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Heintz N, Gong S. Working with Bacterial Artificial Chromosomes (BACs) and Other High-Capacity Vectors. Cold Spring Harb Protoc 2020; 2020:2020/10/pdb.top097998. [PMID: 33004554 DOI: 10.1101/pdb.top097998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Genetic targeting of specific cell types is fundamentally important for modern molecular-genetic studies. The development of simple methods to engineer high-capacity vectors-in particular, bacterial artificial chromosomes (BACs)-for the preparation of transgenic lines that accurately express a gene of interest has resulted in commonplace usage of transgenic techniques in a wide variety of experimental systems. Here we provide a brief description of each of the four major types of large-capacity vectors, with a focus on the use of BAC vectors.
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2
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Ma X, Fu D, Chu M, Ding X, Wu X, Guo X, Kalwar Q, Pei J, Bao P, Liang C, Yan P. Genome-Wide Analysis Reveals Changes in Polled Yak Long Non-coding RNAs in Skeletal Muscle Development. Front Genet 2020; 11:365. [PMID: 32351548 PMCID: PMC7176074 DOI: 10.3389/fgene.2020.00365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/25/2020] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been extensively studied in recent years. Numerous lncRNAs have been identified in mice, rats, and humans, some of which play important roles in muscle formation and development. However, little is known about lncRNA regulators that affect muscle development in yak (Bos grunniens). LncRNA expression during skeletal muscle development in yak was analyzed by RNA sequencing at three development stages: 3 years (group A), 6 months (group M), and 90-day-old fetuses (group E). A total of 1180 lncRNAs were identified in the three development stages. Compared with group E, 154 were upregulated and 130 were downregulated in group A. Compared with group A, 31 were upregulated and 29 were downregulated in group M. Compared with group E, 147 were upregulated and 149 were downregulated in group M (padj < 0.001, |log2FC| > 1.2). In addition, functional annotation analysis based on gene ontology (GO) and the Kyoto protocol encyclopedia of genes and genomes (KEGG) database showed that differentially expressed lncRNAs (DElncRNAs) were cis–trans target genes. The results showed that DElncRNAs were mainly involved in PI3K-Akt signaling pathway, focal adhesion, MAPK signaling pathway, apoptosis, and p53 signaling pathway. Furthermore, RTL1, IGF2, MEF2C, Pax7, and other well-known muscle development regulators were included in a co-expression network of differentially expressed target genes and lncRNAs. These data will help to further clarify the function of lncRNAs in the different stages of skeletal muscle developmental in yak.
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Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Donghai Fu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuezhi Ding
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Qudratullah Kalwar
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jie Pei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chunnian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
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3
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Sekigami Y, Kobayashi T, Omi A, Nishitsuji K, Ikuta T, Fujiyama A, Satoh N, Saiga H. Hox gene cluster of the ascidian, Halocynthia roretzi, reveals multiple ancient steps of cluster disintegration during ascidian evolution. ZOOLOGICAL LETTERS 2017; 3:17. [PMID: 28932414 PMCID: PMC5602962 DOI: 10.1186/s40851-017-0078-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/12/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Hox gene clusters with at least 13 paralog group (PG) members are common in vertebrate genomes and in that of amphioxus. Ascidians, which belong to the subphylum Tunicata (Urochordata), are phylogenetically positioned between vertebrates and amphioxus, and traditionally divided into two groups: the Pleurogona and the Enterogona. An enterogonan ascidian, Ciona intestinalis (Ci), possesses nine Hox genes localized on two chromosomes; thus, the Hox gene cluster is disintegrated. We investigated the Hox gene cluster of a pleurogonan ascidian, Halocynthia roretzi (Hr) to investigate whether Hox gene cluster disintegration is common among ascidians, and if so, how such disintegration occurred during ascidian or tunicate evolution. RESULTS Our phylogenetic analysis reveals that the Hr Hox gene complement comprises nine members, including one with a relatively divergent Hox homeodomain sequence. Eight of nine Hr Hox genes were orthologous to Ci-Hox1, 2, 3, 4, 5, 10, 12 and 13. Following the phylogenetic classification into 13 PGs, we designated Hr Hox genes as Hox1, 2, 3, 4, 5, 10, 11/12/13.a, 11/12/13.b and HoxX. To address the chromosomal arrangement of the nine Hox genes, we performed two-color chromosomal fluorescent in situ hybridization, which revealed that the nine Hox genes are localized on a single chromosome in Hr, distinct from their arrangement in Ci. We further examined the order of the nine Hox genes on the chromosome by chromosome/scaffold walking. This analysis suggested a gene order of Hox1, 11/12/13.b, 11/12/13.a, 10, 5, X, followed by either Hox4, 3, 2 or Hox2, 3, 4 on the chromosome. Based on the present results and those previously reported in Ci, we discuss the establishment of the Hox gene complement and disintegration of Hox gene clusters during the course of ascidian or tunicate evolution. CONCLUSIONS The Hox gene cluster and the genome must have experienced extensive reorganization during the course of evolution from the ancestral tunicate to Hr and Ci. Nevertheless, some features are shared in Hox gene components and gene arrangement on the chromosomes, suggesting that Hox gene cluster disintegration in ascidians involved early events common to tunicates as well as later ascidian lineage-specific events.
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Affiliation(s)
- Yuka Sekigami
- Department of Biological Sciences and Technology, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo, 192-0397 Japan
| | - Takuya Kobayashi
- Department of Biological Sciences and Technology, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo, 192-0397 Japan
| | - Ai Omi
- Department of Biological Sciences and Technology, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo, 192-0397 Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495 Japan
| | - Tetsuro Ikuta
- Department of Biological Sciences and Technology, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo, 192-0397 Japan
| | - Asao Fujiyama
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495 Japan
| | - Hidetoshi Saiga
- Department of Biological Sciences and Technology, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo, 192-0397 Japan
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Romano JE, Raussdepp T, Mulon PY, Villadóniga GB. Non-mosaic monosomy 59,X in cattle: a case report. Anim Reprod Sci 2015; 156:83-90. [PMID: 25835572 DOI: 10.1016/j.anireprosci.2015.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 03/03/2015] [Accepted: 03/06/2015] [Indexed: 01/15/2023]
Abstract
A 3-year-old Longhorn heifer was referred to the Veterinary Medical Teaching Hospital of Texas A&M University for inability to get pregnant. Physical examination revealed a small-sized female for age and breed with a normal vulva, vaginal length, and external cervical os. Further assessment by per rectum palpation and trans-rectal ultrasonography revealed a small uterine cervix and cord-like uterine horns with no identifiable ovaries. Additional evaluation including laparoscopy, hormonal evaluation, and genetic analysis allowed ruling out conditions commonly associated with a phenotypic female with infantile or underdeveloped reproductive organs such as freemartin, XY gonadal dysgenesis, testicular feminization, and bilateral ovarian agenesis. Laparoscopy confirmed the presence of a small cervix with small uterine horns and absence of ovaries. Testosterone, progesterone, and 17-β estradiol concentrations were 200.0pg/mL, 1.48ng/mL, and undetectable, respectively. Genetic evaluation determined that the karyotype was 59,X non-mosaic. Evaluation of phenotypically female cattle with infertility and infantile genital organs and absence of ovaries should include cytogenetic analysis to test for possible X monosomy. The 59,X condition should be considered in the differential diagnoses together with freemartin, dysgenesis XY, testicular feminization, and bilateral ovarian agenesis.
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Affiliation(s)
- Juan E Romano
- Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX 77843-4475, USA.
| | - Terje Raussdepp
- Veterinary Integrative Biosciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX 77843-4475, USA
| | - Pierre Y Mulon
- Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX 77843-4475, USA
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5
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Wang F, Ekiert DC, Ahmad I, Yu W, Zhang Y, Bazirgan O, Torkamani A, Raudsepp T, Mwangi W, Criscitiello MF, Wilson IA, Schultz PG, Smider VV. Reshaping antibody diversity. Cell 2013; 153:1379-93. [PMID: 23746848 DOI: 10.1016/j.cell.2013.04.049] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 02/15/2013] [Accepted: 04/23/2013] [Indexed: 11/16/2022]
Abstract
Some species mount a robust antibody response despite having limited genome-encoded combinatorial diversity potential. Cows are unusual in having exceptionally long CDR H3 loops and few V regions, but the mechanism for creating diversity is not understood. Deep sequencing reveals that ultralong CDR H3s contain a remarkable complexity of cysteines, suggesting that disulfide-bonded minidomains may arise during repertoire development. Indeed, crystal structures of two cow antibodies reveal that these CDR H3s form a very unusual architecture composed of a β strand "stalk" that supports a structurally diverse, disulfide-bonded "knob" domain. Diversity arises from somatic hypermutation of an ultralong DH with a severe codon bias toward mutation to cysteine. These unusual antibodies can be elicited to recognize defined antigens through the knob domain. Thus, the bovine immune system produces an antibody repertoire composed of ultralong CDR H3s that fold into a diversity of minidomains generated through combinations of somatically generated disulfides.
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Affiliation(s)
- Feng Wang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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Abstract
The vision of Morris Soller was instrumental in launching the field of bovine genomics. This study is a review of the early years of bovine gene mapping leading up to the sequencing and assembly of the bovine genome in 2009. A historical perspective of parasexual, linkage and physical mapping is provided with a focus on the contribution of these maps to the eventual assignment and orientation of genes and sequence to cattle chromosomes.
