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Jaratlerdsiri W, Deakin J, Godinez RM, Shan X, Peterson DG, Marthey S, Lyons E, McCarthy FM, Isberg SR, Higgins DP, Chong AY, John JS, Glenn TC, Ray DA, Gongora J. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. PLoS One 2014; 9:e114631. [PMID: 25503521 PMCID: PMC4263668 DOI: 10.1371/journal.pone.0114631] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/11/2014] [Indexed: 12/22/2022] Open
Abstract
The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.
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Affiliation(s)
- Weerachai Jaratlerdsiri
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Janine Deakin
- Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2601, Australia
| | - Ricardo M. Godinez
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, United States of America
- Department of Genetics, Harvard Medical School, 77 Louis Pasteur Ave., Boston, Massachusetts 02115, United States of America
| | - Xueyan Shan
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, United States of America
| | - Daniel G. Peterson
- Institute for Genomics, Biocomputing and Biotechnology (IGBB), Mississippi State University, Mississippi State, Mississippi 39762, United States of America
| | - Sylvain Marthey
- Animal Genetics and Integrative Biology, INRA, UMR 1313 Jouy-en-Josas 78352, France
| | - Eric Lyons
- School of Plant Science, University of Arizona, Tucson, Arizona 85721, United States of America
| | - Fiona M. McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States of America
| | - Sally R. Isberg
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
- Center for Crocodile Research, P.O. Box 329, Noonamah, Northern Territory 0837, Australia
| | - Damien P. Higgins
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Amanda Y. Chong
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
| | - John St John
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, United States of America
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, Georgia 30602, United States of America
| | - David A. Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, United States of America
- Institute for Genomics, Biocomputing and Biotechnology (IGBB), Mississippi State University, Mississippi State, Mississippi 39762, United States of America
| | - Jaime Gongora
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
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A bacterial artificial chromosome library for the Chinese alligator (Alligator sinensis). Gene 2012; 507:74-8. [PMID: 22759519 DOI: 10.1016/j.gene.2012.06.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 06/06/2012] [Accepted: 06/20/2012] [Indexed: 11/21/2022]
Abstract
Chinese alligator (Alligator sinensis) is a rare and endangered species endemic to China. To better understand genetic details of the Chinese alligator genomic structure, a highly redundant bacterial artificial chromosome (BAC) library was constructed. This library consists of 216,238 clones with an average insert size of about 90 kb, indicating that the library contains 6.8-fold genome equivalents. Subsequently, we constructed a 516 kb contig map for the Chinese alligator olfactory receptor (OR) genes, which spans nine BAC clones, and subjected the BACs to full sequencing. The sequence analysis revealed that this contig contained 16 OR functional genes and meanwhile demonstrated that the nine BACs, which constituted the contig, overlapped correctly, proving the usability of this genome library. As a result, this BAC library could provide a useful platform for physical mapping, genome sequencing or complex analysis of targeted genomic regions for this rare species.
