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Xiao Y, Xiao Z, Liu L, Ma Y, Zhao H, Wu Y, Huang J, Xu P, Liu J, Li J. Innovative approach for high-throughput exploiting sex-specific markers in Japanese parrotfish Oplegnathus fasciatus. Gigascience 2024; 13:giae045. [PMID: 39028586 PMCID: PMC11258905 DOI: 10.1093/gigascience/giae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/21/2024] [Accepted: 06/22/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND The use of sex-specific molecular markers has become a prominent method in enhancing fish production and economic value, as well as providing a foundation for understanding the complex molecular mechanisms involved in fish sex determination. Over the past decades, research on male and female sex identification has predominantly employed molecular biology methodologies such as restriction fragment length polymorphism, random amplification of polymorphic DNA, simple sequence repeat, and amplified fragment length polymorphism. The emergence of high-throughput sequencing technologies, particularly Illumina, has led to the utilization of single nucleotide polymorphism and insertion/deletion variants as significant molecular markers for investigating sex identification in fish. The advancement of sex-controlled breeding encounters numerous challenges, including the inefficiency of current methods, intricate experimental protocols, high costs of development, elevated rates of false positives, marker instability, and cumbersome field-testing procedures. Nevertheless, the emergence and swift progress of PacBio high-throughput sequencing technology, characterized by its long-read output capabilities, offers novel opportunities to overcome these obstacles. FINDINGS Utilizing male/female assembled genome information in conjunction with short-read sequencing data survey and long-read PacBio sequencing data, a catalog of large-segment (>100 bp) insertion/deletion genetic variants was generated through a genome-wide variant site-scanning approach with bidirectional comparisons. The sequence tagging sites were ranked based on the long-read depth of the insertion/deletion site, with markers exhibiting lower long-read depth being considered more effective for large-segment deletion variants. Subsequently, a catalog of bulk primers and simulated PCR for the male/female variant loci was developed, incorporating primer design for the target region and electronic PCR (e-PCR) technology. The Japanese parrotfish (Oplegnathus fasciatus), belonging to the Oplegnathidae family within the Centrarchiformes order, holds significant economic value as a rocky reef fish indigenous to East Asia. The criteria for rapid identification of male and female differences in Japanese parrotfish were established through agarose gel electrophoresis, which revealed 2 amplified bands for males and 1 amplified band for females. A high-throughput identification catalog of sex-specific markers was then constructed using this method, resulting in the identification of 3,639 (2,786 INS/853 DEL, ♀ as reference) and 3,672 (2,876 INS/833 DEL, ♂ as reference) markers in conjunction with 1,021 and 894 high-quality genetic sex identification markers, respectively. Sixteen differential loci were randomly chosen from the catalog for validation, with 11 of them meeting the criteria for male/female distinctions. The implementation of cost-effective and efficient technological processes would facilitate the rapid advancement of genetic breeding through expediting the high-throughput development of sex genetic markers for various species. CONCLUSIONS Our study utilized assembled genome information from male and female individuals obtained from PacBio, in addition to data from short-read sequencing data survey and long-read PacBio sequencing data. We extensively employed genome-wide variant site scanning and identification, high-throughput primer design of target regions, and e-PCR batch amplification, along with statistical analysis and ranking of the long-read depth of the variant sites. Through this integrated approach, we successfully compiled a catalog of large insertion/deletion sites (>100 bp) in both male and female Japanese parrotfish.
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Affiliation(s)
- Yongshuang Xiao
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhizhong Xiao
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Weihai Hao Huigan Marine Biotechnology Co., Weihai, 26449, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd, East Lake High-Tech Zone, Wuhan, 430073, China
| | - Yuting Ma
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Haixia Zhao
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yanduo Wu
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jinwei Huang
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Pingrui Xu
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jing Liu
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jun Li
- Center for Ocean Mega-Science, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
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Chen J, Guo JT. Structural and functional analysis of somatic coding and UTR indels in breast and lung cancer genomes. Sci Rep 2021; 11:21178. [PMID: 34707120 PMCID: PMC8551294 DOI: 10.1038/s41598-021-00583-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/14/2021] [Indexed: 11/24/2022] Open
Abstract
Insertions and deletions (Indels) represent one of the major variation types in the human genome and have been implicated in diseases including cancer. To study the features of somatic indels in different cancer genomes, we investigated the indels from two large samples of cancer types: invasive breast carcinoma (BRCA) and lung adenocarcinoma (LUAD). Besides mapping somatic indels in both coding and untranslated regions (UTRs) from the cancer whole exome sequences, we investigated the overlap between these indels and transcription factor binding sites (TFBSs), the key elements for regulation of gene expression that have been found in both coding and non-coding sequences. Compared to the germline indels in healthy genomes, somatic indels contain more coding indels with higher than expected frame-shift (FS) indels in cancer genomes. LUAD has a higher ratio of deletions and higher coding and FS indel rates than BRCA. More importantly, these somatic indels in cancer genomes tend to locate in sequences with important functions, which can affect the core secondary structures of proteins and have a bigger overlap with predicted TFBSs in coding regions than the germline indels. The somatic CDS indels are also enriched in highly conserved nucleotides when compared with germline CDS indels.
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Affiliation(s)
- Jing Chen
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jun-Tao Guo
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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Sukumar S, Krishnan A, Banerjee S. An Overview of Bioinformatics Resources for SNP Analysis. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Kennedy T, Rinker D, Broadie K. Genetic background mutations drive neural circuit hyperconnectivity in a fragile X syndrome model. BMC Biol 2020; 18:94. [PMID: 32731855 PMCID: PMC7392683 DOI: 10.1186/s12915-020-00817-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/19/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Neural circuits are initially assembled during development when neurons synapse with potential partners and later refined as appropriate connections stabilize into mature synapses while inappropriate contacts are eliminated. Disruptions to this synaptogenic process impair connectivity optimization and can cause neurodevelopmental disorders. Intellectual disability (ID) and autism spectrum disorder (ASD) are often characterized by synaptic overgrowth, with the maintenance of immature or inappropriate synapses. Such synaptogenic defects can occur through mutation of a single gene, such as fragile X mental retardation protein (FMRP) loss causing the neurodevelopmental disorder fragile X syndrome (FXS). FXS represents the leading heritable cause of ID and ASD, but many other genes that play roles in ID and ASD have yet to be identified. RESULTS In a Drosophila FXS disease model, one dfmr150M null mutant stock exhibits previously unreported axonal overgrowths at developmental and mature stages in the giant fiber (GF) escape circuit. These excess axon projections contain both chemical and electrical synapse markers, indicating mixed synaptic connections. Extensive analyses show these supernumerary synapses connect known GF circuit neurons, rather than new, inappropriate partners, indicating hyperconnectivity within the circuit. Despite the striking similarities to well-characterized FXS synaptic defects, this new GF circuit hyperconnectivity phenotype is driven by genetic background mutations in this dfmr150M stock. Similar GF circuit synaptic overgrowth is not observed in independent dfmr1 null alleles. Bulked segregant analysis (BSA) was combined with whole genome sequencing (WGS) to identify the quantitative trait loci (QTL) linked to neural circuit hyperconnectivity. The results reveal 8 QTL associated with inappropriate synapse formation and maintenance in the dfmr150M mutant background. CONCLUSIONS Synaptogenesis is a complex, precisely orchestrated neurodevelopmental process with a large cohort of gene products coordinating the connectivity, synaptic strength, and excitatory/inhibitory balance between neuronal partners. This work identifies a number of genetic regions that contain mutations disrupting proper synaptogenesis within a particularly well-mapped neural circuit. These QTL regions contain potential new genes involved in synapse formation and refinement. Given the similarity of the synaptic overgrowth phenotype to known ID and ASD inherited conditions, identifying these genes should increase our understanding of these devastating neurodevelopmental disease states.
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Affiliation(s)
- Tyler Kennedy
- Department of Biological Sciences, Vanderbilt University and Medical Center, Nashville, TN, 37235, USA
| | - David Rinker
- Department of Biological Sciences, Vanderbilt University and Medical Center, Nashville, TN, 37235, USA
| | - Kendal Broadie
- Department of Biological Sciences, Vanderbilt University and Medical Center, Nashville, TN, 37235, USA.
- Department of Cell and Developmental Biology, Vanderbilt University and Medical Center, Nashville, TN, 37235, USA.
- Vanderbilt Brain Institute, Vanderbilt University and Medical Center, Nashville, TN, 37235, USA.
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Hu Y, Sui Z, Zhou W, Wang J, Jiang M, Chen H, Zhang J, Zhang W, Feng X, Lei Y, Xiao B, Guo P. Heterozygous Single Nucleotide Polymorphic Loci in Haploid Gametophytes of Gracilariopsis lemaneiformis (Rhodophyta). Front Genet 2020; 10:1256. [PMID: 31921299 PMCID: PMC6915112 DOI: 10.3389/fgene.2019.01256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/14/2019] [Indexed: 12/18/2022] Open
Abstract
Gracilariopsis lemaneiformis is an important commercial macroalga. Whole-genome resequencing was conducted to identify single nucleotide polymorphisms (SNPs) in parental gametophytes and 60 F1 gametophytes of Gp. lemaneiformis in this study, and 9,989 SNPs located in nonrepetitive sequences were obtained. Among these SNPs, 92.02% of loci were identified as having a heterozygous genotype in at least one gametophyte, and 48.07% of loci had identical heterozygous genotypes in the 62 gametophytes. For each gametophyte, the proportions of homozygous and heterozygous loci ranged between 13.74 and 21.61% (mean of 17.04%) and between 66.36 and 83.59% (mean of 77.12%), respectively. The remainder were missing loci, representing an average 5.84%. Sources of heterozygous SNPs were free of exogenous DNA contamination, cross contamination among individuals, plastid and mitochondrial sequences, chimeras of different thallus parts or different cells, and repetitive sequences. Genotypes of heterozygous SNPs were verified by Sanger sequencing of PCR products and monoclones. Duplications of chromosomal rearrangements in the genome of Gp. lemaneiformis might explain the presence of heterozygous SNPs in haploid gametophytes.
