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Zhuang X, Murphy KR, Ghigliotti L, Pisano E, Cheng CHC. Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod. Mar Genomics 2018; 39:73-84. [PMID: 29510906 DOI: 10.1016/j.margen.2018.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/21/2018] [Accepted: 02/21/2018] [Indexed: 10/17/2022]
Abstract
Antifreeze glycoproteins (AFGPs) are a novel evolutionary innovation in members of the northern cod fish family (Gadidae), crucial in preventing death from inoculative freezing by environmental ice in their frigid Arctic and sub-Arctic habitats. However, the genomic origin and molecular mechanism of evolution of this novel life-saving adaptive genetic trait remained to be definitively determined. To this end, we constructed large insert genomic DNA BAC (bacterial artificial chromosome) libraries for two AFGP-bearing gadids, the high-Arctic polar cod Boreogadus saida and the cold-temperate Atlantic tomcod Microgadus tomcod, to isolate and sequence their AFGP genomic regions for fine resolution evolutionary analyses. The BAC library construction encountered poor cloning efficiency initially, which we resolved by pretreating the agarose-embedded erythrocyte DNA with a cationic detergent, a method that may be of general use to BAC cloning for teleost species and/or where erythrocytes are the source of input DNA. The polar cod BAC library encompassed 92,160 clones with an average insert size of 94.7 kbp, and the Atlantic tomcod library contained 73,728 clones with an average insert size of 89.6 kbp. The genome sizes of B. saida and M. tomcod were estimated by cell flow cytometry to be 836 Mbp and 645 Mbp respectively, thus their BAC libraries have approximately 10- and 9.7-fold genome coverage respectively. The inclusiveness and depth of coverage were empirically confirmed by screening the libraries with three housekeeping genes. The BAC clones that mapped to the AFGP genomic loci of the two gadids were then isolated by screening the BAC libraries with gadid AFGP gene probes. Eight minimal tiling path (MTP) clones were identified for B. saida, sequenced, and assembled. The B. saida AFGP locus reconstruction produced both haplotypes, and the locus comprises three distinct AFGP gene clusters, containing a total of 16 AFGP genes and spanning a combined distance of 512 kbp. The M. tomcod AFGP locus is much smaller at approximately 80 kbp, and contains only three AFGP genes. Fluorescent in situ hybridization with an AFGP gene probe showed the AFGP locus in both species occupies a single chromosomal location. The large AFGP locus with its high gene dosage in B. saida is consistent with its chronically freezing high Arctic habitats, while the small gene family in M. tomcod correlates with its milder habitats in lower latitudes. The results from this study provided the data for fine resolution sequence analyses that would yield insight into the molecular mechanisms and history of gadid AFGP gene evolution driven by northern hemisphere glaciation.
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Affiliation(s)
- Xuan Zhuang
- Department of Animal Biology, University of Illinois at Urbana - Champaign, 515 Morrill Hall, Urbana, IL 61801, USA; Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
| | - Katherine R Murphy
- Department of Animal Biology, University of Illinois at Urbana - Champaign, 515 Morrill Hall, Urbana, IL 61801, USA
| | - Laura Ghigliotti
- Institute of Marine Sciences (ISMAR), National Research Council (CNR), Genoa 16149, Italy
| | - Eva Pisano
- Institute of Marine Sciences (ISMAR), National Research Council (CNR), Genoa 16149, Italy
| | - C-H Christina Cheng
- Department of Animal Biology, University of Illinois at Urbana - Champaign, 515 Morrill Hall, Urbana, IL 61801, USA.
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Spirhanzlova P, Dhorne-Pollet S, Fellah J, Da Silva C, Tlapakova T, Labadie K, Weissenbach J, Poulain J, Jaffredo T, Wincker P, Krylov V, Pollet N. Construction and characterization of a BAC library for functional genomics in Xenopus tropicalis. Dev Biol 2017; 426:255-260. [DOI: 10.1016/j.ydbio.2016.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/18/2016] [Accepted: 05/10/2016] [Indexed: 12/20/2022]
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Riemer S, Bontems F, Krishnakumar P, Gömann J, Dosch R. A functional Bucky ball-GFP transgene visualizes germ plasm in living zebrafish. Gene Expr Patterns 2015; 18:44-52. [PMID: 26143227 DOI: 10.1016/j.gep.2015.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 05/08/2015] [Accepted: 05/09/2015] [Indexed: 10/23/2022]
Abstract
In many animals, the germline is specified by maternal RNA-granules termed germ plasm. The correct localization of germ plasm during embryogenesis is therefore crucial for the specification of germ cells. In zebrafish, we previously identified Bucky ball (Buc) as a key regulator of germ plasm formation. Here, we used a Buc antibody to describe its continuous germ plasm localization. Moreover, we generated a transgenic Buc-GFP line for live imaging, which visualizes germ plasm from its assembly during oogenesis up to the larval stages. Live imaging of Buc-GFP generated stunning movies, as they highlighted the dynamic details of germ plasm movements. Moreover, we discovered that Buc was still detected in primordial germ cells 2 days after fertilization. Interestingly, the transgene rescued buc mutants demonstrating genetically that the Buc-GFP fusion protein is functional. These results show that Buc-GFP exerts all biochemical interactions essential for germline development and highlight the potential of this line to analyze the molecular regulation of germ plasm formation.