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Affiliation(s)
- James E Womack
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843-4467, USA
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7
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Reyes-Valdés MH, Ji Y, Crane CF, Islam-Faridi MN, Price HJ, Stelly DM, Taylor JF. ISH-facilitated analysis of meiotic bivalent pairing. Genome 2012; 39:784-92. [PMID: 18469936 DOI: 10.1139/g96-098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chiasmata constitute one of the cornerstones of sexual reproduction in most eukaryotes. They mediate the reciprocal genetic exchange between homologues and are essential to the proper orientation of the homologous centromeres in meiosis I. As markers of recombination, they offer a cytological means of mapping. Rather than trying to accurately count individual chiasmata, we have examined properties of the mathematical relationship between frequencies of nonadorned disomic configurations in meiosis (ring, rods, and univalents) and the probabilities at which arms of the respective chromosomes are chiasmate (one or more chiasma per arm). Numerical analyses indicated that conventionally analyzed bivalents with nonidentified arms yield statistically biased estimates of chiasma probabilities under a broad range of circumstances. We subsequently analyzed estimators derived from adorned configurations with ISH-marked arms, which were found to be statistically far superior, and with no assumptions concerning interference across the centromere. We applied this methodology in the study of chromosomes 16 and 23 of cotton (Gossypium hirsutum), and estimated their arm lengths in centimorgans. The results for chromosome 23, the only one of the two chromosomes with a documented RFLP map, were consistent with the literature. Similar molecular-meiotic configuration analyses can be used for a wide variety of eukaryotic organisms and purposes: for example, providing far more powerful meiotic comparisons of genomes of chromosomes, and a rapid means of evaluating effects on recombination. Key words : meiotic configurations, chiasma frequencies, in situ hybridization, cotton.
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8
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Stafuzza NB, Abbey CA, Gill CA, Womack JE, Amaral MEJ. Construction and preliminary characterization of a river buffalo bacterial artificial chromosome library. GENETICS AND MOLECULAR RESEARCH 2012; 11:3013-9. [PMID: 22653673 DOI: 10.4238/2012.may.22.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
River buffalo genome analyses have advanced significantly in the last decade, and the genome sequence of Bubalus bubalis will be available shortly. Nonetheless, large-insert DNA library resources such as bacterial artificial chromosomes (BAC) are still required for validation and accurate assembly of the genome sequence. We constructed a river buffalo BAC library containing 52,224 clones with an average insert size of 97 kb, representing 1.7 × coverage of the genome. This genomic resource for river buffalo will facilitate further studies in this economically important species allowing for instance, whole genome physical mapping and isolation of genes and gene clusters, contributing to the elucidation of gene organization and identification of regulatory elements.
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Affiliation(s)
- N B Stafuzza
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual de São Paulo "Júlio de Mesquita Filho", São José do Rio Preto, SP, Brazil
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9
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Construction of a llama bacterial artificial chromosome library with approximately 9-fold genome equivalent coverage. J Biomed Biotechnol 2012; 2012:371414. [PMID: 22811594 PMCID: PMC3395300 DOI: 10.1155/2012/371414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 05/21/2012] [Accepted: 06/04/2012] [Indexed: 11/18/2022] Open
Abstract
The Ilama is an important agricultural livestock in much of South America. The llama is increasing in popularity in the United States as a companion animal. Little work has been done to improve llama production using modern technology. A paucity of information is available regarding the llama genome. We report the construction of a llama bacterial artificial chromosome (BAC) library of about 196,224 clones in the vector pECBAC1. Using flow cytometry and bovine, human, mouse, and chicken as controls, we determined the llama genome size to be 2.4 × 109 bp. The average insert size of the library is 137.8 kb corresponding to approximately 9-fold genome coverage. Further studies are needed to further characterize the library and llama genome. We anticipate that this new library will help facilitate future genomic studies in the llama.
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Schulte D, Ariyadasa R, Shi B, Fleury D, Saski C, Atkins M, deJong P, Wu CC, Graner A, Langridge P, Stein N. BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.). BMC Genomics 2011; 12:247. [PMID: 21595870 PMCID: PMC3224359 DOI: 10.1186/1471-2164-12-247] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 05/19/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although second generation sequencing (2GS) technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequisite for whole genome sequencing for genomes like barley. To start such an endeavor, large insert genomic libraries, i.e. Bacterial Artificial Chromosome (BAC) libraries, which are unbiased and representing deep haploid genome coverage, need to be ready in place. RESULT Five new BAC libraries were constructed for barley (Hordeum vulgare L.) cultivar Morex. These libraries were constructed in different cloning sites (HindIII, EcoRI, MboI and BstXI) of the respective vectors. In order to enhance unbiased genome representation and to minimize the number of gaps between BAC contigs, which are often due to uneven distribution of restriction sites, a mechanically sheared library was also generated. The new BAC libraries were fully characterized in depth by scrutinizing the major quality parameters such as average insert size, degree of contamination (plate wide, neighboring, and chloroplast), empty wells and off-scale clones (clones with <30 or >250 fragments). Additionally a set of gene-based probes were hybridized to high density BAC filters and showed that genome coverage of each library is between 2.4 and 6.6 X. CONCLUSION BAC libraries representing >20 haploid genomes are available as a new resource to the barley research community. Systematic utilization of these libraries in high-throughput BAC fingerprinting should allow developing a genome-wide physical map for the barley genome, which will be instrumental for map-based gene isolation and genome sequencing.
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Affiliation(s)
- Daniela Schulte
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
- KWS SAAT AG, Grimsehlstr. 31, 37555 Einbeck, Germany
| | - Ruvini Ariyadasa
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Bujun Shi
- Australian Centre of Plant Functional Genomics, University of Adelaide, PMB 1 Glen Osmond SA 5064, Australia
| | - Delphine Fleury
- Australian Centre of Plant Functional Genomics, University of Adelaide, PMB 1 Glen Osmond SA 5064, Australia
| | - Chris Saski
- Clemson University Genomics Institute (CUGI), 51 New Cherry St. BRC 310, Clemson, SC 29634, USA
| | - Michael Atkins
- Clemson University Genomics Institute (CUGI), 51 New Cherry St. BRC 310, Clemson, SC 29634, USA
| | - Pieter deJong
- BACPAC Resources, Children's Hospital Oakland, 747 52nd St. Oakland, CA 94609, USA
| | - Cheng-Cang Wu
- Lucigen Corporation, 2120 West Greenview Dr., Middleton, WI 53562, USA
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Peter Langridge
- Australian Centre of Plant Functional Genomics, University of Adelaide, PMB 1 Glen Osmond SA 5064, Australia
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
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Kim DW, Choi SH, Kim RN, Kim SH, Paik SG, Nam SH, Kim DW, Kim A, Kang A, Park HS. Comparative genomic analysis of the false killer whale (Pseudorca crassidens) LMBR1 locus. Genome 2010; 53:658-66. [PMID: 20924415 DOI: 10.1139/g10-043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The sequencing and comparative genomic analysis of LMBR1 loci in mammals or other species, including human, would be very important in understanding evolutionary genetic changes underlying the evolution of limb development. In this regard, comparative genomic annotation of the false killer whale LMBR1 locus could shed new light on the evolution of limb development. We sequenced two false killer whale BAC clones, corresponding to 156 kb and 144 kb, respectively, harboring the tightly linked RNF32, LMBR1, and NOM1 genes. Our annotation of the false killer whale LMBR1 gene showed that it consists of 17 exons (1473 bp), in contrast to 18 exons (1596 bp) in human, and it displays 93.1% and 95.6% nucleotide and amino acid sequence similarity, respectively, compared with the human gene. In particular, we discovered that exon 10, deleted in the false killer whale LMBR1 gene, is present only in primates, and this fact strongly implies that exon 10 might be crucial in determining primate-specific limb development. ZRS and TFBS sequences have been well conserved across 11 species, suggesting that these regions could be involved in an important function of limb development and limb patterning. The neighboring gene RNF32 showed several lineage-conserved exons, such as exons 2 through 9 conserved in eutherian mammals, exons 3 through 9 conserved in mammals, and exons 5 through 9 conserved in vertebrates. The other neighboring gene, NOM1, had undergone a substitution (ATG→GTA) at the start codon, giving rise to a 36 bp shorter N-terminal sequence compared with the human sequence. Our comparative analysis of the false killer whale LMBR1 genomic locus provides important clues regarding the genetic regions that may play crucial roles in limb development and patterning.
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Affiliation(s)
- Dae-Won Kim
- Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
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Biber A, Kaufmann H, Linde M, Spiller M, Terefe D, Debener T. Molecular markers from a BAC contig spanning the Rdr1 locus: a tool for marker-assisted selection in roses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:765-73. [PMID: 19911159 DOI: 10.1007/s00122-009-1197-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 10/17/2009] [Indexed: 05/03/2023]
Abstract
We constructed a BAC contig of about 300 kb spanning the Rdr1 locus for black spot resistance in Rosa multiflora hybrids, using a new BIBAC library from DNA of this species. From this contig, we developed broadly applicable simple sequence repeat (SSR) markers tightly linked to Rdr1, which are suitable for genetic analyses and marker-assisted selection in roses. As a source for the high molecular weight DNA, we chose the homozygous resistant R. multiflora hybrid 88/124-46. For the assembly of the BAC contig, we made use of molecular markers derived from a previously established R. rugosa contig. In order to increase the resolution for fine mapping, the size of the population was increased to 974 plants. The genomic region spanning Rdr1 is now genetically restricted to 0.2 cM, corresponding to a physical distance of about 300 kb. One single-stranded conformational polymorphism (SSCP) and one SSR marker cosegregate with the Rdr1-mediated black spot resistance, while one SSR and several cleaved amplified polymorphic sequence or SSCP markers are very tightly linked with one to three recombinants among the 974 plants. The benefits of the molecular markers developed from the R. multiflora contig for the genetic analysis of roses and the integration of rose genetic maps are discussed.
