student’s t-test with a locally weighted polynomial regression and binary hypotheses. We applied the NIFTY test to 903 pregnancies and compared the diagnostic results with those of full karyotyping. Results 16 of 16 trisomy 21, 12 of 12 trisomy 18, two of two trisomy 13, three of four 45, X, one of one XYY and two of two XXY abnormalities were correctly identified. But one false positive case of trisomy 18 and one false negative case of 45, X were observed. The test performed with 100% sensitivity and 99.9% specificity for autosomal aneuploidies and 85.7% sensitivity and 99.9% specificity for sex chromosomal aneuploidies. Compared with three previously reported z-score approaches with/without GC-bias removal and with internal control, the NIFTY test was more accurate and robust for the detection of both autosomal and sex chromosomal aneuploidies in fetuses. Conclusion Our study demonstrates a powerful and reliable methodology for noninvasive prenatal diagnosis.

Published
2011

4. The sequence and de novo assembly of the giant panda genome

Author

Xiao Sun, Xiaosen Guo, Xiao Liu, Qibin Li, Siu-Ming Yiu, Ning Qu, Jing Wang, Zhaolei Zhang, Anlong Xu, Carolin Kosiol, Yiran Guo, Xiaodong Fang, Yanling Chen, Tomas Vinar, Jianjun Cao, Desheng Li, Ming Wen, Gane Ka-Shu Wong, Hao Zhang, Bo Li, Feng Tian, Yajun Wang, Wei Fan, Shiping Liu, Bo Mu, Qingle Cai, Zhentao Yang, Oliver A. Ryder, Min Jian, Qing Liu, Lin Fang, Kathleen Cook, Shancen Zhao, Gao Shan, Jingxiang Li, Jing Zhao, Lin He, Mingwei Wang, Qi Wu, Haiyin Wang, Wen Wang, Hongmei Zhu, Michael William Bruford, Junyi Wang, Quanfei Huang, Wanjun Gu, Yuanyuan Ren, Jing Cai, Jing Tian, Yang Zheng, Guohua Yang, Yingrui Li, Huiqing Liang, Guojie Zhang, Yonggui Fu, Yinqi Bai, Qinghui Zhang, Juanbin Zhang, Maynard V. Olson, Songgang Li, Shifeng Cheng, Guo-Dong Wang, Jianwen Li, Chang Yu, Zhongbin Shi, Chen Ye, Na An, Heng Li, Zhi Jiang, Huisong Zheng, Cynthia C. Steiner, Ruiqiang Li, Wubin Qian, Yujie Hu, Wenbo Hu, Hongde Liu, Rasmus Nielsen, Xueying Xie, Tommy Tsan-Yuk Lam, Hemin Zhang, Yongyong Shi, Frederick C. Leung, Jun Wang, Peixiang Ni, Xiuqing Zhang, Dong Dong, Xiaoli Ren, Fuwen Wei, Jiumeng Min, Jue Ruan, Runmao Lin, Zhiqiang Li, Wenhui Nie, Lars Bolund, Dawei Li, Fujun Shen, Zuhong Lu, Ya-Ping Zhang, Karsten Kristiansen, Dejin Zhang, Geng Tian, Nan Qin, Siyuan Lin, Tak-Wah Lam, Xia Wang, Jinhuan Wang, Binghang Liu, Li Li, Xiaoling Wang, Lijia Ma, Yan Zhou, Zhihe Zhang, Zhaoling Xuan, Zhigang Wu, Lizhi Xu, Guoqing Li, Rong Hou, Huanming Yang, Bo Wang, Hancheng Zheng, Jun Li, Yan Huang, and Timing Gong

Subjects
Cancer genome sequencing, Heterozygote, China, Sequence assembly, Receptors, G-Protein-Coupled - genetics, Genomics, Biology, Genome, Polymorphism, Single Nucleotide, Synteny, Article, Receptors, G-Protein-Coupled, Evolution, Molecular, Contig Mapping, Dogs, Tandem repeat, biology.animal, Animals, Humans, Diet - veterinary, Ursidae - classification - genetics - physiology, Conserved Sequence, Ailuropoda melanoleuca, Genetics, Multidisciplinary, Contig, Sequence Analysis, DNA, Genome - genetics, Polymorphism, Single Nucleotide - genetics, Diet, Fertility, Multigene Family, Multigene Family - genetics, Fertility - genetics - physiology, Synteny - genetics, Female, Sequence Alignment, Ursidae, Algorithms, Reference genome, Conserved Sequence - genetics
Abstract

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes. © 2010 Macmillan Publishers Limited. All rights reserved., link_to_OA_fulltext

Published
2009
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5. The genome of the cucumber, Cucumis sativus L

Author

Jian Wu, Jie Guo, Xiaowu Wang, Yuhong Yang, Guangcun Li, Lijia Ma, Zhang Baoxi, Zhouchao Cheng, Shifang Liu, Jianwen Li, Shenhao Wang, Shuang Yang, Lars Bolund, Kui Lin, Shiqiang Liu, Li Li, Hongmei Zhu, Wei Fan, Jing Wang, Lin Fang, Qiuxiang Shi, Zhuo Li, Yang Wu, Xuefeng Li, Ying Li, Ruiqiang Li, Mingwei Wang, Yao Lu, Yingrui Li, Bingyan Xie, Won Kyong Cho, Jue Ruan, Hongkun Zheng, Wubin Qian, Jack E. Staub, Jing Zhao, Bo Li, Xiaodong Fang, Ming Wen, Zhaoling Xuan, Han Miao, Xingfang Gu, Weiwei Jin, Zhigang Wu, Zhentao Yang, Hui Liu, Shengping Zhang, Man Li, Zhangjun Fei, Shaochuan Li, Quanfei Huang, Jae-Yean Kim, Bowen Zhao, Guohua Yang, Zhonghua Zhang, Geng Tian, Dongyuan Liu, Jianjun Cao, Nan Qin, Jun He, Xiaoli Ren, Yi Ren, Huiqing Liang, Min Jian, Zhiqi Jia, Yong Xu, Houxiang Kang, Peixiang Ni, Guojie Zhang, Katarzyna Heller-Uszynska, Guoqing Li, Huanming Yang, Rifei Sun, Sanwen Huang, William J. Lucas, Qingle Cai, Hancheng Zheng, Yuanyuan Ren, Jun Li, Yong Zhang, Yongchen Du, Hailong Yang, Jun Wang, Karsten Kristiansen, Rui Chen, Andrzej Kilian, Shuzhi Jiang, Juanbin Zhang, Songgang Li, Yan Zhou, Asan, Edwin A. G. van der Vossen, Yinqi Bai, Xiuqing Zhang, Yonghua Han, and Zhongbin Shi

Subjects
DNA, Plant, Molecular Sequence Data, arabidopsis-thaliana, Biology, Plant disease resistance, Genes, Plant, Genome, Synteny, phloem, diversity, resistance, PRI Biodiversiteit en Veredeling, Gene Duplication, Botany, expression, Genetics, Arabidopsis thaliana, gene, Gene, Plant Diseases, Repetitive Sequences, Nucleic Acid, Whole genome sequencing, plants, Nucleic acid sequence, food and beverages, ethylene biosynthesis, sequence, biology.organism_classification, Immunity, Innate, PRI Biodiversity and Breeding, DNA Transposable Elements, EPS, Cucumis sativus, Cucumis, rice genome, Genome, Plant
Abstract

Udgivelsesdato: 2009-Dec Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativus var. sativus L., assembled using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies to obtain 72.2-fold genome coverage. The absence of recent whole-genome duplication, along with the presence of few tandem duplications, explains the small number of genes in the cucumber. Our study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, biosynthesis of cucurbitacin and 'fresh green' odor. We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system.

Published
2009
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6. Erratum: The sequence and de novo assembly of the giant panda genome

Author

Mingwei Wang, Desheng Li, Carolin Kosiol, Xiao Sun, Na An, Yang Zheng, Min Jian, Qingle Cai, Yan Huang, Chang Yu, Chen Ye, Peixiang Ni, Juanbin Zhang, Timing Gong, Yiran Guo, Guo-Dong Wang, Zuhong Lu, Guojie Zhang, Lars Bolund, Yongyong Shi, Songgang Li, Gao Shan, Frederick C. Leung, Yajun Wang, Geng Tian, Jun Wang, Xiaoli Ren, Wenhui Nie, Zhiqiang Li, Karsten Kristiansen, Yinqi Bai, Feng Tian, Jing Tian, Tomas Vinar, Tak-Wah Lam, Rasmus Nielsen, Wanjun Gu, Qinghui Zhang, Xiao Liu, Michael William Bruford, Quanfei Huang, Hancheng Zheng, Fujun Shen, Bo Li, Zhi Jiang, Xia Wang, Jianwen Li, Xiaodong Fang, Jun Li, Guohua Yang, Hongde Liu, Qing Liu, Ning Qu, Li Li, Shifeng Cheng, Shancen Zhao, Rong Hou, Heng Li, Jing Cai, Fuwen Wei, Zhu Hongmei, Lin Fang, Ming Wen, Huiqing Liang, Huisong Zheng, Yingrui Li, Jingxiang Li, Jing Zhao, Nan Qin, Junyi Wang, Jinhuan Wang, Binghang Liu, Huanming Yang, Runmao Lin, Maynard V. Olson, Xiaosen Guo, Xiaoling Wang, Tommy Tsan-Yuk Lam, Hao Zhang, Zhaolei Zhang, Zhongbin Shi, Dejin Zhang, Cynthia C. Steiner, Jiumeng Min, Ruiqiang Li, Siyuan Lin, Kathleen Cook, Jue Ruan, Lizhi Xu, Yujie Hu, Xiuqing Zhang, Bo Wang, Siu-Ming Yiu, Wei Fan, Lin He, Guoqing Li, Zhihe Zhang, Yan Zhou, Anlong Xu, Zhigang Wu, Zhaoling Xuan, Dong Dong, Dawei Li, Zhentao Yang, Lijia Ma, Haiyin Wang, Xueying Xie, Gane Ka-Shu Wong, Hemin Zhang, Ya-Ping Zhang, Wubin Qian, Bo Mu, Oliver A. Ryder, Qi Wu, Qibin Li, Wen Wang, Yonggui Fu, Yuanyuan Ren, Jianjun Cao, Jian Wang, Yanling Chen, Shiping Liu, and Wenbo Hu

Subjects
Genetics, Multidisciplinary, biology, Species name, biology.animal, Correct name, Ailuropoda, Sequence assembly, biology.organism_classification, Genome, Ailuropoda melanoleuca, Sequence (medicine)
Abstract

Nature 463, 311–317 (2010) In this Article, the Latin species name of the giant panda was written incorrectly as Ailuropoda melanoleura. The correct name is Ailuropoda melanoleuca.

Published
2010
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