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Affiliation(s)
- Stephan Riemer
- Institut für Entwicklungsbiochemie, GZMB, Universitätsmedizin Göttingen, Georg-August-Universität, Göttingen, Germany
| | - Franck Bontems
- Laboratory of Metabolism, Department of Internal Medicine Specialties, Faculty of Medicine, University of Geneva, Switzerland
| | - Pritesh Krishnakumar
- Institut für Entwicklungsbiochemie, GZMB, Universitätsmedizin Göttingen, Georg-August-Universität, Göttingen, Germany
| | - Jasmin Gömann
- Institut für Entwicklungsbiochemie, GZMB, Universitätsmedizin Göttingen, Georg-August-Universität, Göttingen, Germany
| | - Roland Dosch
- Institut für Entwicklungsbiochemie, GZMB, Universitätsmedizin Göttingen, Georg-August-Universität, Göttingen, Germany.
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Protein genes in repetitive sequence-antifreeze glycoproteins in Atlantic cod genome. BMC Genomics 2012; 13:293. [PMID: 22747999 PMCID: PMC3441883 DOI: 10.1186/1471-2164-13-293] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 06/15/2012] [Indexed: 01/20/2023] Open
Abstract
Background Highly repetitive sequences are the bane of genome sequence assembly, and the short read lengths produced by current next generation sequencing technologies further exacerbates this obstacle. An adopted practice is to exclude repetitive sequences in genome data assembly, as the majority of repeats lack protein-coding genes. However, this could result in the exclusion of important genotypes in newly sequenced non-model species. The absence of the antifreeze glycoproteins (AFGP) gene family in the recently sequenced Atlantic cod genome serves as an example. Results The Atlantic cod (Gadus morhua) genome was assembled entirely from Roche 454 short reads, demonstrating the feasibility of this approach. However, a well-known major adaptive trait, the AFGP, essential for survival in frigid Arctic marine habitats was absent in the annotated genome. To assess whether this resulted from population difference, we performed Southern blot analysis of genomic DNA from multiple individuals from the North East Arctic cod population that the sequenced cod belonged, and verified that the AFGP genotype is indeed present. We searched the raw assemblies of the Atlantic cod using our G. morhua AFGP gene, and located partial AFGP coding sequences in two sequence scaffolds. We found these two scaffolds constitute a partial genomic AFGP locus through comparative sequence analyses with our newly assembled genomic AFGP locus of the related polar cod, Boreogadus saida. By examining the sequence assembly and annotation methodologies used for the Atlantic cod genome, we deduced the primary cause of the absence of the AFGP gene family from the annotated genome was the removal of all repetitive Roche 454 short reads before sequence assembly, which would exclude most of the highly repetitive AFGP coding sequences. Secondarily, the model teleost genomes used in projection annotation of the Atlantic cod genome have no antifreeze trait, perpetuating the unawareness that the AFGP gene family is missing. Conclusions We recovered some of the missing AFGP coding sequences and reconstructed a partial AFGP locus in the Atlantic cod genome, bringing to light that not all repetitive sequences lack protein coding information. Also, reliance on genomes of model organisms as reference for annotating protein-coding gene content of a newly sequenced non-model species could lead to omission of novel genetic traits.