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Affiliation(s)
- Anja Biber
- Institute for Plant Genetics, Leibniz University Hannover, Herrenhaeuser Strasse 2, Hannover, Germany
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13
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Ratnakumar A, Barris W, McWilliam S, Brauning R, McEwan JC, Snelling WM, Dalrymple BP. A multiway analysis for identifying high integrity bovine BACs. BMC Genomics 2009; 10:46. [PMID: 19166603 PMCID: PMC2660975 DOI: 10.1186/1471-2164-10-46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 01/23/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In large genomics projects involving many different types of analyses of bacterial artificial chromosomes (BACs), such as fingerprinting, end sequencing (BES) and full BAC sequencing there are many opportunities for the identities of BACs to become confused. However, by comparing the results from the different analyses, inconsistencies can be identified and a set of high integrity BACs preferred for future research can be defined. RESULTS The location of each bovine BAC in the BAC fingerprint-based genome map and in the genome assembly were compared based on the reported BESs, and for a smaller number of BACs the full sequence. BACs with consistent positions in all three datasets, or if the full sequence was not available, for both the fingerprint map and BES-based alignments, were deemed to be correctly positioned. BACs with consistent BES-based and fingerprint-based locations, but with conflicting locations based on the fully sequenced BAC, appeared to have been misidentified during sequencing, and included a number of apparently swapped BACs. Inconsistencies between BES-based and fingerprint map positions identified thirty one plates from the CHORI-240 library that appear to have suffered substantial systematic problems during the end-sequencing of the BACs. No systematic problems were identified in the fingerprinting of the BACs. Analysis of BACs overlapping in the assembly identified a small overrepresentation of clones with substantial overlap in the library and a substantial enrichment of highly overlapping BACs on the same plate in the CHORI-240 library. More than half of these BACs appear to have been present as duplicates on the original BAC-library plates and thus should be avoided in subsequent projects. CONCLUSION Our analysis shows that approximately 95% of the bovine CHORI-240 library clones with both a BAC fingerprint and two BESs mapping to the genome in the expected orientations (approximately 27% of all BACs) have consistent locations in the BAC fingerprint map and the genome assembly. We have developed a broadly applicable methodology for checking the integrity of BAC-based datasets even where only incomplete and partially assembled genomic sequence is available.
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Affiliation(s)
- Abhirami Ratnakumar
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, QLD 4067, Australia.
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14
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Hu X, Gao Y, Feng C, Liu Q, Wang X, Du Z, Wang Q, Li N. Advanced technologies for genomic analysis in farm animals and its application for QTL mapping. Genetica 2008; 136:371-86. [DOI: 10.1007/s10709-008-9338-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 11/19/2008] [Indexed: 12/25/2022]
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15
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Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Aerts J, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jann O, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas FW, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel RD, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor JF, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S. A physical map of the bovine genome. Genome Biol 2008; 8:R165. [PMID: 17697342 PMCID: PMC2374996 DOI: 10.1186/gb-2007-8-8-r165] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 07/20/2007] [Accepted: 08/14/2007] [Indexed: 11/10/2022] Open
Abstract
A new physical map of the bovine genome has been constructed by integrating data from genetic and radiation hybrid maps, and a new bovine BAC map, with the bovine genome draft assembly. Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project. Results A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly. Conclusion Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.
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Affiliation(s)
- Warren M Snelling
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Readman Chiu
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Jacqueline E Schein
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Matthew Hobbs
- Cooperative Research Centre for Innovative Dairy Products, Reprogen, Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | | | | | - Jan Aerts
- Roslin Institute, Roslin, Midlothian EH25 9PS, UK
| | - Gary L Bennett
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Ian E Bosdet
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Mekki Boussaha
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | | | - Alexandre R Caetano
- Embrapa Recursos Geneticos e Biotecnologia, Parque Estacao Biologica, Final Av. W/5 Norte, Brasilia-DF, CP 02372 70770-900, Brasil
| | - Marcos M Costa
- Embrapa Recursos Geneticos e Biotecnologia, Parque Estacao Biologica, Final Av. W/5 Norte, Brasilia-DF, CP 02372 70770-900, Brasil
| | | | - Brian P Dalrymple
- CSIRO Livestock Industries, Carmody Road, St Lucia, Queensland 4067, Australia
| | - André Eggen
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | | | - Sandrine Floriot
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | - Mathieu Gautier
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | - Clare A Gill
- Texas A&M University, College Station, TX 77843, USA
| | - Ronnie D Green
- USDA-ARS - National Program Staff, Beltsville, MD 20705-5134, USA
| | - Robert Holt
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Oliver Jann
- Roslin Institute, Roslin, Midlothian EH25 9PS, UK
| | - Steven JM Jones
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Steven M Kappes
- USDA-ARS - National Program Staff, Beltsville, MD 20705-5134, USA
| | - John W Keele
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Pieter J de Jong
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
| | - Denis M Larkin
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Harris A Lewin
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Stephanie McKay
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Marco A Marra
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Carrie A Mathewson
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Stephen S Moore
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Brenda Murdoch
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Frank W Nicholas
- Cooperative Research Centre for Innovative Dairy Products, Reprogen, Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | - Kazutoyo Osoegawa
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
| | - Alice Roy
- Genoscope, rue Gaston Cremieux, 91057 Evry, France
| | - Hanni Salih
- Texas A&M University, College Station, TX 77843, USA
| | - Laurent Schibler
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | - Robert D Schnabel
- Animal Science Research Center, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Licia Silveri
- Istituto di Zootecnica Università Cattolica del S Cuore, via E Parmense, 84 29100 Piacenza, Italy
| | - Loren C Skow
- Texas A&M University, College Station, TX 77843, USA
| | - Timothy PL Smith
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Tad S Sonstegard
- USDA, ARS, BARC Bovine Functional Genomics Laboratory, Maryland, USA
| | - Jeremy F Taylor
- Animal Science Research Center, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Ross Tellam
- CSIRO Livestock Industries, Carmody Road, St Lucia, Queensland 4067, Australia
| | | | - John L Williams
- Roslin Institute, Roslin, Midlothian EH25 9PS, UK
- Current address: Parco Tecnologico Padano, Via Einstein, Polo Universitario, Lodi 26900, Italy
| | | | - Natasja H Wye
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - George Yang
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Shaying Zhao
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
- Current address: Department of Biochemistry and Molecular Biology, University of Georgia, Green Street, Athens, GA 30602-7229, USA
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A PCR-based high-throughput screen with multiround sample pooling: application to somatic cell gene targeting. Nat Protoc 2008; 2:2865-74. [PMID: 18007621 DOI: 10.1038/nprot.2007.409] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Here, we describe a method of systematic PCR screening with multiround sample pooling for the isolation of rare PCR-positive samples. As an example, we have applied this protocol to the recovery of gene-targeted clones in human somatic cells comprising only 0.02-0.17% of cells transduced with targeting vectors. Initially, cells infected with targeting vectors are seeded and grown in fourteen 96-well tissue culture plates. Samples are then collected from these plates and subjected to two rounds of pooling to yield twelve 'superpools' used for an initial PCR. After identifying PCR-positive samples, de-pooling is carried out with successive rounds of PCR screening, using samples of decreasing complexity. Single-cell cloning is subsequently performed to isolate gene-targeted clones. The entire protocol can be completed in 4-8 weeks depending on the proliferative capacity of the cell line.
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17
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Novel bacterial artificial chromosome vector pUvBBAC for use in studies of the functional genomics of Listeria spp. Appl Environ Microbiol 2008; 74:1892-901. [PMID: 18223114 DOI: 10.1128/aem.00415-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial artificial chromosome (BAC) vectors are important tools for microbial genome research. We constructed a novel BAC vector, pUvBBAC, for replication in both gram-negative and gram-positive bacterial hosts. The pUvBBAC vector was used to generate a BAC library for the facultative intracellular pathogen Listeria monocytogenes EGD-e. The library had insert sizes ranging from 68 to 178 kb. We identified two recombinant BACs from the L. monocytogenes pUvBBAC library that each contained the entire virulence gene cluster (vgc) of L. monocytogenes and transferred them to a nonpathogenic Listeria innocua strain. Recombinant L. innocua strains harboring pUvBBAC+vgc1 and pUvBBAC+vgc2 produced the vgc-specific listeriolysin (LLO) and actin assembly protein ActA and represent the first reported cloning of the vgc locus in its entirety. The use of the novel broad-host-range BAC vector pUvBBAC extends the versatility of this technology and provides a powerful platform for detailed functional genomics of gram-positive bacteria as well as its use in explorative functional metagenomics.
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18
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Klisch K, Thomsen PD, Dantzer V, Leiser R. Genome multiplication is a generalised phenomenon in placentomal and interplacentomal trophoblast giant cells in cattle. Reprod Fertil Dev 2007. [PMID: 15304202 DOI: 10.1071/rd03101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The frequency of polyploidisation in bovine binucleate trophoblast giant cells (TGC) from placentomes (PL) and the interplacentomal allantochorion (AL) of six male fetuses with a crown-rump length between 3.5 and 103 cm was determined by in situ hybridisation with a chromosome-7-specific probe, using a probe specific for the Y chromosome to distinguish between maternal and fetal nuclei. The results showed that polyploid nuclei were essentially always of fetal origin. The frequency of tetraploid nuclei varied between 3% and 15% in both the placentomal and interplacentomal samples, with mean frequencies of 8.8% and 10.0% respectively. Octoploid nuclei were observed with a mean frequency of 1.1% in the interplacentomal samples, but were absent in samples from placentomes. Subsequent determination of nuclear DNA content by cytophotometric measurement of Feulgen-stained nuclei revealed that the frequency of nuclei with an 8C DNA content was several fold higher (AL 5.4%; PL 7.8%) than the frequency of octoploidy, suggesting that tetraploid TGC cells are arrested in the G2 phase of the cell cycle.
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Affiliation(s)
- Karl Klisch
- Microscopical Anatomy, Medical School of Hannover, Hannover, Germany.
