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1. Complete Genome Sequence of the Apicomplexan, Cryptosporidium parvum

Author

Abrahamsen, Mitchell S., Templeton, Thomas J., Enomoto, Shinichiro, Abrahante, Juan E., Zhu, Guan, Lancto, Cheryl A., Deng, Mingqi, Liu, Chang, Widmer, Giovanni, Tzipori, Saul, Buck, Gregory A., Xu, Ping, Bankier, Alan T., Dear, Paul H., Konfortov, Bernard A., Spriggs, Helen F., Iyer, Lakshminarayan, Anantharaman, Vivek, Aravind, L., and Kapur, Vivek

Published
2004

3. Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome

Author

Hamilton, Eileen P, Dear, Paul H, Rowland, Teisha, Saks, Karen, Eisen, Jonathan A, and Orias, Eduardo

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Animals, Genetic Linkage, Genetic Markers, Genome, Protozoan, Macronucleus, Physical Chromosome Mapping, Reproducibility of Results, Telomere, Tetrahymena thermophila, assembly closure, chromosome breakage sequence, germ-line nucleus, internally eliminated sequence, link validation, macronuclear chromosomes, sequence scaffolds, somatic nucleus, telomeres, whole-genome-shotgun sequence, Information Systems, Genetics & Heredity
Abstract

Tetrahymena thermophila is the best studied of the ciliates, a diversified and successful lineage of eukaryotic protists. Mirroring the way in which many metazoans partition their germ line and soma into distinct cell types, ciliates separate germ line and soma into two distinct nuclei in a single cell. The diploid, transcriptionally silent micronucleus undergoes meiosis and fertilization during sexual reproduction and determines the genotype of the progeny; in contrast, the expressed macronucleus contains many copies of hundreds of small chromosomes, determines the cell's phenotype, and is inherited only through vegetative reproduction. Here we demonstrate the power of HAPPY physical mapping to aid the complete assembly of T. thermophila macronuclear chromosomes from shotgun sequence scaffolds. The finished genome, one of only two ciliate genomes shotgun sequenced, will shed valuable additional light upon the biology of this extraordinary, diverse, and, from a genomics standpoint, as yet largely unexplored evolutionary branch of eukaryotes.

Published
2006

7. The genome of Cryptosporidium hominis

Author

Xu, Ping, Widmer, Giovanni, Wang, Yingping, Ozaki, Luiz S., Alves, Joao M., Serrano, Myrna G., Puiu, Daniela, Manque, Patricio, Akiyoshi, Donna, Mackey, Aaron J., Pearson, William R., Dear, Paul H., Bankier, Alan T., Peterson, Darrell L., Abrahamsen, Mitchell S., Kapur, Vivek, Tzipori, Saul, and Buck, Gregory A.

Abstract

Author(s): Ping Xu [1, 2, 3, 12]; Giovanni Widmer [4, 12]; Yingping Wang [1, 2]; Luiz S. Ozaki [1, 2]; Joao M. Alves [1, 2]; Myrna G. Serrano [1, 2]; [...]

Published
2004
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9. Sequence and analysis of chromosome 2 of Dictyostelium discoideum

Author

Glöckner, Gernot, Eichinger, Ludwig, Szafranski, Karol, Pachebat, Justin A., Bankier, Alan T., Dear, Paul H., Lehmann, Rüdiger, Baumgart, Cornelia, Parra, Genís, Abril, Josep F., Guigó, Roderic, Kumpf, Kai, Tunggal, Budi, Cox, Edward, Quail, Michael A., Platzer, Matthias, Rosenthal, André, Noegel, Angelika A., Barrell, Bart G., Rajandream, Marie-Adèle, Williams, Jeffrey G., Kay, Robert R., Kuspa, Adam, Gibbs, Richard, Sucgang, Richard, Muzny, Donna, Desany, Brian, Zeng, Kathy, Zhu, Baoli, de Jong, Pieter, Dingermann, Theodor, Gerisch, Günther, Philippsen, Peter, Schleicher, Michael, Schuster, Stephan C., and Winckler, Thomas

Published
2002
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12. Single-molecule DNA sequencing of widely varying GC-content using nucleotide release, capture and detection in microdroplets