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Ye Q, He K, Wu SY, Wan QH. Isolation of a 97-kb minimal essential MHC B locus from a new reverse-4D BAC library of the golden pheasant. PLoS One 2012; 7:e32154. [PMID: 22403630 PMCID: PMC3293878 DOI: 10.1371/journal.pone.0032154] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 01/19/2012] [Indexed: 12/02/2022] Open
Abstract
The bacterial artificial chromosome (BAC) system is widely used in isolation of large genomic fragments of interest. Construction of a routine BAC library requires several months for picking clones and arraying BACs into superpools in order to employ 4D-PCR to screen positive BACs, which might be time-consuming and laborious. The major histocompatibility complex (MHC) is a cluster of genes involved in the vertebrate immune system, and the classical avian MHC-B locus is a minimal essential one, occupying a 100-kb genomic region. In this study, we constructed a more effective reverse-4D BAC library for the golden pheasant, which first creates sub-libraries and then only picks clones of positive sub-libraries, and identified several MHC clones within thirty days. The full sequencing of a 97-kb reverse-4D BAC demonstrated that the golden pheasant MHC-B locus contained 20 genes and showed good synteny with that of the chicken. The notable differences between these two species were the numbers of class II B loci and NK genes and the inversions of the TAPBP gene and the TAP1-TAP2 region. Furthermore, the inverse TAP2-TAP1 was unique in the golden pheasant in comparison with that of chicken, turkey, and quail. The newly defined genomic structure of the golden pheasant MHC will give an insight into the evolutionary history of the avian MHC.
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Affiliation(s)
| | | | - Shao-Ying Wu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qiu-Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
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St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ, Glenn TC, Green RE, Ray DA. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol 2012; 13:415. [PMID: 22293439 PMCID: PMC3334581 DOI: 10.1186/gb-2012-13-1-415] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.
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Detrich HW, Amemiya CT. Antarctic notothenioid fishes: genomic resources and strategies for analyzing an adaptive radiation. Integr Comp Biol 2010; 50:1009-17. [PMID: 21082069 DOI: 10.1093/icb/icq071] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species-flock in the cold Southern Ocean that surrounds Antarctica. To facilitate genome-level studies of the diversification of these fishes, we present estimates of the genome sizes of 11 Antarctic species and describe the production of high-quality bacterial artificial chromosome (BAC) libraries for two, the red-blooded notothen Notothenia coriiceps and the white-blooded icefish Chaenocephalus aceratus. Our results indicate that evolution of phylogenetically derived notothenioid families (e.g., the crown group Channichthyidae [icefishes]), was accompanied by genome expansion. Six species from the basal family Nototheniidae had C-values between 0.98 and 1.20 pg, a range that is consistent with the genome sizes of proposed outgroups (e.g., percids) of the notothenioid suborder. In contrast, four icefishes had C-values in the range 1.66-1.83 pg. The BAC libraries VMRC-19 (N. coriiceps) and VMRC-21 (C. aceratus) comprise 12× and 10× coverage of the respective genomes and have average insert sizes of 138 and 168 kb. Paired BAC-end reads representing ∼0.1% of each genome showed that the repetitive element landscapes of the two genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus) were similar. The availability of these high-quality and well-characterized BAC libraries sets the stage for targeted genomic analyses of the unusual anatomical and physiological adaptations of the notothenioids, some of which mimic human diseases. Here we consider the evolution of secondary pelagicism by various taxa of the group and illustrate the utility of Antarctic icefishes as an evolutionary-mutant model of human osteopenia (low-mineral density of bones).
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Affiliation(s)
- H W Detrich
- Department of Biology, Northeastern University, Boston, MA 02115, USA.
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Development and analysis of a germline BAC resource for the sea lamprey, a vertebrate that undergoes substantial chromatin diminution. Chromosoma 2010; 119:381-9. [PMID: 20195622 DOI: 10.1007/s00412-010-0263-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 01/27/2010] [Accepted: 01/28/2010] [Indexed: 01/05/2023]
Abstract
Over the last several years, the sea lamprey (Petromyzon marinus) has grown substantially as a model for understanding the evolutionary fundaments and capacity of vertebrate developmental and genome biology. Recent work on the lamprey genome has resulted in a preliminary assembly of the lamprey genome and led to the realization that nearly all somatic cell lineages undergo extensive programmed rearrangements. Here we describe the development of a bacterial artificial chromosome (BAC) resource for lamprey germline DNA and use sequence information from this resource to probe the subchromosomal structure of the lamprey genome. The arrayed germline BAC library represents approximately 10x coverage of the lamprey genome. Analyses of BAC-end sequences reveal that the lamprey genome possesses a high content of repetitive sequences (relative to human), which show strong clustering at the subchromosomal level. This pattern is not unexpected given that the sea lamprey genome is dispersed across a large number of chromosomes (n approximately 99) and suggests a low-copy DNA targeting strategy for efficiently generating informative paired-BAC-end linkages from highly repetitive genomes. This library therefore represents a new and biologically informed resource for understanding the structure of the lamprey genome and the biology of programmed genome rearrangement.