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19
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Bridger PS, Haupt S, Klisch K, Leiser R, Tinneberg HR, Pfarrer C. Validation of primary epitheloid cell cultures isolated from bovine placental caruncles and cotyledons. Theriogenology 2007; 68:592-603. [PMID: 17580088 DOI: 10.1016/j.theriogenology.2007.05.046] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Revised: 04/04/2007] [Accepted: 05/05/2007] [Indexed: 11/18/2022]
Abstract
In order to study feto-maternal interactions in the bovine synepitheliochorial placenta primary cell cultures of both placentomal components throughout pregnancy, namely caruncular epithelial cells and trophoblast cells were developed. The aim of this study was to validate and improve a method to culture caruncular epithelial cells and fetal trophoblast from manually separated placentomes. Prior to seeding the presence of fetal cells in caruncular samples and vice-versa could be demonstrated by the detection of the Y-chromosome via fluorescence in situ hybridization (FISH) provided the fetus was male. Epitheloid shaped cells present in both cultures (cotyledon and caruncle) were characterized on a morphological basis as well as by immunofluorescence and Western blot thereby detecting cytokeratin, zonula occludens-1 and vimentin but not alpha-smooth muscle actin and desmin. The absence of the Y-chromosome demonstrated the caruncular origin of epitheloid cells. In addition, a population of polygonally shaped cells derived from the cotyledon was propagated and displayed the same cytoskeletal characteristics as described above. The presence of the Y-chromosome confirmed the fetal origin of these cells and the lacking uptake of fluorescence conjugated low density lipoprotein, specific for endothelial cells, identified polygonally shaped cells as fetal trophoblast cells. In conclusion, the cross-contamination of maternal and fetal cells in manually separated placentomes should be considered in future experiments as it may lead to false positive results dependent on the sensitivity of the method applied. This study highlights the importance of an appropriate cell characterization and identification, especially when isolating primary cells.
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Affiliation(s)
- P S Bridger
- Department of Veterinary Anatomy, Histology and Embryology, Justus-Liebig-University, Frankfurter Str 98, Giessen, Germany
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20
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Knorr C, Beuermann C, Beck J, Brenig B. Characterization of the porcine multicopy ribosomal protein SA/37-kDa laminin receptor gene family. Gene 2007; 395:135-43. [PMID: 17434268 DOI: 10.1016/j.gene.2007.02.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Revised: 02/09/2007] [Accepted: 02/19/2007] [Indexed: 11/16/2022]
Abstract
Prions represent a new class of infectious agents. The pathogenic prion protein (PrPSc) is known as the trigger of bovine transmissible spongiform encephalopathy (TSE). By contrast, an oral transmission of PrPSc and an ensuing infection seems to be blocked in non-ruminants such as pigs. Several investigations postulate that the ribosomal protein SA (RPSA) previously named 37-kDa laminin receptor precursor (LRP)/67-kDa laminin receptor (LR) is the candidate for binding and internalization of externally added cellular prion protein in the gut. We isolated a porcine ribosomal protein SA cDNA that consists of 1064 bp with an open reading frame of 885 bp encoding a 295 aa protein. The alignment of vertebrate ribosomal protein SA sequences displayed interspecies differences between cattle and pigs at positions 241 and 272 in the putative indirect PrP interaction site (aa 180-285) on RPSA. A PAC library screen revealed the existence of two processed ribosomal protein SA pseudogenes (RPSAP1 and RPSAP3) and of one non-processed pseudogene (RPSAP2). The pseudogenes have been assigned to SSC6 and SSC1 by hybrid panel analyses and FISH. Compared with the porcine cDNA 3, 7, and 13 insdels, 36, 25, and 57 single nucleotide exchanges and 6, 10, and 8 premature stop codons have been deciphered for RPSAP1, RPSAP2, and RPSAP3. In the 5', 3', and intron like regions, 2 (RPSAP1), 10 (RPSAP2), and 4 (RPSAP3) repeats have been detected. Basically, the repeats belong to one of the class/family LINE/L1, SINE/tRNA-Glu and DNA/MER1_type. We conclude that the pig genome contains multiple copies of the RPSA sequence probably as a consequence to maintain the multifunctionality of the mature protein.
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Affiliation(s)
- Christoph Knorr
- Institute of Veterinary Medicine, Georg-August-University of Goettingen, Goettingen, Germany
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21
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Hansen GR, Abbey CA, Gaile DP, Raudsepp T, Chowdhary BP, Womack JE, Gill CA. Assignment of six genes to bovine chromosomes 5 and 16 by fluorescence in situ hybridization, radiation hybrid mapping and genetic linkage analysis. Cytogenet Genome Res 2007; 116:194-7. [PMID: 17317959 DOI: 10.1159/000098186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Accepted: 11/08/2006] [Indexed: 11/19/2022] Open
Abstract
Several quantitative trait loci for beef carcass traits have been mapped to bovine chromosome 5. The objective of this study was to map six candidate genes for these traits by fluoresence in situ hybridization, genetic linkage analysis and radiation hybrid mapping. MYF5 and MYF6 were assigned to 5q13, WIF1 to 5q23 and MMP19 to 5q25. A paralog of MYF5 (putatively MYOG) was assigned to 16q12. A novel microsatellite placed MYF5 and MYF6 10.4 cM from BM6026 and 19.1 cM from BL23 on the genetic linkage map. MYF5 (62.6 cR), WNT10B (319.5 cR), WIF1 (500.8 cR) and MMP19 (701.2 cR) were also integrated into the 5000(Rad) radiation hybrid map.
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Affiliation(s)
- G R Hansen
- Department of Animal Science, Texas A&M University, College Station, TX, USA.
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Wunderlich KR, Abbey CA, Clayton DR, Song Y, Schein JE, Georges M, Coppieters W, Adelson DL, Taylor JF, Davis SL, Gill CA. A 2.5-Mb contig constructed from Angus, Longhorn and horned Hereford DNA spanning the polled interval on bovine chromosome 1. Anim Genet 2007; 37:592-4. [PMID: 17121607 DOI: 10.1111/j.1365-2052.2006.01538.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The polled locus has been mapped by genetic linkage analysis to the proximal region of bovine chromosome 1. As an intermediate step in our efforts to identify the polled locus and the underlying causative mutation for the polled phenotype, we have constructed a BAC-based physical map of the interval containing the polled locus. Clones containing genes and markers in the critical interval were isolated from the TAMBT (constructed from Angus and Longhorn genomic DNA) and CHORI-240 (constructed from horned Hereford genomic DNA) BAC libraries and ordered based on fingerprinting and the presence or absence of 80 STS markers. A single contig spanning 2.5 Mb was assembled. Comparison of the physical order of STSs to the corresponding region of human chromosome 21 revealed the same order of genes within the polled critical interval. This contig of overlapping BAC clones from horned and polled breeds is a useful resource for SNP discovery and characterization of positional candidate genes.
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Affiliation(s)
- K R Wunderlich
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA
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Wang Z, Miyake T, Edwards SV, Amemiya CT. Tuatara (Sphenodon) Genomics: BAC Library Construction, Sequence Survey, and Application to the DMRT Gene Family. J Hered 2006; 97:541-8. [PMID: 17135461 DOI: 10.1093/jhered/esl040] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The tuatara (Sphenodon punctatus) is of "extraordinary biological interest" as the most distinctive surviving reptilian lineage (Rhyncocephalia) in the world. To provide a genomic resource for an understanding of genome evolution in reptiles, and as part of a larger project to produce genomic resources for various reptiles (evogen.jgi.doe.gov/second_levels/BACs/our_libraries.html), a large-insert bacterial artificial chromosome (BAC) library from a male tuatara was constructed. The library consists of 215 424 individual clones whose average insert size was empirically determined to be 145 kb, yielding a genomic coverage of approximately 6.3x. A BAC-end sequencing analysis of 121 420 bp of sequence revealed a genomic GC content of 46.8%, among the highest observed thus far for vertebrates, and identified several short interspersed repetitive elements (mammalian interspersed repeat-type repeats) and long interspersed repetitive elements, including chicken repeat 1 element. Finally, as a quality control measure the arrayed library was screened with probes corresponding to 2 conserved noncoding regions of the candidate sex-determining gene DMRT1 and the DM domain of the related DMRT2 gene. A deep coverage contig spanning nearly 300 kb was generated, supporting the deep coverage and utility of the library for exploring tuatara genomics.
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Affiliation(s)
- Zhenshan Wang
- Department of Biology, University of Washington, Seattle, WA 98195, USA.
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Liu W, Zhao Y, Liu Z, Zhang Y, Lian Z, Li N. Construction of a 7-fold BAC library and cytogenetic mapping of 10 genes in the giant panda (Ailuropoda melanoleuca). BMC Genomics 2006; 7:294. [PMID: 17109760 PMCID: PMC1664575 DOI: 10.1186/1471-2164-7-294] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Accepted: 11/17/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to promote research on this genome, a bacterial artificial chromosome (BAC) library of the giant panda was constructed in this study. RESULTS This BAC library contains 198,844 clones with an average insert size of 108 kb, which represents approximately seven equivalents of the giant panda haploid genome. Screening the library with 15 genes and 8 microsatellite markers demonstrates that it is representative and has good genome coverage. Furthermore, ten BAC clones harbouring AGXT, GHR, FSHR, IRBP, SOX14, TTR, BDNF, NT-4, LH and ZFX1 were mapped to 8 pairs of giant panda chromosomes by fluorescence in situ hybridization (FISH). CONCLUSION This is the first large-insert genomic DNA library for the giant panda, and will contribute to understanding this endangered species in the areas of genome sequencing, physical mapping, gene cloning and comparative genomic studies. We also identified the physical locations of ten genes on their relative chromosomes by FISH, providing a preliminary framework for further development of a high resolution cytogenetic map of the giant panda.