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Affiliation(s)
- Yiyi Hu
- Key Laboratory of Marine Genetics and Breeding (Ocean Univeristy of China), Ministry of Education, Qingdao, China
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding (Ocean Univeristy of China), Ministry of Education, Qingdao, China
| | - Wei Zhou
- Key Laboratory of Marine Genetics and Breeding (Ocean Univeristy of China), Ministry of Education, Qingdao, China
| | - Jinguo Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean Univeristy of China), Ministry of Education, Qingdao, China
| | - Minjie Jiang
- Key Laboratory of Marine Genetics and Breeding (Ocean Univeristy of China), Ministry of Education, Qingdao, China
| | - Haihong Chen
- Key Laboratory of Marine Genetics and Breeding (Ocean Univeristy of China), Ministry of Education, Qingdao, China
| | - Jingyu Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean Univeristy of China), Ministry of Education, Qingdao, China
| | - Wei Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean Univeristy of China), Ministry of Education, Qingdao, China
| | - Xiaoqing Feng
- Key Laboratory of Marine Genetics and Breeding (Ocean Univeristy of China), Ministry of Education, Qingdao, China
| | - Yuehua Lei
- Key Laboratory of Marine Genetics and Breeding (Ocean Univeristy of China), Ministry of Education, Qingdao, China
| | - Baoheng Xiao
- Key Laboratory of Marine Genetics and Breeding (Ocean Univeristy of China), Ministry of Education, Qingdao, China
| | - Peng Guo
- Key Laboratory of Marine Genetics and Breeding (Ocean Univeristy of China), Ministry of Education, Qingdao, China
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Fu Y, Zhong X, Pan J, Liang K, Liu Y, Peng B, Hu X, Huang N. QTLs identification for nitrogen and phosphorus uptake-related traits using ultra-high density SNP linkage. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110209. [PMID: 31521212 DOI: 10.1016/j.plantsci.2019.110209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
To understand the genetic basis of nitrogen and phosphorus uptake in the cultivated rice, quantitative trait loci (QTL) analysis for 7 nitrogen and phosphorus uptake-related traits including above-ground biomass (AGB), leaf colour value (SPAD) in heading stage, grain nitrogen concentration (GNC), grain nitrogen content of the plant, total nitrogen content (TNC), grain phosphorus concentration, total phosphorus content (TPC) were conducted using SNP markers in a F2 population derived from a cross between GH128 and W6827. A total of 21 QTLs for nitrogen and phosphorus uptake-related traits distributed in 16 regions along 6 chromosomes were detected using a high density genetic map consisting of 1582 bin markers, with QTLs maximum explaining 8.19% of the phenotypic variation. Nine QTLs (42.9% of total QTLs) were detected on chromosome 2. Among them, two QTL clusters including AGB, TNC, TPC and GNC were also detected in the region bin 140 and bin 146 on the chromosome 2. The distance between the two clusters was only 4.1 cM. The presence of QTL clusters has important significance and could be useful in molecular marker assisted breeding. These genomic regions might be deployed for the simultaneous improving the use efficiency of nitrogen and phosphorus in rice breeding.
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Affiliation(s)
- Youqiang Fu
- The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangzhou 510640, China
| | - Xuhua Zhong
- The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangzhou 510640, China
| | - Junfeng Pan
- The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangzhou 510640, China
| | - Kaiming Liang
- The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangzhou 510640, China
| | - Yanzhuo Liu
- The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangzhou 510640, China
| | - Bilin Peng
- The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangzhou 510640, China
| | - Xiangyu Hu
- The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangzhou 510640, China
| | - Nongrong Huang
- The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangzhou 510640, China.
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Ogi S, Matsuda A, Otsuka Y, Liu Z, Satoh T, Satoh AK. Syndapin constricts microvillar necks to form a united rhabdomere in Drosophila photoreceptors. Development 2019; 146:dev.169292. [PMID: 31371377 DOI: 10.1242/dev.169292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/22/2019] [Indexed: 01/24/2023]
Abstract
Drosophila photoreceptors develop from polarized epithelial cells that have apical and basolateral membranes. During morphogenesis, the apical membranes subdivide into a united bundle of photosensory microvilli (rhabdomeres) and a surrounding supporting membrane (stalk). By EMS-induced mutagenesis screening, we found that the F-Bin/Amphiphysin/Rvs (F-BAR) protein syndapin is essential for apical membrane segregation. The analysis of the super-resolution microscopy, STORM and the electron microscopy suggest that syndapin localizes to the neck of the microvilli at the base of the rhabdomere. Syndapin and moesin are required to constrict the neck of the microvilli to organize the membrane architecture at the base of the rhabdomere, to exclude the stalk membrane. Simultaneous loss of syndapin along with the microvilli adhesion molecule chaoptin significantly enhanced the disruption of stalk-rhabdomere segregation. However, loss of the factors involving endocytosis do not interfere. These results indicated syndapin is most likely functioning through its membrane curvature properties, and not through endocytic processes for stalk-rhabdomere segregation. Elucidation of the mechanism of this unconventional domain formation will provide novel insights into the field of cell biology.
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Affiliation(s)
- Sakiko Ogi
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1, Kagamiyama, Higashi-hiroshima, Hiroshima 739-8521, Japan
| | - Atsushi Matsuda
- National Institute of Information and Communications Technology, Advanced ICT Research Institute, 588-2, Iwaoka, Nishi-ku, Kobe 651-2492, Japan
| | - Yuna Otsuka
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1, Kagamiyama, Higashi-hiroshima, Hiroshima 739-8521, Japan
| | - Ziguang Liu
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1, Kagamiyama, Higashi-hiroshima, Hiroshima 739-8521, Japan.,Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Xuefu Road No. 368, Nangang District, Harbin, Heilongjiang 150-086, China
| | - Takunori Satoh
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1, Kagamiyama, Higashi-hiroshima, Hiroshima 739-8521, Japan
| | - Akiko K Satoh
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1, Kagamiyama, Higashi-hiroshima, Hiroshima 739-8521, Japan
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Crespo-Piazuelo D, Criado-Mesas L, Revilla M, Castelló A, Fernández AI, Folch JM, Ballester M. Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs. PLoS One 2019; 14:e0218862. [PMID: 31246983 PMCID: PMC6597088 DOI: 10.1371/journal.pone.0218862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
The selection in commercial swine breeds for meat-production efficiency has been increasing among the past decades, reducing the intramuscular fat content, which has changed the sensorial and technological properties of pork. Through processes of natural adaptation and selective breeding, the accumulation of mutations has driven the genetic divergence between pig breeds. The most common and well-studied mutations are single-nucleotide polymorphisms (SNPs). However, insertions and deletions (indels) usually represents a fifth part of the detected mutations and should also be considered for animal breeding. In the present study, three different programs (Dindel, SAMtools mpileup, and GATK) were used to detect indels from Whole Genome Sequencing data of Iberian boars and Landrace sows. A total of 1,928,746 indels were found in common with the three programs. The VEP tool predicted that 1,289 indels may have a high impact on protein sequence and function. Ten indels inside genes related with lipid metabolism were genotyped in pigs from three different backcrosses with Iberian origin, obtaining different allelic frequencies on each backcross. Genome-Wide Association Studies performed in the Longissimus dorsi muscle found an association between an indel located in the C1q and TNF related 12 (C1QTNF12) gene and the amount of eicosadienoic acid (C20:2(n-6)).
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Affiliation(s)
- Daniel Crespo-Piazuelo
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- * E-mail:
| | - Lourdes Criado-Mesas
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
| | - Manuel Revilla
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Anna Castelló
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Ana I. Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Josep M. Folch
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Maria Ballester
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, Spain
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Arslan M, Devisetty UK, Porsch M, Große I, Müller JA, Michalski SG. RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. BMC Genomics 2019; 20:489. [PMID: 31195970 PMCID: PMC6567414 DOI: 10.1186/s12864-019-5886-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 06/05/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Juncus effusus L. (family: Juncaceae; order: Poales) is a helophytic rush growing in temperate damp or wet terrestrial habitats and is of almost cosmopolitan distribution. The species has been studied intensively with respect to its interaction with co-occurring plants as well as microbes being involved in major biogeochemical cycles. J. effusus has biotechnological value as component of Constructed Wetlands where the plant has been employed in phytoremediation of contaminated water. Its genome has not been sequenced. RESULTS In this study we carried out functional annotation and polymorphism analysis of de novo assembled RNA-Seq data from 18 genotypes using 249 million paired-end Illumina HiSeq reads and 2.8 million 454 Titanium reads. The assembly comprised 158,591 contigs with a mean contig length of 780 bp. The assembly was annotated using the dammit! annotation pipeline, which queries the databases OrthoDB, Pfam-A, Rfam, and runs BUSCO (Benchmarking Single-Copy Ortholog genes). In total, 111,567 contigs (70.3%) were annotated with functional descriptions, assigned gene ontology terms, and conserved protein domains, which resulted in 30,932 non-redundant gene sequences. Results of BUSCO and KEGG pathway analyses were similar for J. effusus as for the well-studied members of the Poales, Oryza sativa and Sorghum bicolor. A total of 566,433 polymorphisms were identified in transcribed regions with an average frequency of 1 polymorphism in every 171 bases. CONCLUSIONS The transcriptome assembly was of high quality and genome coverage was sufficient for global analyses. This annotated knowledge resource can be utilized for future gene expression analysis, genomic feature comparisons, genotyping, primer design, and functional genomics in J. effusus.
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Affiliation(s)
- Muhammad Arslan
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr, 15, Leipzig, Germany.,Institute for Biology V (Environmental Research), RWTH Aachen University, Templergraben 55, 52062, Aachen, Germany
| | | | - Martin Porsch
- Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saale), Germany.,Core Facility Deep Sequencing, Martin-Luther-University Halle-Wittenberg, Magdeburger Str. 2, 06112, Halle (Saale), Germany
| | - Ivo Große
- Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Jochen A Müller
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr, 15, Leipzig, Germany.
| | - Stefan G Michalski
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Str. 4, 06120, Halle (Saale), Germany
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Big Lessons from Tiny Flies: Drosophila melanogaster as a Model to Explore Dysfunction of Dopaminergic and Serotonergic Neurotransmitter Systems. Int J Mol Sci 2018; 19:ijms19061788. [PMID: 29914172 PMCID: PMC6032372 DOI: 10.3390/ijms19061788] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 12/31/2022] Open
Abstract
The brain of Drosophila melanogaster is comprised of some 100,000 neurons, 127 and 80 of which are dopaminergic and serotonergic, respectively. Their activity regulates behavioral functions equivalent to those in mammals, e.g., motor activity, reward and aversion, memory formation, feeding, sexual appetite, etc. Mammalian dopaminergic and serotonergic neurons are known to be heterogeneous. They differ in their projections and in their gene expression profile. A sophisticated genetic tool box is available, which allows for targeting virtually any gene with amazing precision in Drosophila melanogaster. Similarly, Drosophila genes can be replaced by their human orthologs including disease-associated alleles. Finally, genetic manipulation can be restricted to single fly neurons. This has allowed for addressing the role of individual neurons in circuits, which determine attraction and aversion, sleep and arousal, odor preference, etc. Flies harboring mutated human orthologs provide models which can be interrogated to understand the effect of the mutant protein on cell fate and neuronal connectivity. These models are also useful for proof-of-concept studies to examine the corrective action of therapeutic strategies. Finally, experiments in Drosophila can be readily scaled up to an extent, which allows for drug screening with reasonably high throughput.