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9
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Shan X, Ray DA, Bunge JA, Peterson DG. A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization. BMC Genomics 2009; 10 Suppl 2:S9. [PMID: 19607660 PMCID: PMC2966330 DOI: 10.1186/1471-2164-10-s2-s9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored. To facilitate comparative genomics within Crocodylia and between crocodilians and other archosaurs, we have constructed a bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile, Crocodylus porosus. This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian. Results The C. porosus BAC library consists of 101,760 individually archived clones stored in 384-well microtiter plates. NotI digestion of random clones indicates an average insert size of 102 kb. Based on a genome size estimate of 2778 Mb, the library affords 3.7 fold (3.7×) coverage of the C. porosus genome. To investigate the utility of the library in studying sequence distribution, probes derived from CR1a and CR1b, two crocodilian CR1-like retrotransposon subfamilies, were hybridized to C. porosus macroarrays. The results indicate that there are a minimum of 20,000 CR1a/b elements in C. porosus and that their distribution throughout the genome is decidedly non-random. To demonstrate the utility of the library in gene isolation, we probed the C. porosus macroarrays with an overgo designed from a C-mos (oocyte maturation factor) partial cDNA. A BAC containing C-mos was identified and the C-mos locus was sequenced. Nucleotide and amino acid sequence alignment of the C. porosus C-mos coding sequence with avian and reptilian C-mos orthologs reveals greater sequence similarity between C. porosus and birds (specifically chicken and zebra finch) than between C. porosus and squamates (green anole). Conclusion We have demonstrated the utility of the Crocodylus porosus BAC library as a tool in genomics research. The BAC library should expedite complete genome sequencing of C. porosus and facilitate detailed analysis of genome evolution within Crocodylia and between crocodilians and diverse amniote lineages including birds, mammals, and other non-avian reptiles.
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Affiliation(s)
- Xueyan Shan
- Mississippi Genome Exploration Laboratory, Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, USA.
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Hinton DE, Hardman RC, Kullman SW, (Mac) Law JM, Schmale MC, Walter RB, Winn RN, Yoder JA. Aquatic animal models of human disease: selected papers and recommendations from the 4th Conference. Comp Biochem Physiol C Toxicol Pharmacol 2009; 149:121-8. [PMID: 19150511 PMCID: PMC2676715 DOI: 10.1016/j.cbpc.2008.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- David E. Hinton
- Division of Environmental Sciences and Policy, Nicholas School of the Environment, Duke University, Box 90328, A333B LSRC, Durham, NC 27708-0328, USA, Email address: , Tel.: +1 919 613 8038, Fax.: +1 919 684 8741
| | - Ron C. Hardman
- Division of Environmental Sciences and Policy, Nicholas School of the Environment, Duke University, Box 90328, A333A LSRC, Durham, NC 27708-0328, USA, Email address: , Tel.: +1 919 613 8038, Fax.: +1 919 684 8741
| | - Seth W. Kullman
- Department of Environmental and Molecular Toxicology, Box 7633, North Carolina State University, Raleigh, NC 27695-7633, Email address: , Tel.: +1 919 515 2274, Fax.: +1 919 515 7169
| | - Jerry M. (Mac) Law
- Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, Email address: , Tel.: +1 919 515 7411, Fax.: +1 919 515 3044
| | - Michael C. Schmale
- Division of Marine Biology and Fisheries, Rosentiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Cswy. Miami, FL 33149, USA, Email address: , Tel.:+1 305 421 4140, Fax.: +1 305 421 4600
| | - Ronald B. Walter
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, Email address: , Tel.: +1 512 245 0357, Fax.: +1 512 245 1922
| | - Richard N. Winn
- Aquatic Biotechnology and Environmental Lab (ABEL), 2580 Devil’s Ford Road, Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA, Email address: , Tel.: +1 706 369 5858, Fax.: +1 706 353 2620
| | - Jeffrey A. Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606 USA, Email address: , Tel.: +1 919 515 7406, Fax.: +1 919 513 7301
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Okoruwa OE, Weston MD, Sanjeevi DC, Millemon AR, Fritzsch B, Hallworth R, Beisel KW. Evolutionary insights into the unique electromotility motor of mammalian outer hair cells. Evol Dev 2008; 10:300-15. [PMID: 18460092 DOI: 10.1111/j.1525-142x.2008.00239.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Prestin (SLC26A5) is the molecular motor responsible for cochlear amplification by mammalian cochlea outer hair cells and has the unique combined properties of energy-independent motility, voltage sensitivity, and speed of cellular shape change. The ion transporter capability, typical of SLC26A members, was exchanged for electromotility function and is a newly derived feature of the therian cochlea. A putative minimal essential motif for the electromotility motor (meEM) was identified through the amalgamation of comparative genomic, evolution, and structural diversification approaches. Comparisons were done among nonmammalian vertebrates, eutherian mammalian species, and the opossum and platypus. The opossum and platypus SLC26A5 proteins were comparable to the eutherian consensus sequence. Suggested from the point-accepted mutation analysis, the meEM motif spans all the transmembrane segments and represented residues 66-503. Within the eutherian clade, the meEM was highly conserved with a substitution frequency of only 39/7497 (0.5%) residues, compared with 5.7% in SLC26A4 and 12.8% in SLC26A6 genes. Clade-specific substitutions were not observed and there was no sequence correlation with low or high hearing frequency specialists. We were able to identify that within the highly conserved meEM motif two regions, which are unique to all therian species, appear to be the most derived features in the SLC26A5 peptide.