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Affiliation(s)
- Wei Liu
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing 100094, China
| | - Yonghui Zhao
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing 100094, China
| | - Zhaoliang Liu
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing 100094, China
| | - Ying Zhang
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing 100094, China
| | - Zhengxing Lian
- College of Animal Science and Technology, China Agricultural University, Beijing 100094, China
| | - Ning Li
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing 100094, China
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Roelofs JB, Bouwman EB, Pedersen HG, Rasmussen ZR, Soede NM, Thomsen PD, Kemp B. Effect of time of artificial insemination on embryo sex ratio in dairy cattle. Anim Reprod Sci 2006; 93:366-71. [PMID: 16256282 DOI: 10.1016/j.anireprosci.2005.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Revised: 09/06/2005] [Accepted: 09/12/2005] [Indexed: 10/25/2022]
Abstract
The objective of the present study was to examine whether different intervals between insemination and ovulation have an influence on the sex of seven-day-old embryos in dairy cattle. Cows were inseminated once with semen of one of two bulls of proven fertility between 36 h before ovulation and 12 h after ovulation. Time of ovulation was assessed by ultrasound at 4-h intervals. In total, 64 embryos were determined to be male or female. Of these 64 embryos, 51.6% were female. The sex ratio in the various insemination-ovulation intervals (early: between 36 and 20 h before ovulation; intermediate: between 20 and 8 h before ovulation; late: between 8 h before and 12 h after ovulation) did not significantly differ from the expected 1:1 sex ratio (50, 50 and 55% females, respectively). Bull (Bull A and B) and Parity (primiparous and multiparous) had no influence on the expected 1:1 sex ratio either. The number of cell cycles was similar for male and female (P = 0.23) embryos when quality of the embryo (P < 0.0001) was included in the model. The results of this study indicate that, in cattle, the interval between insemination and ovulation does not influence the sex ratio of seven-day-old embryos.
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Affiliation(s)
- J B Roelofs
- Adaptation Physiology, Department of Animal Science, Wageningen University, P.O. Box 338, 6700 AH Wageningen, The Netherlands
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Yin CC, Chen HY, Zhang Q. Identification of two bovine microsatellite markers in a defined region of BTA6. Anim Genet 2006; 36:527-9. [PMID: 16293137 DOI: 10.1111/j.1365-2052.2005.01371.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- C C Yin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100094, China
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27
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Childers CP, Newkirk HL, Honeycutt DA, Ramlachan N, Muzney DM, Sodergren E, Gibbs RA, Weinstock GM, Womack JE, Skow LC. Comparative analysis of the bovine MHC class IIb sequence identifies inversion breakpoints and three unexpected genes. Anim Genet 2006; 37:121-9. [PMID: 16573526 DOI: 10.1111/j.1365-2052.2005.01395.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The bovine major histocompatibility complex (MHC) or BoLA is organized differently from typical mammalian MHCs in that a large portion of the class II region, called class IIb, has been transposed to a position near the centromere on bovine chromosome 23. Gene mapping indicated that the rearrangement resulted from a single inversion, but the boundaries and gene content of the inverted segment have not been fully determined. Here, we report the genomic sequence of BoLA IIb. Comparative sequence analysis with the human MHC revealed that the proximal inversion breakpoint occurred approximately 2.5 kb from the 3' end of the glutamate-cysteine ligase, catalytic subunit (GCLC) locus and that the distal breakpoint occurred about 2 kb from the 5' end from a divergent class IIDRbeta-like sequence designated DSB. Gene content, order and orientation of BoLA IIb are consistent with the single inversion hypothesis when compared with the corresponding region of the human class II MHC (HLA class II). Differences with HLA include the presence of a single histone H2B gene located between the proteasome subunit, beta type, 9 (PSMB9) and DMB loci and a duplicated TAP2 with a variant splice site. BoLA IIb spans approximately 450 kb DNA, with 20 apparently intact genes and no obvious pseudogenes. The region contains 227 simple sequence repeats (SSRs) and approximately 167 kb of retroviral-related repetitive DNA. Nineteen of the 20 genes identified in silico are supported by bovine EST data indicating that the functional gene content of BoLA IIb has not been diminished because it has been transposed from the remainder of BoLA genes.
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Affiliation(s)
- C P Childers
- College of Veterinary Medicine, Texas A&M University, College Station, TX 77843-4458, USA
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Feng J, Vick BA, Lee MK, Zhang HB, Jan CC. Construction of BAC and BIBAC libraries from sunflower and identification of linkage group-specific clones by overgo hybridization. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:23-32. [PMID: 16612648 DOI: 10.1007/s00122-006-0265-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 03/09/2006] [Indexed: 05/04/2023]
Abstract
Complementary BAC and BIBAC libraries were constructed from nuclear DNA of sunflower cultivar HA 89. The BAC library, constructed with BamHI in the pECBAC1 vector, contains 107,136 clones and has an average insert size of 140 kb. The BIBAC library was constructed with HindIII in the plant-transformation-competent binary vector pCLD04541 and contains 84,864 clones, with an average insert size of 137 kb. The two libraries combined contain 192,000 clones and are equivalent to approximately 8.9 haploid genomes of sunflower (3,000 Mb/1C), and provide a greater than 99% probability of obtaining a clone of interest. The frequencies of BAC and BIBAC clones carrying chloroplast or mitochondrial DNA sequences were estimated to be 2.35 and 0.04%, respectively, and insert-empty clones were less than 0.5%. To facilitate chromosome engineering and anchor the sunflower genetic map to its chromosomes, one to three single- or low-copy RFLP markers from each linkage group of sunflower were used to design pairs of overlapping oligonucleotides (overgos). Thirty-six overgos were designed and pooled as probes to screen a subset (5.1x) of the BAC and BIBAC libraries. Of the 36 overgos, 33 (92%) gave at least one positive clone and 3 (8%) failed to hit any clone. As a result, 195 BAC and BIBAC clones representing 19 linkage groups were identified, including 76 BAC clones and 119 BIBAC clones, further verifying the genome coverage and utility of the libraries. These BAC and BIBAC libraries and linkage group-specific clones provide resources essential for comprehensive research of the sunflower genome.
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Affiliation(s)
- Jiuhuan Feng
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
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Cavanagh JAL, Tammen I, Hayden MJ, Gill CA, Nicholas FW, Raadsma HW. Characterization of the bovine aggrecan gene: genomic structure and physical and linkage mapping. Anim Genet 2006; 36:452-4. [PMID: 16167996 DOI: 10.1111/j.1365-2052.2005.01340.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- J A L Cavanagh
- Centre for Advanced Technologies in Animal Genetics and Reproduction (Reprogen), Faculty of Veterinary Science, The University of Sydney, Camden NSW 2570, Australia.
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Chen K, Knorr C, Bornemann-Kolatzki K, Ren J, Huang L, Rohrer GA, Brenig B. Targeted oligonucleotide-mediated microsatellite identification (TOMMI) from large-insert library clones. BMC Genet 2005; 6:54. [PMID: 16287508 PMCID: PMC1315340 DOI: 10.1186/1471-2156-6-54] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Accepted: 11/15/2005] [Indexed: 11/10/2022] Open
Abstract
Background In the last few years, microsatellites have become the most popular molecular marker system and have intensively been applied in genome mapping, biodiversity and phylogeny studies of livestock. Compared to single nucleotide polymorphism (SNP) as another popular marker system, microsatellites reveal obvious advantages. They are multi-allelic, possibly more polymorphic and cheaper to genotype. Calculations showed that a multi-allelic marker system always has more power to detect Linkage Disequilibrium (LD) than does a di-allelic marker system [1]. Traditional isolation methods using partial genomic libraries are time-consuming and cost-intensive. In order to directly generate microsatellites from large-insert libraries a sequencing approach with repeat-containing oligonucleotides is introduced. Results Seventeen porcine microsatellite markers were isolated from eleven PAC clones by targeted oligonucleotide-mediated microsatellite identification (TOMMI), an improved efficient and rapid flanking sequence-based approach for the isolation of STS-markers. With the application of TOMMI, an average of 1.55 (CA/GT) microsatellites per PAC clone was identified. The number of alleles, allele size distribution, polymorphism information content (PIC), average heterozygosity (HT), and effective allele number (NE) for the STS-markers were calculated using a sampling of 336 unrelated animals representing fifteen pig breeds (nine European and six Chinese breeds). Sixteen of the microsatellite markers proved to be polymorphic (2 to 22 alleles) in this heterogeneous sampling. Most of the publicly available (porcine) microsatellite amplicons range from approximately 80 bp to 200 bp. Here, we attempted to utilize as much sequence information as possible to develop STS-markers with larger amplicons. Indeed, fourteen of the seventeen STS-marker amplicons have minimal allele sizes of at least 200 bp. Thus, most of the generated STS-markers can easily be integrated into multilocus assays covering a broader separation spectrum. Linkage mapping results of the markers indicate their potential immediate use in QTL studies to further dissect trait associated chromosomal regions. Conclusion The sequencing strategy described in this study provides a targeted, inexpensive and fast method to develop microsatellites from large-insert libraries. It is well suited to generate polymorphic markers for selected chromosomal regions, contigs of overlapping clones and yields sufficient high quality sequence data to develop amplicons greater than 250 bases.