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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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Liu W, Thummasuwan S, Sehgal SK, Chouvarine P, Peterson DG. Characterization of the genome of bald cypress. BMC Genomics 2011; 12:553. [PMID: 22077969 PMCID: PMC3228858 DOI: 10.1186/1471-2164-12-553] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Accepted: 11/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bald cypress (Taxodium distichum var. distichum) is a coniferous tree of tremendous ecological and economic importance. It is a member of the family Cupressaceae which also includes cypresses, redwoods, sequoias, thujas, and junipers. While the bald cypress genome is more than three times the size of the human genome, its 1C DNA content is amongst the smallest of any conifer. To learn more about the genome of bald cypress and gain insight into the evolution of Cupressaceae genomes, we performed a Cot analysis and used Cot filtration to study Taxodium DNA. Additionally, we constructed a 6.7 genome-equivalent BAC library that we screened with known Taxodium genes and select repeats. RESULTS The bald cypress genome is composed of 90% repetitive DNA with most sequences being found in low to mid copy numbers. The most abundant repeats are found in fewer than 25,000 copies per genome. Approximately 7.4% of the genome is single/low-copy DNA (i.e., sequences found in 1 to 5 copies). Sequencing of highly repetitive Cot clones indicates that most Taxodium repeats are highly diverged from previously characterized plant repeat sequences. The bald cypress BAC library consists of 606,336 clones (average insert size of 113 kb) and collectively provides 6.7-fold genome equivalent coverage of the bald cypress genome. Macroarray screening with known genes produced, on average, about 1.5 positive clones per probe per genome-equivalent. Library screening with Cot-1 DNA revealed that approximately 83% of BAC clones contain repetitive sequences iterated 103 to 104 times per genome. CONCLUSIONS The BAC library for bald cypress is the first to be generated for a conifer species outside of the family Pinaceae. The Taxodium BAC library was shown to be useful in gene isolation and genome characterization and should be an important tool in gymnosperm comparative genomics, physical mapping, genome sequencing, and gene/polymorphism discovery. The single/low-copy (SL) component of bald cypress is 4.6 times the size of the Arabidopsis genome. As suggested for other gymnosperms, the large amount of SL DNA in Taxodium is likely the result of divergence among ancient repeat copies and gene/pseudogene duplication.
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Affiliation(s)
- Wenxuan Liu
- Mississippi Genome Exploration Laboratory and Department of Plant & Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA
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Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine. PLoS One 2011; 6:e16214. [PMID: 21283709 PMCID: PMC3025025 DOI: 10.1371/journal.pone.0016214] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 12/10/2010] [Indexed: 11/19/2022] Open
Abstract
Loblolly pine (LP; Pinus taeda L.) is the most economically important tree in the U.S. and a cornerstone species in southeastern forests. However, genomics research on LP and other conifers has lagged behind studies on flowering plants due, in part, to the large size of conifer genomes. As a means to accelerate conifer genome research, we constructed a BAC library for the LP genotype 7-56. The LP BAC library consists of 1,824,768 individually-archived clones making it the largest single BAC library constructed to date, has a mean insert size of 96 kb, and affords 7.6X coverage of the 21.7 Gb LP genome. To demonstrate the efficacy of the library in gene isolation, we screened macroarrays with overgos designed from a pine EST anchored on LP chromosome 10. A positive BAC was sequenced and found to contain the expected full-length target gene, several gene-like regions, and both known and novel repeats. Macroarray analysis using the retrotransposon IFG-7 (the most abundant repeat in the sequenced BAC) as a probe indicates that IFG-7 is found in roughly 210,557 copies and constitutes about 5.8% or 1.26 Gb of LP nuclear DNA; this DNA quantity is eight times the Arabidopsis genome. In addition to its use in genome characterization and gene isolation as demonstrated herein, the BAC library should hasten whole genome sequencing of LP via next-generation sequencing strategies/technologies and facilitate improvement of trees through molecular breeding and genetic engineering. The library and associated products are distributed by the Clemson University Genomics Institute (www.genome.clemson.edu).
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Dittmar T, Zänker KS. Horizontal gene transfers with or without cell fusions in all categories of the living matter. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 714:5-89. [PMID: 21506007 PMCID: PMC7120942 DOI: 10.1007/978-94-007-0782-5_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.
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Affiliation(s)
- Thomas Dittmar
- Inst. Immunologie, Universität Witten/Herdecke, Stockumer Str. 10, Witten, 58448 Germany
| | - Kurt S. Zänker
- Institute of Immunologie, University of Witten/Herdecke, Stockumer Str. 10, Witten, 58448 Germany
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Janes DE, Organ CL, Fujita MK, Shedlock AM, Edwards SV. Genome evolution in Reptilia, the sister group of mammals. Annu Rev Genomics Hum Genet 2010; 11:239-64. [PMID: 20590429 DOI: 10.1146/annurev-genom-082509-141646] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomes of birds and nonavian reptiles (Reptilia) are critical for understanding genome evolution in mammals and amniotes generally. Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in the comparative genomics era. The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral amniote genome--predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system--to the small and highly streamlined genomes of birds. Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals.
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Affiliation(s)
- Daniel E Janes
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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