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11
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Abstract
The CRISPR-CRISPR-associated (Cas) nuclease system offers the ability to perform unprecedented functional genetic experiments and the promise of therapy for a variety of genetic disorders. The understanding of factors contributing to CRISPR targeting efficacy and specificity continues to evolve. As CRISPR systems rely on Watson-Crick base pairing to ultimately mediate genomic cleavage, it logically follows that genetic variation would affect CRISPR targeting by increasing or decreasing sequence homology at on-target and off-target sites or by altering protospacer adjacent motifs. Numerous efforts have been made to document the extent of human genetic variation, which can serve as resources to understand and mitigate the effect of genetic variation on CRISPR targeting. Here, we review efforts to elucidate the effect of human genetic variation on CRISPR targeting at on-target and off-target sites with considerations for laboratory experiments and clinical translation of CRISPR-based therapies.
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Affiliation(s)
- Matthew C. Canver
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - J. Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
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12
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Hakeda-Suzuki S, Takechi H, Kawamura H, Suzuki T. Two receptor tyrosine phosphatases dictate the depth of axonal stabilizing layer in the visual system. eLife 2017; 6:31812. [PMID: 29116043 PMCID: PMC5683756 DOI: 10.7554/elife.31812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/03/2017] [Indexed: 11/13/2022] Open
Abstract
Formation of a functional neuronal network requires not only precise target recognition, but also stabilization of axonal contacts within their appropriate synaptic layers. Little is known about the molecular mechanisms underlying the stabilization of axonal connections after reaching their specifically targeted layers. Here, we show that two receptor protein tyrosine phosphatases (RPTPs), LAR and Ptp69D, act redundantly in photoreceptor afferents to stabilize axonal connections to the specific layers of the Drosophila visual system. Surprisingly, by combining loss-of-function and genetic rescue experiments, we found that the depth of the final layer of stable termination relied primarily on the cumulative amount of LAR and Ptp69D cytoplasmic activity, while specific features of their ectodomains contribute to the choice between two synaptic layers, M3 and M6, in the medulla. These data demonstrate how the combination of overlapping downstream but diversified upstream properties of two RPTPs can shape layer-specific wiring.
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Affiliation(s)
- Satoko Hakeda-Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroki Takechi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hinata Kawamura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Takashi Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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13
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Iquebal MA, Jaiswal S, Mahato AK, Jayaswal PK, Angadi UB, Kumar N, Sharma N, Singh AK, Srivastav M, Prakash J, Singh SK, Khan K, Mishra RK, Rajan S, Bajpai A, Sandhya BS, Nischita P, Ravishankar KV, Dinesh MR, Rai A, Kumar D, Sharma TR, Singh NK. MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation. Sci Rep 2017; 7:14968. [PMID: 29097776 PMCID: PMC5668432 DOI: 10.1038/s41598-017-14998-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/20/2017] [Indexed: 01/20/2023] Open
Abstract
Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world’s first web-based genomic resources for genetic improvement and germplasm management of mango.
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Affiliation(s)
- M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Ajay Kumar Mahato
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Pawan K Jayaswal
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Neeraj Kumar
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Nimisha Sharma
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anand K Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Jai Prakash
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S K Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kasim Khan
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | - Rupesh K Mishra
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | - Shailendra Rajan
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | - Anju Bajpai
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | - B S Sandhya
- ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | | | - K V Ravishankar
- ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - M R Dinesh
- ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India.
| | - Tilak R Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Nagendra K Singh
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
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14
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Ren X, Holsteens K, Li H, Sun J, Zhang Y, Liu LP, Liu Q, Ni JQ. Genome editing in Drosophila melanogaster: from basic genome engineering to the multipurpose CRISPR-Cas9 system. SCIENCE CHINA-LIFE SCIENCES 2017; 60:476-489. [PMID: 28527116 DOI: 10.1007/s11427-017-9029-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/05/2017] [Indexed: 12/16/2022]
Abstract
Nowadays, genome editing tools are indispensable for studying gene function in order to increase our knowledge of biochemical processes and disease mechanisms. The extensive availability of mutagenesis and transgenesis tools make Drosophila melanogaster an excellent model organism for geneticists. Early mutagenesis tools relied on chemical or physical methods, ethyl methane sulfonate (EMS) and X-rays respectively, to randomly alter DNA at a nucleotide or chromosomal level. Since the discovery of transposable elements and the availability of the complete fly genome, specific genome editing tools, such as P-elements, zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), have undergone rapid development. Currently, one of the leading and most effective contemporary tools is the CRISPR-cas9 system made popular because of its low cost, effectiveness, specificity and simplicity of use. This review briefly addresses the most commonly used mutagenesis and transgenesis tools in Drosophila, followed by an in-depth review of the multipurpose CRISPR-Cas9 system and its current applications.
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Affiliation(s)
- Xingjie Ren
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Kristof Holsteens
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Haiyi Li
- French International School of Hong Kong, Hong Kong SAR, 999000, China
| | - Jin Sun
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yifan Zhang
- Department of Biology, University of California, San Diego, 92093, USA
| | - Lu-Ping Liu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Qingfei Liu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
| | - Jian-Quan Ni
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, 100084, China.
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15
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Abstract
The fruit fly Drosophila melanogaster offers a host of advantages for studying the biology of aging: a well-understood biology, a wide range of genetic reagents, well-defined dietary requirements, and a relatively short life span, with a median of ~80 days and maximum ~100 days. Several phenotypes can be used to assess the aging process, but the simplest and most widely used metric is length of life. Here we describe a standard life span assay for Drosophila housed on a simple sugar/yeast diet.
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Affiliation(s)
- Matthew D. W. Piper
- Institute of Healthy Ageing and Department Genetics, Evolution and
Environment, University College London, Gower St, London, UK ,School of Biological Sciences, Monash University, Clayton, Victoria 3800 Australia
| | - Linda Partridge
- Institute of Healthy Ageing and Department Genetics, Evolution and
Environment, University College London, Gower St, London, UK ,Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Köln, Germany
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16
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Wang Q, Heizer E, Rosa BA, Wildman SA, Janetka JW, Mitreva M. Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 39:201-211. [PMID: 26829384 PMCID: PMC4789095 DOI: 10.1016/j.meegid.2016.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/29/2015] [Accepted: 01/28/2016] [Indexed: 01/18/2023]
Abstract
Insertions and deletions (indels) are important sequence variants that are considered as phylogenetic markers that reflect evolutionary adaptations in different species. In an effort to systematically study indels specific to the phylum Nematoda and their structural impact on the proteins bearing them, we examined over 340,000 polypeptides from 21 nematode species spanning the phylum, compared them to non-nematodes and identified indels unique to nematode proteins in more than 3000 protein families. Examination of the amino acid composition revealed uneven usage of amino acids for insertions and deletions. The amino acid composition and cost, along with the secondary structure constitution of the indels, were analyzed in the context of their biological pathway associations. Species-specific indels could enable indel-based targeting for drug design in pathogens/parasites. Therefore, we screened the spatial locations of the indels in the parasite's protein 3D structures, determined the location of the indel and identified potential unique drug targeting sites. These indels could be confirmed by RNA-Seq data. Examples are presented illustrating the close proximity of some indels to established small-molecule binding pockets that can potentially facilitate selective targeting to the parasites and bypassing their host, thus reducing or eliminating the toxicity of the potential drugs. This study presents an approach for understanding the adaptation of pathogens/parasites at a molecular level, and outlines a strategy to identify such nematode-selective targets that remain essential to the organism. With further experimental characterization and validation, it opens a possible channel for the development of novel treatments with high target specificity, addressing both host toxicity and resistance concerns.
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Affiliation(s)
- Qi Wang
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Esley Heizer
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Bruce A Rosa
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Scott A Wildman
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - James W Janetka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Ave., St. Louis, MO, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA; Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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17
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Iwanami N, Nakamura Y, Satoh T, Liu Z, Satoh AK. Rab6 Is Required for Multiple Apical Transport Pathways but Not the Basolateral Transport Pathway in Drosophila Photoreceptors. PLoS Genet 2016; 12:e1005828. [PMID: 26890939 PMCID: PMC4758697 DOI: 10.1371/journal.pgen.1005828] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 01/05/2016] [Indexed: 11/30/2022] Open
Abstract
Polarized membrane trafficking is essential for the construction and maintenance of multiple plasma membrane domains of cells. Highly polarized Drosophila photoreceptors are an excellent model for studying polarized transport. A single cross-section of Drosophila retina contains many photoreceptors with 3 clearly differentiated plasma membrane domains: a rhabdomere, stalk, and basolateral membrane. Genome-wide high-throughput ethyl methanesulfonate screening followed by precise immunohistochemical analysis identified a mutant with a rare phenotype characterized by a loss of 2 apical transport pathways with normal basolateral transport. Rapid gene identification using whole-genome resequencing and single nucleotide polymorphism mapping identified a nonsense mutation of Rab6 responsible for the apical-specific transport deficiency. Detailed analysis of the trafficking of a major rhabdomere protein Rh1 using blue light-induced chromophore supply identified Rab6 as essential for Rh1 to exit the Golgi units. Rab6 is mostly distributed from the trans-Golgi network to a Golgi-associated Rab11-positive compartment that likely recycles endosomes or transport vesicles going to recycling endosomes. Furthermore, the Rab6 effector, Rich, is required for Rab6 recruitment in the trans-Golgi network. Moreover, a Rich null mutation phenocopies the Rab6 null mutant, indicating that Rich functions as a guanine nucleotide exchange factor for Rab6. The results collectively indicate that Rab6 and Rich are essential for the trans-Golgi network–recycling endosome transport of cargoes destined for 2 apical domains. However, basolateral cargos are sorted and exported from the trans-Golgi network in a Rab6-independent manner. Cells in animal bodies have multiple plasma membrane domains; this polarized characteristic of cells is essential for their specific functions. Selective membrane transport pathways play key roles in the construction and maintenance of polarized structures. Drosophila photoreceptors with multiple plasma membrane domains are an excellent model of polarized transport. We performed genetic screening and identified a Rab6 null mutant with a rare phenotype characterized by a loss of 2 apical transport pathways with normal basolateral transport. Although Rab6 functions in the Golgi are well known, its function in polarized transport was unexpected. Here, we found that Rab6 and its effector, Rich, are required for multiple apical transport pathways but not the basolateral transport pathway. Our findings strongly indicate that the membrane proteins delivered to multiple polarized domains are not sorted simultaneously: basolateral cargos are segregated before the Rab6-dependent process, and cargos going to multiple apical domains are sorted after Rab6-dependent transport from the trans-Golgi network to the Golgi-associated Rab11-positive compartment, which presumably recycles endosomes. Our finding of the function of Rab6 in polarized transport will elucidate the molecular mechanisms of polarized transport.
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Affiliation(s)
- Nozomi Iwanami
- Division of Life Science, Graduate School of Integral Arts and Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yuri Nakamura
- Division of Life Science, Graduate School of Integral Arts and Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takunori Satoh
- Division of Life Science, Graduate School of Integral Arts and Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Ziguang Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Akiko K. Satoh
- Division of Life Science, Graduate School of Integral Arts and Science, Hiroshima University, Higashi-Hiroshima, Japan
- * E-mail:
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18
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Wang F, Jiang L, Chen Y, Haelterman NA, Bellen HJ, Chen R. FlyVar: a database for genetic variation in Drosophila melanogaster. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav079. [PMID: 26289428 PMCID: PMC4541374 DOI: 10.1093/database/bav079] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 07/20/2015] [Indexed: 11/12/2022]
Abstract
FlyVar is a publicly and freely available platform that addresses the increasing need of next generation sequencing data analysis in the Drosophila research community. It is composed of three parts. First, a database that contains 5.94 million DNA polymorphisms found in Drosophila melanogaster derived from whole genome shotgun sequencing of 612 genomes of D. melanogaster. In addition, a list of 1094 dispensable genes has been identified. Second, a graphical user interface (GUI) has been implemented to allow easy and flexible queries of the database. Third, a set of interactive online tools enables filtering and annotation of genomic sequences obtained from individual D. melanogaster strains to identify candidate mutations. FlyVar permits the analysis of next generation sequencing data without the need of extensive computational training or resources. Database URL: www.iipl.fudan.edu.cn/FlyVar.
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Affiliation(s)
- Fei Wang
- Shanghai Key Lab of Intelligent Information Processing, School of Computer Science and Technology, Fudan University, Shanghai, China;
| | - Lichun Jiang
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, and
| | - Yong Chen
- Shanghai Key Lab of Intelligent Information Processing, School of Computer Science and Technology, Fudan University, Shanghai, China
| | - Nele A Haelterman
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, and Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA; Howard Hughes Medical Institute
| | - Rui Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, and
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19
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Identification of Laying-Related SNP Markers in Geese Using RAD Sequencing. PLoS One 2015; 10:e0131572. [PMID: 26181055 PMCID: PMC4504669 DOI: 10.1371/journal.pone.0131572] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 06/03/2015] [Indexed: 12/18/2022] Open
Abstract
Laying performance is an important economical trait of goose production. As laying performance is of low heritability, it is of significance to develop a marker-assisted selection (MAS) strategy for this trait. Definition of sequence variation related to the target trait is a prerequisite of quantitating MAS, but little is presently known about the goose genome, which greatly hinders the identification of genetic markers for the laying traits of geese. Recently developed restriction site-associated DNA (RAD) sequencing is a possible approach for discerning large-scale single nucleotide polymorphism (SNP) and reducing the complexity of a genome without having reference genomic information available. In the present study, we developed a pooled RAD sequencing strategy for detecting geese laying-related SNP. Two DNA pools were constructed, each consisting of equal amounts of genomic DNA from 10 individuals with either high estimated breeding value (HEBV) or low estimated breeding value (LEBV). A total of 139,013 SNP were obtained from 42,291,356 sequences, of which 18,771,943 were for LEBV and 23,519,413 were for HEBV cohorts. Fifty-five SNP which had different allelic frequencies in the two DNA pools were further validated by individual-based AS-PCR genotyping in the LEBV and HEBV cohorts. Ten out of 55 SNP exhibited distinct allele distributions in these two cohorts. These 10 SNP were further genotyped in a goose population of 492 geese to verify the association with egg numbers. The result showed that 8 of 10 SNP were associated with egg numbers. Additionally, liner regression analysis revealed that SNP Record-111407, 106975 and 112359 were involved in a multiplegene network affecting laying performance. We used IPCR to extend the unknown regions flanking the candidate RAD tags. The obtained sequences were subjected to BLAST to retrieve the orthologous genes in either ducks or chickens. Five novel genes were cloned for geese which harbored the candidate laying-related SNP, including membrane associated guanylate kinase (MAGI-1), KIAA1462, Rho GTPase activating protein 21 (ARHGAP21), acyl-CoA synthetase family member 2 (ACSF2), astrotactin 2 (ASTN2). Collectively, our data suggests that 8 SNP and 5 genes might be promising candidate markers or targets for marker-assisted selection of egg numbers in geese.
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20
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Haelterman NA, Jiang L, Li Y, Bayat V, Sandoval H, Ugur B, Tan KL, Zhang K, Bei D, Xiong B, Charng WL, Busby T, Jawaid A, David G, Jaiswal M, Venken KJT, Yamamoto S, Chen R, Bellen HJ. Large-scale identification of chemically induced mutations in Drosophila melanogaster. Genome Res 2015; 24:1707-18. [PMID: 25258387 PMCID: PMC4199363 DOI: 10.1101/gr.174615.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Forward genetic screens using chemical mutagens have been successful in defining the function of thousands of genes in eukaryotic model organisms. The main drawback of this strategy is the time-consuming identification of the molecular lesions causative of the phenotypes of interest. With whole-genome sequencing (WGS), it is now possible to sequence hundreds of strains, but determining which mutations are causative among thousands of polymorphisms remains challenging. We have sequenced 394 mutant strains, generated in a chemical mutagenesis screen, for essential genes on the Drosophila X chromosome and describe strategies to reduce the number of candidate mutations from an average of ∼3500 to 35 single-nucleotide variants per chromosome. By combining WGS with a rough mapping method based on large duplications, we were able to map 274 (∼70%) mutations. We show that these mutations are causative, using small 80-kb duplications that rescue lethality. Hence, our findings demonstrate that combining rough mapping with WGS dramatically expands the toolkit necessary for assigning function to genes.
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Affiliation(s)
- Nele A Haelterman
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lichun Jiang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Vafa Bayat
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hector Sandoval
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Berrak Ugur
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kai Li Tan
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ke Zhang
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Danqing Bei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bo Xiong
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wu-Lin Charng
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Theodore Busby
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Adeel Jawaid
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gabriela David
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Manish Jaiswal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Koen J T Venken
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Verna and Mars Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA
| | - Rui Chen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA; Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
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21
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Satoh T, Ohba A, Liu Z, Inagaki T, Satoh AK. dPob/EMC is essential for biosynthesis of rhodopsin and other multi-pass membrane proteins in Drosophila photoreceptors. eLife 2015; 4. [PMID: 25715730 PMCID: PMC4341237 DOI: 10.7554/elife.06306] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 01/26/2015] [Indexed: 12/22/2022] Open
Abstract
In eukaryotes, most integral membrane proteins are synthesized, integrated into the membrane, and folded properly in the endoplasmic reticulum (ER). We screened the mutants affecting rhabdomeric expression of rhodopsin 1 (Rh1) in the Drosophila photoreceptors and found that dPob/EMC3, EMC1, and EMC8/9, Drosophila homologs of subunits of ER membrane protein complex (EMC), are essential for stabilization of immature Rh1 in an earlier step than that at which another Rh1-specific chaperone (NinaA) acts. dPob/EMC3 localizes to the ER and associates with EMC1 and calnexin. Moreover, EMC is required for the stable expression of other multi-pass transmembrane proteins such as minor rhodopsins Rh3 and Rh4, transient receptor potential, and Na+K+-ATPase, but not for a secreted protein or type I single-pass transmembrane proteins. Furthermore, we found that dPob/EMC3 deficiency induces rhabdomere degeneration in a light-independent manner. These results collectively indicate that EMC is a key factor in the biogenesis of multi-pass transmembrane proteins, including Rh1, and its loss causes retinal degeneration. DOI:http://dx.doi.org/10.7554/eLife.06306.001 The membranes that surround cells contain many proteins, and those that span the entire width of the membrane are known as transmembrane proteins. Rhodopsin is one such transmembrane protein that is found in the light-sensitive ‘photoreceptor’ cells of the eye, where it plays an essential role in vision. Transmembrane proteins are made inside the cell and are inserted into the membrane surrounding a compartment called the endoplasmic reticulum. Here, they mature and ‘fold’ into their correct three-dimensional shape with help from chaperone proteins. Once correctly folded, the transmembrane proteins can be transported to the cell membrane. Incorrect folding of proteins can have severe consequences; if rhodopsin is incorrectly folded the photoreceptor cells can die, leading to blindness in humans and other animals. Experiments carried out in zebrafish have shown that the chaperone protein Pob is required for the survival of photoreceptor cells. Pob is part of a group or ‘complex’ of chaperone proteins in the endoplasmic reticulum called the EMC complex. This suggests that the EMC complex may be involved in folding rhodopsin, but the details remain unclear. Here, Satoh et al. studied the role of the EMC complex in the folding of rhodopsin in fruit flies. This involved examining hundreds of flies that carried a variety of genetic mutations and that also had low levels of rhodopsin. The experiments show that dPob—the fly version of Pob—and two other proteins in the EMC complex are required for newly-made rhodopsin to be stabilized. If photoreceptor cells are missing proteins from the complex, the light-sensitive structures in the eye degenerate. Rhodopsin is known as a ‘multi-pass’ membrane protein because it crosses the membrane multiple times. Satoh et al. found that the EMC complex is also required for the folding of other multi-pass membrane proteins in photoreceptor cells. The next challenge will be to reveal how the EMC complex is able to specifically target this type of transmembrane protein. DOI:http://dx.doi.org/10.7554/eLife.06306.002
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Affiliation(s)
- Takunori Satoh
- Graduate School of Integrated Arts and Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Aya Ohba
- Graduate School of Integrated Arts and Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Ziguang Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Tsuyoshi Inagaki
- Graduate School of Integrated Arts and Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Akiko K Satoh
- Graduate School of Integrated Arts and Science, Hiroshima University, Higashi-Hiroshima, Japan
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22
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Abstract
The power of Drosophila melanogaster as a model organism lies in its ability to be used for large-scale genetic screens with the capacity to uncover the genetic basis of biological processes. In particular, genetic screens for circadian behavior, which have been performed since 1971, allowed researchers to make groundbreaking discoveries on multiple levels: they discovered that there is a genetic basis for circadian behavior, they identified the so-called core clock genes that govern this process, and they started to paint a detailed picture of the molecular functions of these clock genes and their encoded proteins. Since the discovery that fruit flies sleep in 2000, researchers have successfully been using genetic screening to elucidate the many questions surrounding this basic animal behavior. In this chapter, we briefly recall the history of circadian rhythm and sleep screens and then move on to describe techniques currently employed for mutagenesis and genetic screening in the field. The emphasis lies on comparing the newer approaches of transgenic RNA interference (RNAi) to classical forms of mutagenesis, in particular in their application to circadian behavior and sleep. We discuss the different screening approaches in light of the literature and published and unpublished sleep and rhythm screens utilizing ethyl methanesulfonate mutagenesis and transgenic RNAi from our lab.
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Affiliation(s)
- Sofia Axelrod
- Laboratory of Genetics, The Rockefeller University, New York, USA
| | - Lino Saez
- Laboratory of Genetics, The Rockefeller University, New York, USA
| | - Michael W Young
- Laboratory of Genetics, The Rockefeller University, New York, USA.
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Sakuma C, Kawauchi T, Haraguchi S, Shikanai M, Yamaguchi Y, Gelfand VI, Luo L, Miura M, Chihara T. Drosophila Strip serves as a platform for early endosome organization during axon elongation. Nat Commun 2014; 5:5180. [PMID: 25312435 PMCID: PMC4197811 DOI: 10.1038/ncomms6180] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/05/2014] [Indexed: 12/19/2022] Open
Abstract
Early endosomes are essential for regulating cell signalling and controlling the amount of cell surface molecules during neuronal morphogenesis. Early endosomes undergo retrograde transport (clustering) before their homotypic fusion. Small GTPase Rab5 is known to promote early endosomal fusion, but the mechanism linking the transport/clustering with Rab5 activity is unclear. Here we show that Drosophila Strip is a key regulator for neuronal morphogenesis. strip knockdown disturbs the early endosome clustering and Rab5-positive early endosomes become smaller and scattered. Strip genetically and biochemically interacts with both Glued (the regulator of dynein-dependent transport) and Sprint (the guanine nucleotide exchange factor for Rab5), suggesting that Strip is a molecular linker between retrograde transport and Rab5 activation. Overexpression of an active form of Rab5 in strip mutant neurons suppresses the axon elongation defects. Thus, Strip acts as a molecular platform for the early endosome organization that plays important roles in neuronal morphogenesis.
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Affiliation(s)
- Chisako Sakuma
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeshi Kawauchi
- 1] Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan [2] PRESTO, Japan Science and Technology Agency (JST), 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Shuka Haraguchi
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mima Shikanai
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yoshifumi Yamaguchi
- 1] Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] PRESTO, Japan Science and Technology Agency (JST), 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Vladimir I Gelfand
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Masayuki Miura
- 1] Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] CREST, Japan Science and Technology Agency (JST), 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Takahiro Chihara
- 1] Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] PRESTO, Japan Science and Technology Agency (JST), 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan [3] CREST, Japan Science and Technology Agency (JST), 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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24
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Giagtzoglou N. Genetic screens to identify new Notch pathway mutants in Drosophila. Methods Mol Biol 2014; 1187:15-28. [PMID: 25053478 DOI: 10.1007/978-1-4939-1139-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Notch signaling controls a wide range of developmental processes, including proliferation, apoptosis, and cell fate specification during both development and adult tissue homeostasis. The functional versatility of the Notch signaling pathway is tightly linked with the complexity of its regulation in different cellular contexts. To unravel the complexity of Notch signaling, it is important to identify the different components of the Notch signaling pathway. A powerful strategy to accomplish this task is based on genetic screens. Given that the developmental context of signaling is important, these screens should be customized to specific cell populations or tissues. Here, I describe how to perform F1 clonal forward genetic screens in Drosophila to identify novel components of the Notch signaling pathway. These screens combine a classical EMS (ethyl methanesulfonate) chemical mutagenesis protocol along with clonal analysis via FRT-mediated mitotic recombination. These F1 clonal screens allow rapid phenotypic screening within clones of mutant cells induced at specific developmental stages and in tissues of interest, bypassing the pleiotropic effects of isolated mutations. More importantly, since EMS mutations have been notoriously difficult to map to specific genes in the past, I briefly discuss mapping methods that allow rapid identification of the causative mutations.
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Affiliation(s)
- Nikolaos Giagtzoglou
- Department of Neurology, Jan and Dan Duncan Neurological Institute, Baylor College of Medicine, 1250 Moursund St. Ste. 1150, Houston, TX, 77030, USA,
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Domanitskaya E, Anllo L, Schüpbach T. Phantom, a cytochrome P450 enzyme essential for ecdysone biosynthesis, plays a critical role in the control of border cell migration in Drosophila. Dev Biol 2013; 386:408-18. [PMID: 24373956 DOI: 10.1016/j.ydbio.2013.12.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 12/05/2013] [Accepted: 12/10/2013] [Indexed: 10/25/2022]
Abstract
The border cells of Drosophila are a model system for coordinated cell migration. Ecdysone signaling has been shown to act as the timing signal to initiate the migration process. Here we find that mutations in phantom (phm), encoding an enzyme in the ecdysone biosynthesis pathway, block border cell migration when the entire follicular epithelium of an egg chamber is mutant, even when the associated germline cells (nurse cells and oocyte) are wild-type. Conversely, mutant germline cells survive and do not affect border cell migration, as long as the surrounding follicle cells are wild-type. Interestingly, even small patches of wild-type follicle cells in a mosaic epithelium are sufficient to allow the production of above-threshold levels of ecdysone to promote border cell migration. The same phenotype is observed with mutations in shade (shd), encoding the last enzyme in the pathway that converts ecdysone to the active 20-hydroxyecdysone. Administration of high 20-hydroxyecdysone titers in the medium can also rescue the border cell migration phenotype in cultured egg chambers with an entirely phm mutant follicular epithelium. These results indicate that in normal oogenesis, the follicle cell epithelium of each individual egg chamber must supply sufficient ecdysone precursors, leading ultimately to high enough levels of mature 20-hydroxyecdysone to the border cells to initiate their migration. Neither the germline, nor the neighboring egg chambers, nor the surrounding hemolymph appear to provide threshold amounts of 20-hydroxyecdysone to do so. This "egg chamber autonomous" ecdysone synthesis constitutes a useful way to regulate the individual maturation of the asynchronous egg chambers present in the Drosophila ovary.
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Affiliation(s)
- Elena Domanitskaya
- Howard Hughes Medical Institute, Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States
| | - Lauren Anllo
- Howard Hughes Medical Institute, Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States
| | - Trudi Schüpbach
- Howard Hughes Medical Institute, Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States.
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26
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Agunbiade TA, Sun W, Coates BS, Djouaka R, Tamò M, Ba MN, Binso-Dabire C, Baoua I, Olds BP, Pittendrigh BR. Development of reference transcriptomes for the major field insect pests of cowpea: a toolbox for insect pest management approaches in west Africa. PLoS One 2013; 8:e79929. [PMID: 24278221 PMCID: PMC3838393 DOI: 10.1371/journal.pone.0079929] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 09/27/2013] [Indexed: 11/19/2022] Open
Abstract
Cowpea is a widely cultivated and major nutritional source of protein for many people that live in West Africa. Annual yields and longevity of grain storage is greatly reduced by feeding damage caused by a complex of insect pests that include the pod sucking bugs, Anoplocnemis curvipes Fabricius (Hemiptera: Coreidae) and Clavigralla tomentosicollis Stål (Hemiptera: Coreidae); as well as phloem-feeding cowpea aphids, Aphis craccivora Koch (Hemiptera: Aphididae) and flower thrips, Megalurothrips sjostedti Trybom (Thysanoptera: Thripidae). Efforts to control these pests remain a challenge and there is a need to understand the structure and movement of these pest populations in order to facilitate the development of integrated pest management strategies (IPM). Molecular tools have the potential to help facilitate a better understanding of pest populations. Towards this goal, we used 454 pyrosequencing technology to generate 319,126, 176,262, 320,722 and 227,882 raw reads from A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti, respectively. The reads were de novo assembled into 11,687, 7,647, 10,652 and 7,348 transcripts for A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti, respectively. Functional annotation of the resulting transcripts identified genes putatively involved in insecticide resistance, pathogen defense and immunity. Additionally, sequences that matched the primary aphid endosymbiont, Buchnera aphidicola, were identified among A. craccivora transcripts. Furthermore, 742, 97, 607 and 180 single nucleotide polymorphisms (SNPs) were respectively predicted among A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti transcripts, and will likely be valuable tools for future molecular genetic marker development. These results demonstrate that Roche 454-based transcriptome sequencing could be useful for the development of genomic resources for cowpea pest insects in West Africa.
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Affiliation(s)
- Tolulope A. Agunbiade
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
| | - Weilin Sun
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Brad S. Coates
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | | | - Manuele Tamò
- International Institute of Tropical Agriculture, Cotonou, Benin
| | - Malick N. Ba
- Institut de l’Environnement et de Recherches Agricoles, Ouagadougou, Burkina Faso
| | | | - Ibrahim Baoua
- Institut National de la Recherche Agronomique du Niger, Maradi, Niger
| | - Brett P. Olds
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Barry R. Pittendrigh
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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27
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Lenz S, Karsten P, Schulz JB, Voigt A. Drosophila as a screening tool to study human neurodegenerative diseases. J Neurochem 2013; 127:453-60. [PMID: 24028575 DOI: 10.1111/jnc.12446] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 08/22/2013] [Accepted: 09/03/2013] [Indexed: 11/28/2022]
Abstract
In an aging society, research involving neurodegenerative disorders is of paramount importance. Over the past few years, research on Alzheimer's and Parkinson's diseases has made tremendous progress. Experimental studies, however, rely mostly on transgenic animal models, preferentially using mice. Although experiments on mice have enormous advantages, they also have some inherent limitations, some of which can be overcome by the use of Drosophila melanogaster as an experimental animal. Among the major advantages of using the fly is its small genome, which can also be modified very easily. The fact that its genome lends itself to diverse alterations (e. g. mutagenesis, transposons) has made the fly a useful organism to perform large-scale and genome-wide screening approaches. This has opened up an entirely new field of experimental research aiming to elucidate genetic interactions and screen for modifiers of disease processes in vivo. Here, we provide a brief overview of how flies can be used to analyze molecular mechanisms underlying human neurodegenerative diseases.
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Affiliation(s)
- Sarah Lenz
- Department of Neurology, University Medical Center, RWTH Aachen, Aachen, Germany
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28
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Shi YY, Sun LX, Huang ZY, Wu XB, Zhu YQ, Zheng HJ, Zeng ZJ. A SNP based high-density linkage map of Apis cerana reveals a high recombination rate similar to Apis mellifera. PLoS One 2013; 8:e76459. [PMID: 24130775 PMCID: PMC3794977 DOI: 10.1371/journal.pone.0076459] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/24/2013] [Indexed: 11/21/2022] Open
Abstract
Background The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. Results F2 workers (N = 103) were genotyped for 126,990 single nucleotide polymorphisms (SNPs). After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM) with the largest linkage group (180 loci) measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. Conclusion We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera.