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Affiliation(s)
- Kefei Chen
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture, Jiangxi Agricultural University, Nanchang 330045, P. R. China
| | - Christoph Knorr
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
| | | | - Jun Ren
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture, Jiangxi Agricultural University, Nanchang 330045, P. R. China
| | - Lusheng Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture, Jiangxi Agricultural University, Nanchang 330045, P. R. China
| | - Gary A Rohrer
- US Meat Animal Research Center, Agricultural Research Service, US Department of Agriculture, Clay Center, NE 68933-0166, USA
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
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Fraser JA, Diezmann S, Subaran RL, Allen A, Lengeler KB, Dietrich FS, Heitman J. Convergent evolution of chromosomal sex-determining regions in the animal and fungal kingdoms. PLoS Biol 2004; 2:e384. [PMID: 15538538 PMCID: PMC526376 DOI: 10.1371/journal.pbio.0020384] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2004] [Accepted: 09/10/2004] [Indexed: 02/03/2023] Open
Abstract
Sexual identity is governed by sex chromosomes in plants and animals, and by mating type (MAT) loci in fungi. Comparative analysis of the MAT locus from a species cluster of the human fungal pathogen Cryptococcus revealed sequential evolutionary events that fashioned this large, highly unusual region. We hypothesize that MAT evolved via four main steps, beginning with acquisition of genes into two unlinked sex-determining regions, forming independent gene clusters that then fused via chromosomal translocation. A transitional tripolar intermediate state then converted to a bipolar system via gene conversion or recombination between the linked and unlinked sex-determining regions. MAT was subsequently subjected to intra- and interallelic gene conversion and inversions that suppress recombination. These events resemble those that shaped mammalian sex chromosomes, illustrating convergent evolution in sex-determining structures in the animal and fungal kingdoms. A comparative genomic analysis of the sex determining region in fungi reveals a remarkable similarity between its evolution and the events which shaped mammalian sex chromosomes
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MESH Headings
- Alleles
- Animals
- Biodiversity
- Chromosomes
- Chromosomes, Artificial, Bacterial
- Chromosomes, Fungal
- Cryptococcus/genetics
- Cryptococcus neoformans/genetics
- Evolution, Molecular
- Fungi/physiology
- Gene Conversion
- Gene Library
- Genes, Mating Type, Fungal
- Genome
- Genome, Fungal
- Humans
- Models, Genetic
- Molecular Sequence Data
- Phylogeny
- Recombination, Genetic
- Sex Chromosomes
- Sex Determination Processes
- Translocation, Genetic
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Affiliation(s)
- James A Fraser
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 2Howard Hughes Medical Institute, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Stephanie Diezmann
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 3Duke Institute for Genomics Sciences and Policy, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Ryan L Subaran
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Andria Allen
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 3Duke Institute for Genomics Sciences and Policy, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Klaus B Lengeler
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 2Howard Hughes Medical Institute, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Fred S Dietrich
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 3Duke Institute for Genomics Sciences and Policy, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Joseph Heitman
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 2Howard Hughes Medical Institute, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 4Department of Medicine, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 5Department of Pharmacology and Cancer Biology, Duke University Medical CenterDurham, North CarolinaUnited States of America
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Szeto IYY, Barton SC, Keverne EB, Surani AM. Analysis of imprinted murine Peg3 locus in transgenic mice. Mamm Genome 2004; 15:284-95. [PMID: 15112106 DOI: 10.1007/s00335-003-3031-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2003] [Accepted: 11/19/2003] [Indexed: 11/25/2022]
Abstract
Peg3 is an imprinted gene exclusively expressed from the paternal allele. It encodes a C(2)H(2) type zinc-finger protein and is involved in maternal behavior. It is important for TNF-NFkB signaling and p53-mediated apoptosis. To investigate the imprinting mechanism and gene expression of Peg3 and its neighboring gene(s), we used a 120 kb Peg3-containing BAC clone to generate transgenic mice. The BAC clone contains 20 kb of 5' and 80 kb of 3' flanking DNA, and we obtained three transgenic lines. In one of the lines harboring one copy of the transgene, Peg3 was imprinted properly. In the other two lines, Peg3 was expressed upon both maternal and paternal transmission. Imprinted expression was linked to the differential methylation of a region (DMR) upstream of the Peg3 gene. A second, maternally expressed gene, Zim1, present on the transgene was expressed irrespective of parental inheritance in all lines. These data suggest that, similar to other imprinted genes within domains, Peg3 and Zim1 are regulated by one or more elements lying at a distance from the genes. The imprinting of Peg3 seen in one line may reflect the presence of a responder sequence. Concerning the expression of the Peg3 transgene, we detected appropriate expression in the adult brain. However, this was not sufficient to rescue the maternal behavior phenotype seen in Peg3 deficient animals.
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Affiliation(s)
- Irene Y Y Szeto
- Wellcome Trust/Cancer Research UK Institute of Cancer and Developmental Biology and Department of Physiology, University of Cambridge, Tennis Court Road, Cambridge, CB2, 1QR, UK
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Chalhoub B, Belcram H, Caboche M. Efficient cloning of plant genomes into bacterial artificial chromosome (BAC) libraries with larger and more uniform insert size. PLANT BIOTECHNOLOGY JOURNAL 2004; 2:181-8. [PMID: 17147609 DOI: 10.1111/j.1467-7652.2004.00065.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The construction of bacterial artificial chromosome (BAC) libraries remains relatively complex and laborious, such that any technological improvement is considered to be highly advantageous. In this study, we addressed several aspects that improved the quality and efficiency of cloning of plant genomes into BACs. We set the 'single tube vector' preparation method with no precipitation or gel electrophoresis steps, which resulted in less vector DNA damage and a remarkable two- to threefold higher transformation efficiency compared with other known vector preparation methods. We used a reduced amount of DNA for partial digestion (up to 5 microg), which resulted in less BAC clones with small inserts. We performed electrophoresis in 0.25 x TBE (Tris, boric acid, ethylenediaminetetraacetic acid) buffer instead of 0.5 x TBE, which resulted in larger and more uniformly sized BAC inserts and, surprisingly, a two- to threefold higher transformation efficiency, probably due to less contamination with borate ions. We adopted a triple size selection that resulted in an increased mean insert size of up to 70 kb and a transformation efficiency comparable with that of double size selection. Overall, the improved protocol presented in this study resulted in a five- to sixfold higher cloning efficiency and larger and more uniformly sized BAC inserts. BAC libraries with the desired mean insert size (up to 200 kb) were constructed from several plant species, including hexaploid wheat. The improved protocol will render the construction of BAC libraries more available in plants and will greatly enhance genome analysis, gene mapping and cloning.
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Affiliation(s)
- Boulos Chalhoub
- Unité de Recherches en Génomique Végétale (URGV), INRA, Evry, France.
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Winter A, Alzinger A, Fries R. Assessment of the gene content of the chromosomal regions flanking bovine DGAT1. Genomics 2004; 83:172-80. [PMID: 14667821 DOI: 10.1016/s0888-7543(03)00238-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
As a first step towards verifying the candidate status of DGAT1 as the causal gene for milk fat percentage in cattle, we constructed a bovine BAC contig spanning 576 kb of the chromosomal region containing DGAT1. High content of NotI sites (21 within the contig) indicated that the region is gene-rich. Twenty-three genes neighboring DGAT1 were mapped, including two bovine cDNA sequences that have no orthologous sequences within the NCBI sequence databases. On average, 2015 bp for each of the 23 neighboring genes were sequenced and entered into EMBL. Likewise, 10 new STS markers were established by BAC-end sequencing. Within the genes and STS markers, 55 polymorphisms were discovered. These will form the basis of future linkage disequilibrium studies to test whether any genes neighboring DGAT1 are associated with variation in milk fat percentage, thereby testing the candidate status of DGAT1.
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Affiliation(s)
- Andreas Winter
- Lehrstuhl für Tierzucht der Technischen Universität München, 85350 Freising-Weihenstephan, Germany
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35
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Liu W, Liu Z, Hu X, Zhang Y, Yuan J, Zhao R, Li Z, Xu W, Gao Y, Deng X, Li N. Construction and Characterization of a Novel 13.34‐Fold Chicken Bacterial Artificial Chromosome Library. Anim Biotechnol 2003; 14:145-53. [PMID: 14703073 DOI: 10.1081/abio-120026484] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A chicken bacterial artificial chromosome (BAC) library consisting of 138,240 clones was constructed in vector pBeloBAC11 with genomic DNA isolated from female white-silk chicken. An average insert size of 118 kb was estimated from 452 randomly isolated clones, which indicate the library to be approximate 13.34-fold genome coverage. For the demonstration of the probability to pick out any unique genes or DNA markers from the library, 8 single-copy genes were screened out and the positive clones were yielded between 2 and 15 with an average of 11.125, in agreement with the estimated high genomic coverage of this library. Positive superpools were obtained for 40 microsatellite markers selected from different regions of chicken genome. The number of positive superpools for each marker varies from 1 to 15 with an average of 9.475.
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Affiliation(s)
- Wei Liu
- State Key Laboratory for Agrobiotechnology, College of Biological Science, China Agriculture University, Beijing, PR China
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36
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Zhao Y, Kacskovics I, Rabbani H, Hammarstrom L. Physical mapping of the bovine immunoglobulin heavy chain constant region gene locus. J Biol Chem 2003; 278:35024-32. [PMID: 12829708 DOI: 10.1074/jbc.m301337200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bovine antibodies have recently attracted increasing attention, as they have been shown to exhibit prophylactic and therapeutic properties in selected infectious diseases in humans. In the present study, we have isolated bacterial artificial chromosomes and cosmid clones containing the bovine JH, mu, delta, gamma 1, gamma 2, gamma 3, epsilon, and alpha genes, which allowed us to make a contig of the genes within the bovine IGHC locus. The genes are arranged in a 5'-JH-7 kb-mu-5 kb-delta-33 kb-gamma 3-20 kb-gamma 1-34 kb-gamma 2-20 kb-epsilon- 13 kb-alpha-3' order, spanning approximately 150 kb DNA. Examination of the bovine germline JH locus revealed six JH segments, two of which, JH1 and JH2, were shown to be functional although there was a strong preference for expression of the former. Sequence alignment of the bovine 5' E mu enhancer core region with those of other mammals, demonstrated an absence of the mu E3 motif and a shortened spacer between the mu A and mu B sites within the bovine E mu enhancer core region. Furthermore, the essential sequence element for class switching, switch mu, spanning approximately 3-kb repetitive sequence and abundant in the switch region motifs CTGGG (187 repeats) and CTGAG (127 repeats), was identified immediately upstream of the mu gene. A further sequence comparison revealed that the bovine IGHC genes display an extensive polymorphism leading to expression of multiple antibody allotypes.
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Affiliation(s)
- Yaofeng Zhao
- Center for Biotechnology, Department of Bioscience at Novum, Karolinska, Institutet, SE-14157, Huddinge, Sweden
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White SN, Taylor KH, Abbey CA, Gill CA, Womack JE. Haplotype variation in bovine Toll-like receptor 4 and computational prediction of a positively selected ligand-binding domain. Proc Natl Acad Sci U S A 2003; 100:10364-9. [PMID: 12915733 PMCID: PMC193567 DOI: 10.1073/pnas.1333957100] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Toll-like receptor 4 (TLR4) is a cell-surface receptor that activates innate and adaptive immune responses. Because it recognizes a broad class of pathogen-associated molecular patterns presented by lipopolysaccharides and lipoteichoic acid, TLR4 is a candidate gene for resistance to a large number of diseases. In particular, mouse models suggest TLR4 as a candidate gene for resistance to major agents in bovine respiratory disease and Johne's disease. The coding sequence of bovine TLR4 is divided into three exons, with intron/exon boundaries and intron sizes similar to those of human TLR4 transcript variant 1. We amplified each exon in 40 individuals from 11 breeds and screened the sequence for single-nucleotide polymorphisms (SNPs). We identified 32 SNPs, 28 of which are in the coding sequence, for an average of one SNP per 90 bp of coding sequence. Eight SNPs were nonsynonymous and potentially alter specificity of pathogen recognition or efficiency of signaling. To evaluate the functional importance of these SNPs, we used codon-substitution models to detect diversifying selection in an extracellular region that may physically interact with ligands. One nonsynonymous SNP is located within this region, and other substitutions are in adjacent regions that may interact with coreceptor molecules. The 32 SNPs were found in 20 haplotypes that can be assigned to geographic ranges of origin. Haplotype-tagging SNP analysis indicated that 12 SNPs need to be genotyped to distinguish these 20 haplotypes. These data provide a basic understanding of bovine TLR4 sequence variation and supply haplotype markers for disease association studies.
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Affiliation(s)
- Stephen N White
- Department of Veterinary Pathobiology and Animal Science, Texas A&M University, College Station, TX 77843, USA
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Kaufmann H, Mattiesch L, Lörz H, Debener T. Construction of a BAC library of Rosa rugosaThunb. and assembly of a contig spanning Rdr1, a gene that confers resistance to blackspot. Mol Genet Genomics 2003; 268:666-74. [PMID: 12589441 DOI: 10.1007/s00438-002-0784-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2002] [Accepted: 11/07/2002] [Indexed: 10/25/2022]
Abstract
A BAC library to serve as a general tool for the physical mapping and positional cloning of rose genes has been constructed from Rosa rugosa DNA. With 27,264 clones the library contains 5.2 genome equivalents. The library was used to assemble a contig of BAC clones spanning Rdr1, a locus that confers resistance to blackspot. For this purpose fine-scale mapping of the target locus was achieved by bulked segregant analysis using 816 AFLP primer combinations. The target region around Rdr1 comprises about 400 kb and is covered by a minimum of six BAC clones. Furthermore, the detection of at least five resistance gene analogs of the TIR-NBS-LRR family on the contig indicates the presence of a cluster of resistance genes around Rdr1. These results will not only allow the isolation and identification of Rdr1 in the near future, but also provide the tools for the physical mapping and positional cloning of other horticulturally interesting genes in roses.
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Affiliation(s)
- H Kaufmann
- Institute of General Botany and Botanical Garden, Applied Molecular Biology of Plants (AMP) II, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
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Meinecke B, Kuiper H, Drögemüller C, Leeb T, Meinecke-Tillmann S. A mola hydatidosa coexistent with a foetus in a bovine freemartin pregnancy. Placenta 2003; 24:107-12. [PMID: 12495666 DOI: 10.1053/plac.2002.0872] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Molar transformations of the bovine placenta are extremly rare phenomenona and the aetiology of this genuine placental disease is still unknown. In the present study, an uncommon case of a German Holstein Friesian foetus co-twinned with a hydatidiform mole is described. Cytogenetic and fluorescence in situ hybridization analysis of cell cultures as well as prove of the presence of the SRY gene sequence revealed a heterosexual twin pregnancy. A chimeric condition of the mole was also established. In addition, an XO cell population was detected in the co-twin as well as in the mole. Upon examination of microsatellites of the parents, the mole and the co-twin an androgenetic origin of the mole is suggested, supporting the hypothesis that molar transformation of the bovine placenta may be caused by an androgenetic origin. Furthermore, the present observation demonstrates that the freemartin condition in cattle can be induced even in cases where severe placental transformations had subsequently occurred and no foetus proper could be detected at delivery.
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Affiliation(s)
- B Meinecke
- Department of Reproductive Medicine, Buenteweg 15, School of Veterinary Medicine Hannover, Germany.
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Zhao Y, Kacskovics I, Pan Q, Liberles DA, Geli J, Davis SK, Rabbani H, Hammarstrom L. Artiodactyl IgD: the missing link. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2002; 169:4408-16. [PMID: 12370374 DOI: 10.4049/jimmunol.169.8.4408] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
IgD has been suggested to be a recently developed Ig class, only present in rodents and primates. However, in this paper the cow, sheep, and pig Ig delta genes have been identified and shown to be transcriptionally active. The deduced amino acid sequences from their cDNAs show that artiodactyl IgD H chains are structurally similar to human IgD, where the cow, sheep, and pig IgD H chain constant regions all contain three domains and a hinge region, sharing homologies of 43.6, 44, and 46.8% with their human counterpart, respectively. According to a phylogenetic analysis, the Cdelta gene appears to have been duplicated from the Cmu gene >300 million yr ago. The ruminant mu CH1 exon and its upstream region was again duplicated before the speciation of the cow and sheep, approximately 20 million yr ago, inserted upstream of the delta gene hinge regions, and later modified by gene conversion. A short Sdelta (switch delta) sequence resulting from the second duplication, is located immediately upstream of the bovine Cdelta gene and directs regular mu-delta class switch recombination in the cow. The presence of Cdelta genes in artiodactyls, possibly in most mammals, suggests that IgD may have some as yet unknown biological properties, distinct from those of IgM, conferring a survival advantage.
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Affiliation(s)
- Yaofeng Zhao
- Center for Biotechnology, Department of Bioscience at Novum, Karolinska Institute, SE-14157 Huddinge, Sweden.
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41
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Antoniou E, Gallagher D. Chromosomal assignment of the bovine ubiquitin-conjugating enzyme E2I (UBE2I ) gene to BTA6q34 defines a new fragment of conserved synteny with human chromosome 16. Anim Genet 2002; 33:388-9. [PMID: 12354154 DOI: 10.1046/j.1365-2052.2002.00896_8.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- E Antoniou
- Animal Sciences Research Center, University of Missouri, Room S140, Columbia, MO 65211, USA.
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Fujisaki S, Mizoguchi Y, Takahashi S, Chen YZ, Suzuki K, Asakawa S, Soeda E, Shimizu N, Sugimoto Y, Yasue H. Construction of a bovine bacterial artificial chromosome library from fibroblasts used for cloned cattle. Anim Genet 2002; 33:379-81. [PMID: 12354149 DOI: 10.1046/j.1365-2052.2002.00896_3.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- S Fujisaki
- Genome Research Department, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan
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Wild J, Hradecna Z, Szybalski W. Conditionally amplifiable BACs: switching from single-copy to high-copy vectors and genomic clones. Genome Res 2002; 12:1434-44. [PMID: 12213781 PMCID: PMC186656 DOI: 10.1101/gr.130502] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The widely used, very-low-copy BAC (bacterial artificial chromosome) vectors are the mainstay of present genomic research. The principal advantage of BACs is the high stability of inserted clones, but an important disadvantage is the low yield of DNA, both for vectors alone and when carrying genomic inserts. We describe here a novel class of single-copy/high-copy (SC/HC) pBAC/oriV vectors that retain all the advantages of low-copy BAC vectors, but are endowed with a conditional and tightly controlled oriV/TrfA amplification system that allows: (1) a yield of ~100 copies of the vector per host cell when conditionally induced with L-arabinose, and (2) analogous DNA amplification (only upon induction and with copy number depending on the insert size) of pBAC/oriV clones carrying >100-kb inserts. Amplifiable clones and libraries facilitate high-throughput DNA sequencing and other applications requiring HC plasmid DNA. To turn on DNA amplification, which is driven by the oriV origin of replication, we used copy-up mutations in the gene trfA whose expression was very tightly controlled by the araC-P(araBAD) promoter/regulator system. This system is inducible by L-arabinose, and could be further regulated by glucose and fucose. Amplification of DNA upon induction with L-arabinose and its modulation by glucose are robust and reliable. Furthermore, we discovered that addition of 0.2% D-glucose to the growth medium helped toward the objective of obtaining a real SC state for all BAC systems, thus enhancing the stability of their maintenance, which became equivalent to cloning into the host chromosome
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Affiliation(s)
- Jadwiga Wild
- McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA
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Wechter WP, Begum D, Presting G, Kim JJ, Wing RA, Kluepfel DA. Physical mapping, BAC-end sequence analysis, and marker tagging of the soilborne nematicidal bacterium, Pseudomonas synxantha BG33R. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2002; 6:11-21. [PMID: 11881828 DOI: 10.1089/15362310252780807] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A bacterial artificial chromosome (BAC) library was constructed for the genome of the rhizosphere-inhabiting fluorescent pseudomonad Pseudomonas synxantha BG33R. Three thousand BAC clones with an average insert size of 140 kbp and representing a 70-fold genomic coverage were generated and arrayed onto nylon membranes. EcoRI fingerprint analysis of 986 BAC clones generated 23 contigs and 75 singletons. Hybridization analysis allowed us to order the 23 contigs and condense them into a single contig, yielding an estimated genome size of 5.1 Mb for P. synxantha BG33R. A minimum-tile path of 47 BACs was generated and end-sequenced. The genetic loci involved in ring nematode egg-kill factor production in BG33R Tn5 mutants, 246 (vgrG homolog), 1122 (sensor kinase homolog), 1233 (UDP-galactose epimerase homolog), 1397 (ferrisiderophore receptor homolog), and 1917 (ribosomal subunit protein homolog), have been mapped onto the minimum-tile BAC library. Two of the genetic regions that flank Tn5 insertions in BG33R egg-kill-negative mutants 1233 and 1397 are separated by a single BAC clone. Fragments isolated by ligation-mediated PCR of the Tn5 mutagenized regions of 29 randomly selected, non-egg-kill-related, insertion mutants have been anchored onto the ordered physical map of P. synxantha.