Author

Puchtler, Tim J, primary, Johnson, Kerr, additional, Palmer, Rebecca N, additional, Talbot, Emma L, additional, Ibbotson, Lindsey A, additional, Powalowska, Paulina K, additional, Knox, Rachel, additional, Shibahara, Aya, additional, M. S. Cunha, Pedro, additional, Newell, Oliver J, additional, Wu, Mei, additional, Chana, Jasmin, additional, Athanasopoulou, Evangelia-Nefeli, additional, Waeber, Andreas M, additional, Stolarek, Magdalena, additional, Silva, Ana-Luisa, additional, Mordaka, Justyna M, additional, Haggis-Powell, Michael, additional, Xyrafaki, Christina, additional, Bush, James, additional, Topkaya, Ibrahim S, additional, Sosna, Maciej, additional, Ingham, Richard J, additional, Huckvale, Thomas, additional, Negrea, Aurel, additional, Breiner, Boris, additional, Šlikas, Justinas, additional, Kelly, Douglas J, additional, Dunning, Alexander J, additional, Bell, Neil M, additional, Dethlefsen, Mark, additional, Love, David M, additional, Dear, Paul H, additional, Kuleshova, Jekaterina, additional, Podd, Gareth J, additional, Isaac, Tom H, additional, Balmforth, Barnaby W, additional, and Frayling, Cameron A, additional

Published
2020
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17. Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization

Author

King-Hwa Ling, Rajandream, Marie-Adele, Rivailler, Pierre, Ivens, Alasdair, Soon-Joo Yap, Madeira, Alda M.B.N., Mungall, Karen, Billington, Karen, Wai-Yan Yee; Bankier, Alan T., Carroll, FionnadhDurham, Alan M.; Peters, Nicholas, Shu-San Loo, Mat Isa, Mohd Noor, Novaes, Jeniffer, Quail, Michael, Rosli, Rozita, Nor Shamsudin, Mariana, Sobreira, Tiago J.P., Tivey, Adrian R., Siew-Fun Wai, White, Sarah, Xikun Wu, Kerhornou, Arnaud, Blake, Damer, Mohamed, Rahmah, Shirley, Martin, Gruber, Arthur, Berriman, Matthew, Tomley, Fiona, Dear, Paul H., and Wan, Kiew-Lian

Subjects
Protozoa -- Genetic aspects, Protozoa -- Research, Chromosomes -- Structure, Chromosomes -- Research, Bacterial genetics -- Research, Health
Abstract

The sequencing and analysis of the first chromosome of Eimeria tenella, a chromosome believed to carry loci associated with drug resistance and known to differ between virulent and attenuated strains of the parasite infecting the intestinal tracts of domestic fowls is reported. The chromosome is found to show most striking segmentation of repeat-rich regions peppered with transposon-like elements and telomere-like repeats, alternating with repeat-free regions.

Published
2007

21. Insights into the genome structure and copy-number variation of Eimeria tenella

Author

Lim Lik-Sin, Tay Yea-Ling, Alias Halimah, Wan Kiew-Lian, and Dear Paul H

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Eimeria is a genus of parasites in the same phylum (Apicomplexa) as human parasites such as Toxoplasma, Cryptosporidium and the malaria parasite Plasmodium. As an apicomplexan whose life-cycle involves a single host, Eimeria is a convenient model for understanding this group of organisms. Although the genomes of the Apicomplexa are diverse, that of Eimeria is unique in being composed of large alternating blocks of sequence with very different characteristics - an arrangement seen in no other organism. This arrangement has impeded efforts to fully sequence the genome of Eimeria, which remains the last of the major apicomplexans to be fully analyzed. In order to increase the value of the genome sequence data and aid in the effort to gain a better understanding of the Eimeria tenella genome, we constructed a whole genome map for the parasite. Results A total of 1245 contigs representing 70.0% of the whole genome assembly sequences (Wellcome Trust Sanger Institute) were selected and subjected to marker selection. Subsequently, 2482 HAPPY markers were developed and typed. Of these, 795 were considered as usable markers, and utilized in the construction of a HAPPY map. Markers developed from chromosomally-assigned genes were then integrated into the HAPPY map and this aided the assignment of a number of linkage groups to their respective chromosomes. BAC-end sequences and contigs from whole genome sequencing were also integrated to improve and validate the HAPPY map. This resulted in an integrated HAPPY map consisting of 60 linkage groups that covers approximately half of the estimated 60 Mb genome. Further analysis suggests that the segmental organization first seen in Chromosome 1 is present throughout the genome, with repeat-poor (P) regions alternating with repeat-rich (R) regions. Evidence of copy-number variation between strains was also uncovered. Conclusions This paper describes the application of a whole genome mapping method to improve the assembly of the genome of E. tenella from shotgun data, and to help reveal its overall structure. A preliminary assessment of copy-number variation (extra or missing copies of genomic segments) between strains of E. tenella was also carried out. The emerging picture is of a very unusual genome architecture displaying inter-strain copy-number variation. We suggest that these features may be related to the known ability of this parasite to rapidly develop drug resistance.

Published
2012
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22. Single-molecule detection of deoxyribonucleoside triphosphates in microdroplets

Author

Breiner, Boris, primary, Johnson, Kerr, additional, Stolarek, Magdalena, additional, Silva, Ana-Luisa, additional, Negrea, