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Li X.,CAS Kunming Institute of Zoology | Fan D.,BGIShenzhen | Zhang W.,University of Chicago | Liu G.,CAS Kunming Institute of Zoology | And 29 more authors.
Nature Communications | Year: 2015

Butterflies are exceptionally diverse but their potential as an experimental system has been limited by the difficulty of deciphering heterozygous genomes and a lack of genetic manipulation technology. Here we use a hybrid assembly approach to construct high-quality reference genomes for Papilio xuthus (contig and scaffold N50: 492kb, 3.4Mb) and Papilio machaon (contig and scaffold N50: 81kb, 1.15Mb), highly heterozygous species that differ in host plant affiliations, and adult and larval colour patterns. Integrating comparative genomics and analyses of gene expression yields multiple insights into butterfly evolution, including potential roles of specific genes in recent diversification. To functionally test gene function, we develop an efficient (up to 92.5%) CRISPR/Cas9 gene editing method that yields obvious phenotypes with three genes, Abdominal-B, ebony and frizzled. Our results provide valuable genomic and technological resources for butterflies and unlock their potential as a genetic model system. © 2015 Macmillan Publishers Limited. All rights reserved.


Chen G.,Guangzhou University of Chinese Medicine | Zhang X.,BGIShenzhen | Li C.,Shenzhen Engineering Laboratory for GenomicsAssisted Animal Breeding | Lin Y.,Guangdong Second ProvincialTraditional Chinese Medicine Hospital | And 2 more authors.
Molecular Medicine Reports | Year: 2014

Tanshinone IIA (TIIA) is widely used for the treatment of a number human diseases, including diabetic nephropathy (DN) (1). The present study was performed to examine the role of the transforming growth factor β (TGFβ)/p65 pathway under TIIA treatment in a glomerular mesangial cell model of DN. Firstly, it was identified that TIIA inhibited the proliferation of HBZY1 cells, while simultaneously suppressing the expression of TGFβ and p65. In addition, glucose-induced HBZY1 cells were treated with TIIA, siTGFβ and sip65. The results revealed that siTGFβ or sip65 were able to inhibit the proliferation of HBZY1 cells as well. Finally, the expression of TGFβ and p65 in a rat model of DN treated with TIIA was detected. The results demonstrated that renal hypertrophy and 24 h urinary protein excretion were ameliorated in TIIA-treated rats with DN. Furthermore, it was revealed that the protein levels of TGFβ and p65 were decreased in the DN rats following TIIA treatment. In conclusion, the present study demonstrated that TGFβ and p65 were activated by TIIA in HBZY1 cells. In addition, the expression of TGFβ and of p65 was downregulated in rats with DN treated with TIIA.


Evans J.D.,U.S. Department of Agriculture | Brown S.J.,Kansas State University | Hackett K.J.J.,U.S. Department of Agriculture | Robinson G.,University of Illinois at Urbana - Champaign | And 23 more authors.
Journal of Heredity | Year: 2013

Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world's terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind. © 2013 Published by Oxford University Press on behalf of The American Genetic Association 2013. This work is written by (a) US Government employee(s) and is in the public domain in the US.


Yang H.,Anhui Agricultural University | Wei C.-L.,Anhui Agricultural University | Liu H.-W.,Anhui Agricultural University | Wu J.-L.,Anhui Agricultural University | And 10 more authors.
PLoS ONE | Year: 2016

Tea is one of the most popular beverages across the world and is made exclusively from cultivars of Camellia sinensis. Many wild relatives of the genus Camellia that are closely related to C. sinensis are native to Southwest China. In this study, we first identified the distinct genetic divergence between C. sinensis and its wild relatives and provided a glimpse into the artificial selection of tea plants at a genome-wide level by analyzing 15,444 genomic SNPs that were identified from 18 cultivated and wild tea accessions using a high-throughput genome-wide restriction site-associated DNA sequencing (RAD-Seq) approach. Six distinct clusters were detected by phylogeny inferrence and principal component and genetic structural analyses, and these clusters corresponded to six Camellia species/varieties. Genetic divergence apparently indicated that C. taliensis var. bangwei is a semi-wild or transient landrace occupying a phylogenetic position between those wild and cultivated tea plants. Cultivated accessions exhibited greater heterozygosity than wild accessions, with the exception of C. taliensis var. bangwei. Thirteen genes with non-synonymous SNPs exhibited strong selective signals that were suggestive of putative artificial selective footprints for tea plants during domestication. The genome-wide SNPs provide a fundamental data resource for assessing genetic relationships, characterizing complex traits, comparing heterozygosity and analyzing putatitve artificial selection in tea plants. © 2016 Yang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Xu Y.,Sun Yat Sen University | Guan L.,BGIShenzhen | Xiao X.,Sun Yat Sen University | Zhang J.,Sun Yat Sen University | And 7 more authors.
Optometry and Vision Science | Year: 2016

Purpose. Mutations in MFRP have been reported to cause autosomal recessive posterior microphthalmia, nanophthalmos, and an ophthalmic syndrome characterized by posterior microphthalmia, high hyperopia, retinitis pigmentosa, foveoschisis, and optic disc drusen. High hyperopia is a consistent sign of this syndrome. The purpose of this study was to detect MFRP mutations in 46 unrelated Chinese probands with high hyperopia. Methods. Clinical data and genomic DNAwere collected from 46 Chinese probands diagnosed as having high hyperopia. Genomic DNA from 42 probands was initially analyzed by whole exome sequencing. MFRP variants were confirmed by Sanger sequencing. The coding sequence of MFRP for four additional probands was also analyzed by Sanger sequencing. Candidate MFRP variants were further validated in available family members and 192 normal individuals. Results. Potential pathogenic compound heterozygous mutations, including c.287-291del (p.P96Lfs 6), c.1615C9T (p.R539C), c.664C9A (p.P222T), c.1150dup (p.H384Pfs 8), and c.1549C9T (p.R517W), were detected in three of the 46 probands included in this study. The clinical data revealed that all patients in this study had high hyperopia of +13.50D or higher and an eye axial length of 16.78mmor less. Electroretinography showed normal responses in a patient with missense mutations and reduced rod responses in another patient with missense and truncation mutations in whomoptical coherence tomography showed developmental cystoid macular degeneration in both eyes. Conclusions. The current study expands our knowledge of the mutation spectrum of MFRP and its associated phenotypes. To our knowledge, this is the first report of MFRP mutations in a Chinese cohort. Copyright © American Academy of Optometry.


Zhang M.,Anhui Medical University | Wu X.,BGIShenzhen | Wu X.,Southern Medical University | Lu W.,Anhui Medical University | And 6 more authors.
Iranian Journal of Basic Medical Sciences | Year: 2015

Objective(s): Genome‐wide association studies have identified a number of genetic variants of telomerase reverse transcriptase (TERT), cleft lip and palate transmembrane1‐like (CLPTM1L) associated with the risk of bladder cancer. Rs401681 polymorphism in TERT‐CLPTM1L was of special interest for bladder cancer risk, whereas the results were inconclusive. Materials and Methods: Publications illustrating the association between rs401681 polymorphism and bladder cancer risk were collected from the Embase, PubMed and Google scholar. Three independent reviewers worked on the data extraction. The meta‐analysis was performed by STATA 12.0. The odds ratio (OR) with 95% confidence interval (CI) was calculated for these data. Results: Six case‐control studies were retrieved reporting a total of 9196 bladder cancer patients and 42570 controls. The strength of the relevance between rs401681 polymorphism and bladder cancer risk was evaluated by Stata 12.0 software. Rs401681[C] allele was identified marginally associated with increased bladder cancer risk, with per allele OR of 1.132 (95% CI=1.080‐1.187, Pheterogeneity=0.701); in the stratified analysis by ethnicity, the increased cancer risk was revealed in Asian and Caucasian groups. Moreover, we also revealed that rs401681 polymorphism was associated with an increased risk of bladder cancer in Asian population with three publications under allele model (OR=3.722, 95% CI=1.311‐10.568, P=0.014), whereas a decreased risk was identified in homozygote model (OR=0.692, 95% CI=0.513‐0.934, P= 0.016) and recessive model (OR=0.728, 95% CI=0.541‐0.980, P=0.036). Conclusion: In summary, our study provided evidence that rs401681 polymorphism is associated with the risk of bladder cancer. © 2015, Mashhad University of Medical Sciences. All rights reserved.


PubMed | BGIShenzhen and Sun Yat Sen University
Type: Journal Article | Journal: International journal of molecular medicine | Year: 2014

Mutations in almost 200 genes are associated with hereditary retinal diseases. Of these diseases, retinitis pigmentosa (RP) is the most common and is genetically and clinically highly heterogeneous. At least 62 genes are associated with RP and mutations in these genes account for approximately half of the cases of disease. In the present study, mutations in the CHM gene, which are known to associate with choroideremia, were identified in six of 157 families with retinitis pigmentosa by whole exome sequencing. No potential pathogenic mutations in the 62 RPassociated genes were found in the six families. Sanger sequencing confirmed the mutations in CHM, including four novel (c.558_559delTT, c.964G>T, c.966delA, c.1166+2T>G) and two known (c.7031G>A and c.1584_1587delTGTT) mutations. Available clinical data suggest an atypical phenotype of choroideremia in these patients compared to that of Caucasians. Overlapping clinical features and atypical phenotypic variation may contribute to the confusion of one another. Awareness of the phenotypic variation and careful clinical examination may facilitate proper clinical diagnosis and genetic counseling of complicated hereditary retinal diseases. Whole exome sequencing therefore is useful in the identification of genetic cause for less clarified hereditary retinal diseases and enriches our understanding of phenotypic variations of gene mutation.