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Affiliation(s)
- W P Wechter
- The Department of Plant Pathology and Physiology, Clemson University, South Carolina 29634-0377, USA
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45
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Xu M, Song J, Cheng Z, Jiang J, Korban SS. A bacterial artificial chromosome (BAC) library of Malus floribunda 821 and contig construction for positional cloning of the apple scab resistance gene Vf. Genome 2001. [DOI: 10.1139/g01-105] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The apple scab resistance gene Vf, originating from the wild species Malus floribunda 821, has been incorporated into a wide variety of apple cultivars through a classical breeding program. With the aim of isolating the Vf gene, a bacterial artificial chromosome (BAC) library consisting of 31 584 clones has been constructed from M. floribunda 821. From the analysis of 88 randomly selected BAC clones, the average insert size is estimated at 125 kb. If it is assumed that the genome size of M. floribunda 821 is 769 Mb/haploid, the library represents about 5× haploid genome equivalents. This provides a 99% probability of finding any specific sequence from this library. PCR-based screening of the library has been carried out using eight random genomic sequence-characterized amplified regions (SCARs), chloroplast- and mitochondria-specific SCARs, and 13 high-density Vf-linked SCAR markers. An average of five positive BAC clones per random SCAR has been obtained, whereas less than 1% of BAC clones are derived from the chloroplast or mitochondrial genomes. Most BAC clones identified with Vf-linked SCAR markers are physically linked. Three BAC contigs along the Vf region have been obtained by assembling physically linked BAC clones based on their fingerprints. The overlapping relatedness of BAC clones has been further confirmed by cytogenetic mapping using fiber fluorescence in situ hybridization (fiber-FISH). The M. floribunda 821 BAC library provides a valuable genetic resource not only for map-based cloning of the Vf gene, but also for finding many other important genes for improving the cultivated apple.Key words: apple, resistance Vf gene, BAC library, sequence-characterized amplified regions (SCARs), fiber fluorescence in situ hybridization (fiber-FISH), positional cloning.
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McShane RD, Gallagher DS, Newkirk H, Taylor JF, Burzlaff JD, Davis SK, Skow LC. Physical localization and order of genes in the class I region of the bovine MHC. Anim Genet 2001; 32:235-9. [PMID: 11683708 DOI: 10.1046/j.1365-2052.2001.00758.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fluorescence in situ hybridization (FISH) analyses were used to order 16 bacterial artificial chromosomes (BAC) clones containing loci from the bovine lymphocyte antigen (BoLA) class I and III regions of bovine chromosome 23 (BTA23). Fourteen of these BACs were assigned to chromosomal band locations of mitotic and pachytene chromosomes by single- and dual-colour FISH. Dual-colour FISH confirmed that class II DYA is proximal to and separated from BoLA class I genes by approximately three chromosome bands. The FISH results showed that tumour necrosis factor alpha (TNFA), heat shock protein 70 (HSP70.1) and 21 steroid dehydrogenase (CYP21) are closely linked in the region of BTA23 band 22 along with BoLA class I genes, and that male enhanced antigen (MEA) mapped between DYA and the CYP21/TNFA/HSP70.1 gene region. All BAC clones containing BoLA class I genes mapped distal to CYP21/TNFA/HSP70.1 and centromeric to prolactin (PRL). Myelin oligodendrocyte glycoprotein (MOG) was shown to be imbedded within the BoLA class I gene cluster. The cytogenetic data confirmed that the disrupted distribution of BoLA genes is most likely the result of a single large chromosomal inversion. Similar FISH results were obtained when BoLA DYA and class I BAC clones were mapped to discrete chromosomal locations on the BTA homologue in white-tailed deer, suggesting that this chromosomal inversion predates divergence of the advanced ruminant families from a common ancestor.
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Affiliation(s)
- R D McShane
- Department of Veterinary Anatomy and Public Health, Texas A & M University, TX 77843, USA
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Mao J, Marcos S, Davis SK, Burzlaff J, Seyfert HM. Genomic distribution of three promoters of the bovine gene encoding acetyl-CoA carboxylase alpha and evidence that the nutritionally regulated promoter I contains a repressive element different from that in rat. Biochem J 2001; 358:127-35. [PMID: 11485560 PMCID: PMC1222040 DOI: 10.1042/0264-6021:3580127] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The enzyme acetyl-CoA carboxylase alpha (ACC-alpha) is rate-limiting for the synthesis of long-chain fatty acids de novo. As a first characterization of the bovine gene encoding this enzyme, we established the entire bovine ACC-alpha cDNA sequence (7041 bp) and used experiments with 5' rapid amplification of cDNA ends to determine the heterogeneous composition of 5' untranslated regions, as expressed from three different promoters (PI, PII and PIII). The individual locations of these promoters have been defined within an area comprising 35 kbp on Bos taurus chromosome 19 ('BTA19'), together with the segmentation of the first 14 exons. Primer extension analyses reveal that the nutritionally regulated PI initiates transcription from at least four sites. PI transcripts are much more abundant in adipose and mammary-gland tissues than in liver or lung. A 2.6 kb promoter fragment drives the expression of reporter genes only weakly in different model cells, irrespective of stimulation with insulin or dexamethasone. Thus bovine PI is basically repressed, like its analogue from rat. Finely graded deletions of PI map two separate elements, which have to be present together in cis to repress bovine PI. The distal component resides within a well-preserved Art2 retroposon element. Thus sequence, structure and evolutionary origin of the main repressor of PI in bovines are entirely different from its functional counterpart in rat, which had been identified as a (CA)(28) microsatellite. We show that, in different mammalian species, unrelated genome segments of different origins have been recruited to express as functionally homologous PI the ancient and otherwise highly conserved ACC-alpha-encoding gene.
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Affiliation(s)
- J Mao
- Research Institute for the Biology of Farm Animals, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
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Katagiri T, Asakawa S, Minagawa S, Shimizu N, Hirono I, Aoki T. Construction and characterization of BAC libraries for three fish species; rainbow trout, carp and tilapia. Anim Genet 2001; 32:200-4. [PMID: 11531698 DOI: 10.1046/j.1365-2052.2001.00764.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacterial artificial chromosome (BAC) libraries are important tools for genomic research. We have constructed seven genomic BAC libraries from three fish species, rainbow trout (Oncorhynchus mykiss), carp (Cyprinus carpio) and tilapia (Oreochromis niloticus). The two rainbow trout BAC libraries have average insert sizes of 58 and 110 kb. The average size of inserts in the carp BAC library is 160 kb. The average insert sizes of the four tilapia BAC libraries are 65, 105, 145 and 194 kb, respectively. These libraries represent good coverage of each genome (2-64 x coverage). The libraries can be screened by conventional colony hybridization and provide a starting point for the construction of high-density filtres or polymerase chain reaction (PCR) screening approaches. These BAC libraries will facilitate the positional cloning of quantitative trait loci (QTLs) for a variety of economically important traits in these species.
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Affiliation(s)
- T Katagiri
- Laboratory of Genetics and Biochemistry, Tokyo University of Fisheries, Konan 4-5-7, Minato-ku, Tokyo 108-8477, Japan
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Barthel R, Feng J, Piedrahita JA, McMurray DN, Templeton JW, Adams LG. Stable transfection of the bovine NRAMP1 gene into murine RAW264.7 cells: effect on Brucella abortus survival. Infect Immun 2001; 69:3110-9. [PMID: 11292730 PMCID: PMC98266 DOI: 10.1128/iai.69.5.3110-3119.2001] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genetically based natural resistance to brucellosis in cattle provides for novel strategies to control zoonotic diseases. Bovine NRAMP1, the homologue of a murine gene (Bcg), has been identified as a major candidate for controlling the in vivo resistant phenotype. We developed an in vitro model for expression of resistance- and susceptibility-associated alleles of bovine NRAMP1 as stable transgenes under the regulatory control of the bovine NRAMP1 promoter in the murine RAW264.7 macrophage cell line (Bcg(s)) to analyze the regulation of the NRAMP1 gene and its role in macrophage function. We demonstrated that the 5'-flanking region of bovine NRAMP1, despite the lack of TATA and CAAT boxes, has a functional promoter capable of driving the expression of a transgene in murine macrophages. A polymorphism within a microsatellite in the 3' untranslated region critically affects the expression of bovine NRAMP1 and the control of in vitro replication of Brucella abortus but not Salmonella enterica serovar Dublin. We did not observe any differences in the production of NO by resting or gamma interferon (IFN-gamma)- and IFN-gamma-lipopolysaccharide (LPS)-treated transfected cell lines, yet the resistant transfected cell lines produced significantly less NO than other cell lines, following stimulation with LPS at 24 and 48 h.
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Affiliation(s)
- R Barthel
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
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50
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Ward TJ, Skow LC, Gallagher DS, Schnabel RD, Nall CA, Kolenda CE, Davis SK, Taylor JF, Derr JN. Differential introgression of uniparentally inherited markers in bison populations with hybrid ancestries. Anim Genet 2001; 32:89-91. [PMID: 11421943 DOI: 10.1046/j.1365-2052.2001.00736.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Historical hybridization between Bison bison (bison) and Bos taurus (cattle) has been well documented and resulted in cattle mitochondrial DNA (mtDNA) introgression, previously identified in six different bison populations. In order to examine Y chromosome introgression, a microsatellite marker (BYM-1) with non-overlapping allele size distributions in bison and cattle was isolated from a bacterial artificial chromosome (BAC) clone, and was physically assigned to the Y chromosome by fluorescence in situ hybridization. BYM-1 genotypes for a sample of 143 male bison from 10 populations, including all six populations where cattle mtDNA haplotypes were previously identified, indicated that cattle Y chromosome introgression had not occurred in these bison populations. The differential permeability of uniparentally inherited markers to introgression is consistent with observations of sterility among first generation hybrid males and a sexual asymmetry in the direction of hybridization favouring matings between male bison and female cattle.
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Affiliation(s)
- T J Ward
- Department of Veterinary Pathobiology, Texas A & M University, College Station, TX, USA
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