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Affiliation(s)
- Oseremen E Okoruwa
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE 68178, USA
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Di Palma F, Kidd C, Borowsky R, Kocher TD. Construction of Bacterial Artificial Chromosome Libraries for The Lake Malawi Cichlid (Metriaclima Zebra), And The Blind Cavefish (Astyanax Mexicanus). Zebrafish 2007; 4:41-7. [DOI: 10.1089/zeb.2006.9996] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Federica Di Palma
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire
| | - Celeste Kidd
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire
| | | | - Thomas D. Kocher
- Department of Biology, University of Maryland, College Park, Maryland
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Amemiya CT, Gomez-Chiarri M. Comparative genomics in vertebrate evolution and development. ACTA ACUST UNITED AC 2006; 305:672-82. [PMID: 16902957 DOI: 10.1002/jez.a.308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The vast quantities of publicly available DNA sequencing data and genome resources are enabling biologists to investigate age-old problems in biology that were not addressable previously. In this review, we discuss how comparative genomics is practiced and how the data can be used to make biological inferences with respect to vertebrate evolution and development. Examples are taken from the well-known HOX clusters, which are always a high-priority target for genomic analyses due to their inferred role in the evolution of metazoans. In addition, we briefly discuss the application of genomic approaches to problems in comparative endocrinology.
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Affiliation(s)
- Chris T Amemiya
- Molecular Genetics Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA.
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Luo M, Kim H, Kudrna D, Sisneros NB, Lee SJ, Mueller C, Collura K, Zuccolo A, Buckingham EB, Grim SM, Yanagiya K, Inoko H, Shiina T, Flajnik MF, Wing RA, Ohta Y. Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey. BMC Genomics 2006; 7:106. [PMID: 16672057 PMCID: PMC1513397 DOI: 10.1186/1471-2164-7-106] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2005] [Accepted: 05/03/2006] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. AIMS In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum. RESULTS The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 x 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6-28 primary positive clones per probe of which 50-90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. CONCLUSION We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.
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Affiliation(s)
- Meizhong Luo
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - HyeRan Kim
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Dave Kudrna
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Nicholas B Sisneros
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - So-Jeong Lee
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Christopher Mueller
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Kristi Collura
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Andrea Zuccolo
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - E Bryan Buckingham
- University of Maryland, Department of Microbiology and Immunology, 655 West Baltimore Street, BRB3-052, Baltimore, MD 21201, USA
| | - Suzanne M Grim
- University of Maryland, Department of Microbiology and Immunology, 655 West Baltimore Street, BRB3-052, Baltimore, MD 21201, USA
| | - Kazuyo Yanagiya
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1143, Japan
| | - Hidetoshi Inoko
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1143, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1143, Japan
| | - Martin F Flajnik
- University of Maryland, Department of Microbiology and Immunology, 655 West Baltimore Street, BRB3-052, Baltimore, MD 21201, USA
| | - Rod A Wing
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Yuko Ohta
- University of Maryland, Department of Microbiology and Immunology, 655 West Baltimore Street, BRB3-052, Baltimore, MD 21201, USA
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Cannon JP, Haire RN, Mueller MG, Litman RT, Eason DD, Tinnemore D, Amemiya CT, Ota T, Litman GW. Ancient divergence of a complex family of immune-type receptor genes. Immunogenetics 2006; 58:362-73. [PMID: 16738934 PMCID: PMC3701310 DOI: 10.1007/s00251-006-0112-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2006] [Accepted: 03/13/2006] [Indexed: 10/24/2022]
Abstract
Multigene families of activating/inhibitory receptors belonging to the immunoglobulin superfamily (IgSF) regulate immunological and other cell-cell interactions. A new family of such genes, termed modular domain immune-type receptors (MDIRs), has been identified in the clearnose skate (Raja eglanteria), a phylogenetically ancient vertebrate. At least five different major forms of predicted MDIR proteins are comprised of four different subfamilies of IgSF ectodomains of the intermediate (I)- or C2-set. The predicted number of individual IgSF ectodomains in MDIRs varies from one to six. MDIR1 contains a positively charged transmembrane residue and MDIR2 and MDIR3 each possesses at least one immunoreceptor tyrosine-based inhibitory motif in their cytoplasmic regions. MDIR4 and MDIR5 lack characteristic activating/inhibitory signalling motifs. MDIRs are encoded in a particularly large and complex multigene family. MDIR domains exhibit distant sequence similarity to mammalian CMRF-35-like molecules, polymeric immunoglobulin receptors, triggering receptors expressed on myeloid cells (TREMs), TREM-like transcripts, NKp44 and FcR homologs, as well as to sequences identified in several different vertebrate genomes. Phylogenetic analyses suggest that MDIRs are representative members of an extended family of IgSF genes that diverged before or very early in evolution of the vertebrates and subsequently came to occupy multiple, fully independent distributions in the present day.
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Affiliation(s)
- John P. Cannon
- Department of Pediatrics, University of South Florida College of Medicine, and USF/ACH Children’s Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Avenue, Tampa, FL 33612, USA
| | - Robert N. Haire
- Department of Pediatrics, University of South Florida College of Medicine, and USF/ACH Children’s Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Avenue, Tampa, FL 33612, USA
| | - M. Gail Mueller
- Department of Molecular Genetics, All Children’s Hospital, 801 Sixth Street South, St. Petersburg, FL 33701, USA
| | - Ronda T. Litman
- Department of Pediatrics, University of South Florida College of Medicine, and USF/ACH Children’s Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA
| | - Donna D. Eason
- Department of Pediatrics, University of South Florida College of Medicine, and USF/ACH Children’s Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Avenue, Tampa, FL 33612, USA
| | - Deborah Tinnemore
- Molecular Genetics Program, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101, USA
| | - Chris T. Amemiya
- Molecular Genetics Program, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101, USA
| | - Tatsuya Ota
- Department of Biosystems Science and Hayama Center for Advanced Studies, The Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa 240-0193, Japan
| | - Gary W. Litman
- Department of Pediatrics, University of South Florida College of Medicine, and USF/ACH Children’s Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Avenue, Tampa, FL 33612, USA
- Department of Molecular Genetics, All Children’s Hospital, 801 Sixth Street South, St. Petersburg, FL 33701, USA, , Tel.: +1-727-5533602, Fax: +1-727-5533610
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16
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Luo M, Yu Y, Kim H, Kudrna D, Itoh Y, Agate RJ, Melamed E, Goicoechea JL, Talag J, Mueller C, Wang W, Currie J, Sisneros NB, Wing RA, Arnold AP. Utilization of a zebra finch BAC library to determine the structure of an avian androgen receptor genomic region. Genomics 2006; 87:181-90. [PMID: 16321505 DOI: 10.1016/j.ygeno.2005.09.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Revised: 09/06/2005] [Accepted: 09/07/2005] [Indexed: 12/16/2022]
Abstract
The zebra finch (Taeniopygia guttata) is an important model organism for studying behavior, neuroscience, avian biology, and evolution. To support the study of its genome, we constructed a BAC library (TG__Ba) using DNA from livers of females. The BAC library consists of 147,456 clones with 98% containing inserts of an average size of 134 kb and represents 15.5 haploid genome equivalents. By sequencing a whole BAC, a full-length androgen receptor open reading frame was identified, the first in an avian species. Comparison of BAC end sequences and the whole BAC sequence with the chicken genome draft sequence showed a high degree of conserved synteny between the zebra finch and the chicken genome.
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Affiliation(s)
- Meizhong Luo
- Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721, USA
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17
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447482 DOI: 10.1002/cfg.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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