Kang X.,University of Chinese Academy of Sciences | Xia J.,University of Chinese Academy of Sciences | Wang Y.,BGIShenzhen | Xu H.,BGIShenzhen | And 12 more authors.
PLoS ONE | Year: 2016

Background: With the speedy development of sequencing technologies, noninvasive prenatal testing (NIPT) has been widely applied in clinical practice for testing for fetal aneuploidy. The cellfree fetal DNA (cffDNA) concentration in maternal plasma is the most critical parameter for this technology because it affects the accuracy of NIPT-based sequencing for fetal trisomies 21, 18 and 13. Several approaches have been developed to calculate the cffDNA fraction of the total cell-free DNA in the maternal plasma. However, most approaches depend on specific single nucleotide polymorphism (SNP) allele information or are restricted to male fetuses. Methods: In this study, we present an innovative method to accurately deduce the concentration of the cffDNA fraction using only maternal plasma DNA. SNPs were classified into four maternal- fetal genotype combinations and three boundaries were added to capture effective SNP loci in which the mother was homozygous and the fetus was heterozygous. The median value of the concentration of the fetal DNA fraction was estimated using the effective SNPs. A depth-bias correction was performed using simulated data and corresponding regression equations for adjustments when the depth of the sequencing data was below 100-fold or the cffDNA fraction is less than 10%. Results: Using our approach, the median of the relative bias was 0.4% in 18 maternal plasma samples with a median sequencing depth of 125-fold. There was a significant association (r = 0.935) between our estimations and the estimations inferred from the Y chromosome. Furthermore, this approach could precisely estimate a cffDNA fraction as low as 3%, using only maternal plasma DNA at the targeted region with a sequencing depth of 65-fold. We also used PCR instead of parallel sequencing to calculate the cffDNA fraction. There was a significant association (r = 98.2%) between our estimations and those inferred from the Y chromosome. © 2016 Kang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


PubMed | Shenzhen Engineering Laboratory for GenomicsAssisted Animal Breeding, Guangzhou University, Guangdong Second Provincial Traditional Chinese Medicine Hospital, BGIShenzhen and Jinan University
Type: Journal Article | Journal: Molecular medicine reports | Year: 2014

TanshinoneA (TA) is widely used for the treatment of a number human diseases, including diabetic nephropathy (DN)(1). The present study was performed to examine the role of the transforming growth factor (TGF)/p65 pathway under TA treatment in a glomerular mesangial cell model of DN. Firstly, it was identified that TA inhibited the proliferation of HBZY1 cells, while simultaneously suppressing the expression of TGF and p65. In addition, glucose-induced HBZY1 cells were treated with TA, siTGF and sip65. The results revealed that siTGF or sip65 were able to inhibit the proliferation of HBZY1 cells as well. Finally, the expression of TGF and p65 in a rat model of DN treated with TA was detected. The results demonstrated that renal hypertrophy and 24h urinary protein excretion were ameliorated in TA-treated rats with DN. Furthermore, it was revealed that the protein levels of TGF and p65 were decreased in the DN rats following TA treatment. In conclusion, the present study demonstrated that TGF and p65 were activated by TA in HBZY1 cells. In addition, the expression of TGF and of p65 was downregulated in rats with DN treated with TA.


Wang Y.,Nanjing Agricultural University | Lu J.,Nanjing Agricultural University | Chen S.,CAS Institute of Genetics and Developmental Biology | Shu L.,BGIShenzhen | And 7 more authors.
Journal of Integrative Plant Biology | Year: 2014

This study was designed to reveal the genome-wide distribution of presence/absence variation (PAV) and to establish a database of polymorphic PAV markers in soybean. The 33 soybeanwhole-genome sequences were compared to each other with that of Williams 82 as a reference genome. A total of 33,127 PAVs were detected and 28,912 PAV markers with their primer sequences were designed as the database NJAUSoyPAV_1.0. The PAVs scattered on whole genome while only 518 (1.8%) overlapped with simple sequence repeats (SSRs) in BARCSOYSSR_1.0 database. In a random sample of 800 PAVs, 713 (89.13%) showed polymorphism among the 12 differential genotypes. Using 126 PAVs and 108 SSRs to test a Chinese soybean germplasm collection composed of 828 Glycine soja Sieb. et Zucc. and Glycine max (L.) Merr. accessions, the per locus allele number and its variation appeared less in PAVs than in SSRs. The distinctness among alleles/bands of PCR (polymerase chain reaction) products showed better in PAVs than in SSRs, potential in accuratemarkerassisted allele selection. The association mapping results showed SSR+PAV was more powerful than any single marker systems. The NJAUSoyPAV_1.0 database has enriched the source of PCR markers, andmay fit the materials with a range of per locus allele numbers, if jointly used with SSR markers. © 2014 Institute of Botany, Chinese Academy of Sciences.

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