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Affiliation(s)
- Yuan Yuan Shi
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Liang Xian Sun
- Molecular Biology and Pharmacology Key Laboratory of Fujian Advanced Education, Quanzhou Normal University, Quanzhou, Fujian, China
| | - Zachary Y. Huang
- Department of Entomology, Michigan State University, East Lansing, Michigan, United States of America
| | - Xiao Bo Wu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yong Qiang Zhu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Hua Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
- * E-mail: (HJZ); (ZJZ)
| | - Zhi Jiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- * E-mail: (HJZ); (ZJZ)
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29
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Lü ZC, Sun HB, Wan FH, Guo JY, Zhang GF. High Variation in Single Nucleotide Polymorphisms (SNPs) and Insertions/Deletions (Indels) in the Highly Invasive Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Middle East-Asia Minor 1 (MEAM1). NEOTROPICAL ENTOMOLOGY 2013; 42:521-526. [PMID: 23949985 DOI: 10.1007/s13744-013-0152-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 07/03/2013] [Indexed: 06/02/2023]
Abstract
Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Middle East-Asia Minor 1 (MEAM1) is invasive and adaptive to varied environments throughout the world. The adaptability is closely related to genomic variation such as single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). In order to elucidate the feature of SNPs and indels in MEAM1, and reveal the association between SNPs/indels and adaptive capacity to various environments, a computational approach with QualitySNP was used to identify reliable SNPs and indels on the basis of 9110-expressed sequence tags of MEAM1 present in the NCBI database. There were 575 SNPs detected with a density of 10.1 SNPs/kb and 6.4 SNPs/contig. Also, 237 transitions (39.3%) and 366 transversions (60.7%) were obtained, where the ratio of transitions to transversions was 0.65:1. In addition, 581 indels with a density of 14.1 indels/kb and 9.2 indels/contig were detected. Collectively, it showed that invasive MEAM1 has high SNPs density, and higher SNPs percentage than non-invasive B. tabaci species. A high SNPs density/percentage in MEAM1 yielded a high genomic variation that might have allowed it to adapt to varied environments, which provides some support to understand the invasive nature of MEAM1 at the genomic level. High levels of genomic variation are implicated in the level of adaptive capacity and invasive species are thought to exhibit higher levels of adaptive capacity than non-invasive species.
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Affiliation(s)
- Z C Lü
- State Key Lab for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
| | - H B Sun
- State Key Lab for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
| | - F H Wan
- State Key Lab for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China.
- Center for Management of Invasive Alien Species, Ministry of Agriculture, Beijing, China.
| | - J Y Guo
- State Key Lab for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
- Center for Management of Invasive Alien Species, Ministry of Agriculture, Beijing, China
| | - G F Zhang
- State Key Lab for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
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30
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Response to the dorsal anterior gradient of EGFR signaling in Drosophila oogenesis is prepatterned by earlier posterior EGFR activation. Cell Rep 2013; 4:791-802. [PMID: 23972992 DOI: 10.1016/j.celrep.2013.07.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/21/2013] [Accepted: 07/26/2013] [Indexed: 11/22/2022] Open
Abstract
Spatially restricted epidermal growth factor receptor (EGFR) activity plays a central role in patterning the follicular epithelium of the Drosophila ovary. In midoogenesis, localized EGFR activation is achieved by the graded dorsal anterior localization of its ligand, Gurken. Graded EGFR activity determines multiple dorsal anterior fates along the dorsal-ventral axis but cannot explain the sharp posterior limit of this domain. Here, we show that posterior follicle cells express the T-box transcription factors Midline and H15, which render cells unable to adopt a dorsal anterior fate in response to EGFR activation. The posterior expression of Midline and H15 is itself induced in early oogenesis by posteriorly localized EGFR signaling, defining a feedback loop in which early induction of Mid and H15 confers a molecular memory that fundamentally alters the outcome of later EGFR signaling. Spatial regulation of the EGFR pathway thus occurs both through localization of the ligand and through localized regulation of the cellular response.
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31
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Plum, an immunoglobulin superfamily protein, regulates axon pruning by facilitating TGF-β signaling. Neuron 2013; 78:456-68. [PMID: 23664613 DOI: 10.1016/j.neuron.2013.03.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2013] [Indexed: 11/22/2022]
Abstract
Axon pruning during development is essential for proper wiring of the mature nervous system, but its regulation remains poorly understood. We have identified an immunoglobulin superfamily (IgSF) transmembrane protein, Plum, that is cell autonomously required for axon pruning of mushroom body (MB) γ neurons and for ectopic synapse refinement at the developing neuromuscular junction in Drosophila. Plum promotes MB γ neuron axon pruning by regulating the expression of Ecdysone Receptor-B1, a key initiator of axon pruning. Genetic analyses indicate that Plum acts to facilitate signaling of Myoglianin, a glial-derived TGF-β, on MB γ neurons upstream of the type-I TGF-β receptor Baboon. Myoglianin, Baboon, and Ecdysone Receptor-B1 are also required for neuromuscular junction ectopic synapse refinement. Our study highlights both IgSF proteins and TGF-β facilitation as key promoters of developmental axon elimination and demonstrates a mechanistic conservation between MB axon pruning during metamorphosis and the refinement of ectopic larval neuromuscular connections.
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32
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Abstract
Genetic analyses in both worm and fly have identified the RhoGAP-like protein Syd-1 as a key positive regulator of presynaptic assembly. In worm, loss of syd-1 can be fully rescued by overexpressing wild-type Liprin-α, suggesting that the primary function of Syd-1 in this process is to recruit Liprin-α. We show that loss of syd-1 from Drosophila R7 photoreceptors causes two morphological defects that occur at distinct developmental time points. First, syd-1 mutant R7 axons often fail to form terminal boutons in their normal M6 target layer. Later, those mutant axons that do contact M6 often project thin extensions beyond it. We find that the earlier defect coincides with a failure to localize synaptic vesicles, suggesting that it reflects a failure in presynaptic assembly. We then analyze the relationship between syd-1 and Liprin-α in R7s. We find that loss of Liprin-α causes a stronger early R7 defect and provide a possible explanation for this disparity: we show that Liprin-α promotes Kinesin-3/Unc-104/Imac-mediated axon transport independently of Syd-1 and that Kinesin-3/Unc-104/Imac is required for normal R7 bouton formation. Unlike loss of syd-1, loss of Liprin-α does not cause late R7 extensions. We show that overexpressing Liprin-α partly rescues the early but not the late syd-1 mutant R7 defect. We therefore conclude that the two defects are caused by distinct molecular mechanisms. We find that Trio overexpression rescues both syd-1 defects and that trio and syd-1 have similar loss- and gain-of-function phenotypes, suggesting that the primary function of Syd-1 in R7s may be to promote Trio activity.
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Kumar S, You FM, Cloutier S. Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries. BMC Genomics 2012; 13:684. [PMID: 23216845 PMCID: PMC3557168 DOI: 10.1186/1471-2164-13-684] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 11/29/2012] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Flax (Linum usitatissimum L.) is a significant fibre and oilseed crop. Current flax molecular markers, including isozymes, RAPDs, AFLPs and SSRs are of limited use in the construction of high density linkage maps and for association mapping applications due to factors such as low reproducibility, intense labour requirements and/or limited numbers. We report here on the use of a reduced representation library strategy combined with next generation Illumina sequencing for rapid and large scale discovery of SNPs in eight flax genotypes. SNP discovery was performed through in silico analysis of the sequencing data against the whole genome shotgun sequence assembly of flax genotype CDC Bethune. Genotyping-by-sequencing of an F6-derived recombinant inbred line population provided validation of the SNPs. RESULTS Reduced representation libraries of eight flax genotypes were sequenced on the Illumina sequencing platform resulting in sequence coverage ranging from 4.33 to 15.64X (genome equivalents). Depending on the relatedness of the genotypes and the number and length of the reads, between 78% and 93% of the reads mapped onto the CDC Bethune whole genome shotgun sequence assembly. A total of 55,465 SNPs were discovered with the largest number of SNPs belonging to the genotypes with the highest mapping coverage percentage. Approximately 84% of the SNPs discovered were identified in a single genotype, 13% were shared between any two genotypes and the remaining 3% in three or more. Nearly a quarter of the SNPs were found in genic regions. A total of 4,706 out of 4,863 SNPs discovered in Macbeth were validated using genotyping-by-sequencing of 96 F6 individuals from a recombinant inbred line population derived from a cross between CDC Bethune and Macbeth, corresponding to a validation rate of 96.8%. CONCLUSIONS Next generation sequencing of reduced representation libraries was successfully implemented for genome-wide SNP discovery from flax. The genotyping-by-sequencing approach proved to be efficient for validation. The SNP resources generated in this work will assist in generating high density maps of flax and facilitate QTL discovery, marker-assisted selection, phylogenetic analyses, association mapping and anchoring of the whole genome shotgun sequence.
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Affiliation(s)
- Santosh Kumar
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada
| | - Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, Manitoba, R3T 2N2, Canada
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St Johnston D. Using mutants, knockdowns, and transgenesis to investigate gene function in Drosophila. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:587-613. [PMID: 24014449 DOI: 10.1002/wdev.101] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The sophisticated genetic techniques available in Drosophila are largely responsible for its success as a model organism. One of the most important of these is the ability to disrupt gene function in vivo and observe the resulting phenotypes. This review considers the ever-increasing repertoire of approaches for perturbing the functions of specific genes in flies, ranging from classical and transposon-mediated mutageneses to newer techniques, such as homologous recombination and RNA interference. Since most genes are used over and over again in different contexts during development, many important advances have depended on being able to interfere with gene function at specific times or places in the developing animal, and a variety of approaches are now available to do this. Most of these techniques rely on being able to create genetically modified strains of Drosophila and the different methods for generating lines carrying single copy transgenic constructs will be described, along with the advantages and disadvantages of each approach.
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Affiliation(s)
- Daniel St Johnston
- The Gurdon Institute and the Department of Genetics, University of Cambridge, Cambridge CB2 1QN, UK.
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Baer MM, Palm W, Eaton S, Leptin M, Affolter M. Microsomal triacylglycerol transfer protein (MTP) is required to expand tracheal lumen in Drosophila in a cell-autonomous manner. J Cell Sci 2012; 125:6038-48. [PMID: 23132924 DOI: 10.1242/jcs.110452] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The Drosophila tracheal system is a useful model for dissecting the molecular mechanisms controlling the assembly and expansion of tubular organs. We have identified microsomal triacylglycerol transfer protein (MTP) as a new player involved in the lumen expansion in unicellular tubes. MTP is an endoplasmic reticulum resident protein that can transfer triglycerides and phospholipids between membranes in vitro. MTP lipid transfer activity is crucial for the assembly and secretion of apoB family lipoproteins, which are carriers of lipids between different tissues. Here we describe an unexpected role of MTP in tracheal development, which we postulate to be independent of its known function in lipoprotein secretion. We propose that, in tracheal cells, MTP is involved in regulation of de novo apical membrane delivery to the existing lumen and thus promotes proper expansion of the larval tracheal system.
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Affiliation(s)
- Magdalena M Baer
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
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The chromosomal passenger complex is required for meiotic acentrosomal spindle assembly and chromosome biorientation. Genetics 2012; 192:417-29. [PMID: 22865736 DOI: 10.1534/genetics.112.143495] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
During meiosis in the females of many species, spindle assembly occurs in the absence of the microtubule-organizing centers called centrosomes. In the absence of centrosomes, the nature of the chromosome-based signal that recruits microtubules to promote spindle assembly as well as how spindle bipolarity is established and the chromosomes orient correctly toward the poles is not known. To address these questions, we focused on the chromosomal passenger complex (CPC). We have found that the CPC localizes in a ring around the meiotic chromosomes that is aligned with the axis of the spindle at all stages. Using new methods that dramatically increase the effectiveness of RNA interference in the germline, we show that the CPC interacts with Drosophila oocyte chromosomes and is required for the assembly of spindle microtubules. Furthermore, chromosome biorientation and the localization of the central spindle kinesin-6 protein Subito, which is required for spindle bipolarity, depend on the CPC components Aurora B and Incenp. Based on these data we propose that the ring of CPC around the chromosomes regulates multiple aspects of meiotic cell division including spindle assembly, the establishment of bipolarity, the recruitment of important spindle organization factors, and the biorientation of homologous chromosomes.
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Stinchfield MJ, Takaesu NT, Quijano JC, Castillo AM, Tiusanen N, Shimmi O, Enzo E, Dupont S, Piccolo S, Newfeld SJ. Fat facets deubiquitylation of Medea/Smad4 modulates interpretation of a Dpp morphogen gradient. Development 2012; 139:2721-9. [PMID: 22745309 DOI: 10.1242/dev.077206] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The ability of secreted Transforming Growth Factor β (TGFβ) proteins to act as morphogens dictates that their influence be strictly regulated. Here, we report that maternally contributed fat facets (faf; a homolog of USP9X/FAM) is essential for proper interpretation of the zygotic Decapentaplegic (Dpp) morphogen gradient that patterns the embryonic dorsal-ventral axis. The data suggest that the loss of faf reduces the activity of Medea (a homolog of Smad4) below the minimum necessary for adequate Dpp signaling and that this is likely due to excessive ubiquitylation on a specific lysine. This study supports the hypothesis that the control of cellular responsiveness to TGFβ signals at the level of Smad4 ubiquitylation is a conserved mechanism required for proper implementation of a morphogen gradient.
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Sievers C, Willing EM, Hoffmann M, Dreyer C, Ramnarine I, Magurran A. Reasons for the invasive success of a guppy (Poecilia reticulata) population in Trinidad. PLoS One 2012; 7:e38404. [PMID: 22693621 PMCID: PMC3365015 DOI: 10.1371/journal.pone.0038404] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 05/04/2012] [Indexed: 11/18/2022] Open
Abstract
The introduction of non-native species into new habitats poses a major threat to native populations. Of particular interest, though often overlooked, are introductions of populations that are not fully reproductively isolated from native individuals and can hybridize with them. To address this important topic we used different approaches in a multi-pronged study, combining the effects of mate choice, shoaling behaviour and genetics. Here we present evidence that behavioural traits such as shoaling and mate choice can promote population mixing if individuals do not distinguish between native and foreign conspecifics. We examined this in the context of two guppy (Poecilia reticulata) populations that have been subject to an introduction and subsequent population mixing event in Trinidad. The introduction of Guanapo River guppies into the Turure River more than 50 years ago led to a marked reduction of the original genotype. In our experiments, female guppies did not distinguish between shoaling partners when given the choice between native and foreign individuals. Introduced fish are therefore likely to benefit from the protection of a shoal and will improve their survival chances as a result. The additional finding that male guppies do not discriminate between females on the basis of origin will further increase the process of population mixing, especially if males encounter mixed shoals. In a mesocosm experiment, in which the native and foreign populations were allowed to mate freely, we found, as expected on the basis of these behavioural interactions, that the distribution of offspring genotypes could be predicted from the proportions of the two types of founding fish. This result suggests that stochastic and environmental processes have reinforced the biological ones to bring about the genetic dominance of the invading population in the Turure River. Re-sampling the Turure for genetic analysis using SNP markers confirmed the population mixing process and showed that it is an on-going process in this river and has led to the nearly complete disappearance of the original genotype.
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Affiliation(s)
- Caya Sievers
- Scottish Oceans Institute, University of St. Andrews, St. Andrews, Fife, United Kingdom.
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Evolutionary Genomics of Colias Phosphoglucose Isomerase (PGI) Introns. J Mol Evol 2012; 74:96-111. [DOI: 10.1007/s00239-012-9492-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
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Domanitskaya E, Schüpbach T. CoREST acts as a positive regulator of Notch signaling in the follicle cells of Drosophila melanogaster. J Cell Sci 2012; 125:399-410. [PMID: 22331351 DOI: 10.1242/jcs.089797] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The Notch signaling pathway plays important roles in a variety of developmental events. The context-dependent activities of positive and negative modulators dramatically increase the diversity of cellular responses to Notch signaling. In a screen for mutations affecting the Drosophila melanogaster follicular epithelium, we isolated a mutation in CoREST that disrupts the Notch-dependent mitotic-to-endocycle switch of follicle cells at stage 6 of oogenesis. We show that Drosophila CoREST positively regulates Notch signaling, acting downstream of the proteolytic cleavage of Notch but upstream of Hindsight activity; the Hindsight gene is a Notch target that coordinates responses in the follicle cells. We show that CoREST genetically interacts with components of the Notch repressor complex, Hairless, C-terminal Binding Protein and Groucho. In addition, we demonstrate that levels of H3K27me3 and H4K16 acetylation are dramatically increased in CoREST mutant follicle cells. Our data indicate that CoREST acts as a positive modulator of the Notch pathway in the follicular epithelium as well as in wing tissue, and suggests a previously unidentified role for CoREST in the regulation of Notch signaling. Given its high degree of conservation among species, CoREST probably also functions as a regulator of Notch-dependent cellular events in other organisms.
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Affiliation(s)
- Elena Domanitskaya
- Howard Hughes Medical Institute, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544-1014, USA
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Joo SP, Kim TS, Lee IK, Kim JT, Park MS, Cho KH. A genome-wide study of moyamoya-type cerebrovascular disease in the korean population. J Korean Neurosurg Soc 2012; 50:486-91. [PMID: 22323933 DOI: 10.3340/jkns.2011.50.6.486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 10/09/2011] [Accepted: 12/05/2011] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE Structural genetic variation, including copy-number variation (CNV), constitutes a substantial fraction of total genetic variability, and the importance of structural variants in modulating susceptibility is increasingly being recognized. CNV can change biological function and contribute to pathophysiological conditions of human disease. Its relationship with common, complex human disease in particular is not fully understood. Here, we searched the human genome to identify copy number variants that predispose to moya-moya type cerebrovascular disease. METHODS We retrospectively analyzed patients who had unilateral or bilateral steno-occlusive lesions at the cerebral artery from March, 2007, to September, 2009. For the 20 subjects, including patients with moyamoya type pathologies and three normal healthy controls, we divided the subjects into 4 groups : typical moyamoya (n=6), unilateral moyamoya (n=9), progression unilateral to typical moyamoya (n=2) and non-moyamoya (n=3). Fragmented DNA was hybridized on Human610Quad v1.0 DNA analysis BeadChips (Illumina). Data analysis was performed with GenomeStudio v2009.1, Genotyping 1.1.9, cnvPartition_v2.3.4 software. Overall call rates were more than 99.8%. RESULTS In total, 1258 CNVs were identified across the whole genome. The average number of CNV was 45.55 per subject (CNV region was 45.4). The gain/loss of CNV was 52/249, having 4.7 fold higher frequencies in loss calls. The total CNV size was 904,657,868, and average size was 993,038. The largest portion of CNVs (613 calls) were 1M-10M in length. Interestingly, significant association between unilateral moyamoya disease (MMD) and progression of unilateral to typical moyamoya was observed. CONCLUSION Significant association between unilateral MMD and progression of unilateral to typical moyamoya was observed. The finding was confirmed again with clustering analysis. These data demonstrate that certain CNV associate with moyamoya-type cerebrovascular disease.
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Affiliation(s)
- Sung-Pil Joo
- Department of Neurosurgery, Chonnam National University Hospital & Medical School, Gwangju, Korea
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Kumar S, Banks TW, Cloutier S. SNP Discovery through Next-Generation Sequencing and Its Applications. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2012; 2012:831460. [PMID: 23227038 PMCID: PMC3512287 DOI: 10.1155/2012/831460] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/08/2012] [Indexed: 05/08/2023]
Abstract
The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference.
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Affiliation(s)
- Santosh Kumar
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
| | - Travis W. Banks
- Department of Applied Genomics, Vineland Research and Innovation Centre, Vineland Station, ON, Canada L0R 2E0
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB, Canada R3T 2M9
- *Sylvie Cloutier:
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Taniguchi K, Maeda R, Ando T, Okumura T, Nakazawa N, Hatori R, Nakamura M, Hozumi S, Fujiwara H, Matsuno K. Chirality in planar cell shape contributes to left-right asymmetric epithelial morphogenesis. Science 2011; 333:339-41. [PMID: 21764746 DOI: 10.1126/science.1200940] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Some organs in animals display left-right (LR) asymmetry. To better understand LR asymmetric morphogenesis in Drosophila, we studied LR directional rotation of the hindgut epithelial tube. Hindgut epithelial cells adopt a LR asymmetric (chiral) cell shape within their plane, and we refer to this cell behavior as planar cell-shape chirality (PCC). Drosophila E-cadherin (DE-Cad) is distributed to cell boundaries with LR asymmetry, which is responsible for the PCC formation. Myosin ID switches the LR polarity found in PCC and in DE-Cad distribution, which coincides with the direction of rotation. An in silico simulation showed that PCC is sufficient to induce the directional rotation of this tissue. Thus, the intrinsic chirality of epithelial cells in vivo is an underlying mechanism for LR asymmetric tissue morphogenesis.
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Affiliation(s)
- Kiichiro Taniguchi
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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Ghabrial AS, Levi BP, Krasnow MA. A systematic screen for tube morphogenesis and branching genes in the Drosophila tracheal system. PLoS Genet 2011; 7:e1002087. [PMID: 21750678 PMCID: PMC3131284 DOI: 10.1371/journal.pgen.1002087] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 04/05/2011] [Indexed: 01/10/2023] Open
Abstract
Many signaling proteins and transcription factors that induce and pattern organs have been identified, but relatively few of the downstream effectors that execute morphogenesis programs. Because such morphogenesis genes may function in many organs and developmental processes, mutations in them are expected to be pleiotropic and hence ignored or discarded in most standard genetic screens. Here we describe a systematic screen designed to identify all Drosophila third chromosome genes (∼40% of the genome) that function in development of the tracheal system, a tubular respiratory organ that provides a paradigm for branching morphogenesis. To identify potentially pleiotropic morphogenesis genes, the screen included analysis of marked clones of homozygous mutant tracheal cells in heterozygous animals, plus a secondary screen to exclude mutations in general “house-keeping” genes. From a collection including more than 5,000 lethal mutations, we identified 133 mutations representing ∼70 or more genes that subdivide the tracheal terminal branching program into six genetically separable steps, a previously established cell specification step plus five major morphogenesis and maturation steps: branching, growth, tubulogenesis, gas-filling, and maintenance. Molecular identification of 14 of the 70 genes demonstrates that they include six previously known tracheal genes, each with a novel function revealed by clonal analysis, and two well-known growth suppressors that establish an integral role for cell growth control in branching morphogenesis. The rest are new tracheal genes that function in morphogenesis and maturation, many through cytoskeletal and secretory pathways. The results suggest systematic genetic screens that include clonal analysis can elucidate the full organogenesis program and that over 200 patterning and morphogenesis genes are required to build even a relatively simple organ such as the Drosophila tracheal system. Elucidating the genetic programs that control formation and maintenance of body organs is a central goal of developmental biology, and understanding how these programs go awry in disease has important implications for medicine. Many such organogenesis genes have been identified, but most are early-acting “patterning genes” encoding signaling proteins and gene regulators that control expression of a poorly characterized set of downstream “morphogenesis genes,” which encode proteins that generate the remarkable organ forms and structures of the constituent cells. We screened ∼40% of the fruit fly Drosophila genome for mutations that affect tracheal (respiratory) system development. We included steps to bypass complexities from mutant effects on other tissues and steps to exclude mutations in general cell “housekeeping genes.” We isolated mutations in ∼70 genes that identify major steps in the organogenesis program including an integral cell growth control step. Many of the new tracheal genes are “morphogenesis genes” that encode proteins involved in cell structure or intracellular transport. The results suggest that genetic screens can elucidate a full organogenesis program and that over 200 patterning and morphogenesis genes are required to build even a relatively simple organ.
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Affiliation(s)
- Amin S. Ghabrial
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Cell and Developmental Biology, University Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (ASG); (MAK)
| | - Boaz P. Levi
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Mark A. Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (ASG); (MAK)
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Han K, Lee TY, Nikitopoulos DE, Soper SA, Murphy MC. A vertically stacked, polymer, microfluidic point mutation analyzer: rapid high accuracy detection of low-abundance K-ras mutations. Anal Biochem 2011; 417:211-9. [PMID: 21771577 DOI: 10.1016/j.ab.2011.06.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/15/2011] [Accepted: 06/23/2011] [Indexed: 01/06/2023]
Abstract
Recognition of point mutations in the K-ras gene can be used for the clinical management of several types of cancers. Unfortunately, several assay and hardware concerns must be addressed to allow users not well trained in performing molecular analyses the opportunity to undertake these measurements. To provide for a larger user base for these types of molecular assays, a vertically stacked microfluidic analyzer with a modular architecture and process automation was developed. The analyzer employs a primary polymerase chain reaction (PCR) coupled to an allele-specific ligase detection reaction (LDR). Each functional device, including continuous flow thermal reactors for the PCR and LDR, passive micromixers, and ExoSAP-IT purification, was designed and tested. Individual devices were fabricated in polycarbonate using hot embossing and were assembled using adhesive bonding for system assembly. The system produced LDR products from a DNA sample in approximately 1h, an 80% reduction in time compared with conventional benchtop instrumentation. Purifying the post-PCR products with the ExoSAP-IT enzyme led to optimized LDR performance, minimizing false-positive signals and producing reliable results. Mutant alleles in genomic DNA were quantified to the level of 0.25 ng of mutant DNA in 50 ng of wild-type DNA for a 25-μl sample, equivalent to DNA from 42 mutant cells.
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Affiliation(s)
- Kyudong Han
- Department of Nanobiomedical Science and WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea.
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Abstract
We describe a molecularly defined duplication kit for the X chromosome of Drosophila melanogaster. A set of 408 overlapping P[acman] BAC clones was used to create small duplications (average length 88 kb) covering the 22-Mb sequenced portion of the chromosome. The BAC clones were inserted into an attP docking site on chromosome 3L using ΦC31 integrase, allowing direct comparison of different transgenes. The insertions complement 92% of the essential and viable mutations and deletions tested, demonstrating that almost all Drosophila genes are compact and that the current annotations of the genome are reasonably accurate. Moreover, almost all genes are tolerated at twice the normal dosage. Finally, we more precisely mapped two regions at which duplications cause diplo-lethality in males. This collection comprises the first molecularly defined duplication set to cover a whole chromosome in a multicellular organism. The work presented removes a long-standing barrier to genetic analysis of the Drosophila X chromosome, will greatly facilitate functional assays of X-linked genes in vivo, and provides a model for functional analyses of entire chromosomes in other species.
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O'Neil ST, Dzurisin JDK, Carmichael RD, Lobo NF, Emrich SJ, Hellmann JJ. Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon. BMC Genomics 2010; 11:310. [PMID: 20478048 PMCID: PMC2887415 DOI: 10.1186/1471-2164-11-310] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 05/17/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several recent studies have demonstrated the use of Roche 454 sequencing technology for de novo transcriptome analysis. Low error rates and high coverage also allow for effective SNP discovery and genetic diversity estimates. However, genetically diverse datasets, such as those sourced from natural populations, pose challenges for assembly programs and subsequent analysis. Further, estimating the effectiveness of transcript discovery using Roche 454 transcriptome data is still a difficult task. RESULTS Using the Roche 454 FLX Titanium platform, we sequenced and assembled larval transcriptomes for two butterfly species: the Propertius duskywing, Erynnis propertius (Lepidoptera: Hesperiidae) and the Anise swallowtail, Papilio zelicaon (Lepidoptera: Papilionidae). The Expressed Sequence Tags (ESTs) generated represent a diverse sample drawn from multiple populations, developmental stages, and stress treatments. Despite this diversity, > 95% of the ESTs assembled into long (> 714 bp on average) and highly covered (> 9.6x on average) contigs. To estimate the effectiveness of transcript discovery, we compared the number of bases in the hit region of unigenes (contigs and singletons) to the length of the best match silkworm (Bombyx mori) protein--this "ortholog hit ratio" gives a close estimate on the amount of the transcript discovered relative to a model lepidopteran genome. For each species, we tested two assembly programs and two parameter sets; although CAP3 is commonly used for such data, the assemblies produced by Celera Assembler with modified parameters were chosen over those produced by CAP3 based on contig and singleton counts as well as ortholog hit ratio analysis. In the final assemblies, 1,413 E. propertius and 1,940 P. zelicaon unigenes had a ratio > 0.8; 2,866 E. propertius and 4,015 P. zelicaon unigenes had a ratio > 0.5. CONCLUSIONS Ultimately, these assemblies and SNP data will be used to generate microarrays for ecoinformatics examining climate change tolerance of different natural populations. These studies will benefit from high quality assemblies with few singletons (less than 26% of bases for each assembled transcriptome are present in unassembled singleton ESTs) and effective transcript discovery (over 6,500 of our putative orthologs cover at least 50% of the corresponding model silkworm gene).
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Affiliation(s)
- Shawn T O'Neil
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, USA
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Identification and mapping of induced chromosomal deletions using sequence polymorphisms. Biotechniques 2010; 48:53-60. [PMID: 20078428 DOI: 10.2144/000113348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
One of the many advantages of Drosophila melanogaster as a model organism is the relative ease with which gene deletions can be generated by imprecise excision of transposon insertions. Here, we describe a simple, fast, and efficient method of screening for single-gene excision events that is not biased by prior assumptions of the mutant phenotype. DNA sequence polymorphisms were used as co-dominant electrophoretic markers to identify candidate deletions in a single generation, and to delimit the breakpoints to within 0.5-1 kb, thereby rapidly identifying deficiencies that affect only the gene of interest. In addition, we used polymorphism profiling to map existing deficiencies. The method can also be applied to map the extent of deletions generated by x-rays and to identify targeted mutations generated by engineered zinc-finger nucleases in Drosophila and other polymorphic model organisms (e.g., zebrafish, mouse, Caenorhabditis elegans).
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Webster DR, Hekele AG, Lauring AS, Fischer KF, Li H, Andino R, DeRisi JL. An enhanced single base extension technique for the analysis of complex viral populations. PLoS One 2009; 4:e7453. [PMID: 19834618 PMCID: PMC2759544 DOI: 10.1371/journal.pone.0007453] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 08/15/2009] [Indexed: 11/24/2022] Open
Abstract
Many techniques for the study of complex populations provide either specific information on a small number of variants or general information on the entire population. Here we describe a powerful new technique for elucidating mutation frequencies at each genomic position in a complex population. This single base extension (SBE) based microarray platform was designed and optimized using poliovirus as the target genotype, but can be easily adapted to assay populations derived from any organism. The sensitivity of the method was demonstrated by accurate and consistent readouts from a controlled population of mutant genotypes. We subsequently deployed the technique to investigate the effects of the nucleotide analog ribavirin on a typical poliovirus population through two rounds of passage. Our results show that this economical platform can be used to investigate dynamic changes occurring at frequencies below 1% within a complex nucleic acid population. Given that many key aspects of the study and treatment of disease are intimately linked to population-level genomic diversity, our SBE-based technique provides a scalable and cost-effective complement to both traditional and next generation sequencing methodologies.
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Affiliation(s)
- Dale R. Webster
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Armin G. Hekele
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Adam S. Lauring
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Kael F. Fischer
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Raul Andino
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (JLD); (RA)
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (JLD); (RA)
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Abstract
Positional cloning of chemically induced mutations is the rate-limiting step in forward genetic screens in Drosophila. Single-nucleotide polymorphisms (SNPs) are useful markers to locate a mutated region in the genome. Here, we provide a protocol for high-throughput, high-resolution SNP mapping that enables rapid and cost-effective positional cloning in Drosophila. In stage 1 of the protocol, we use highly multiplexed tag-array mini-sequencing assays to map mutations to an interval of 1-2 Mb. In these assays, SNPs are genotyped by primer extension using fluorescently labeled dideoxy-nucleotides. Fluorescent primers are captured and detected on a microarray. In stage 2, we selectively isolate recombinants within the identified 1-2 Mb interval for fine mapping of mutations to about 50 kb. We have previously demonstrated the applicability of this protocol by mapping 14 muscle morphogenesis mutants within 4 months, which represents a significant acceleration compared with other commonly used mapping strategies that may take years.
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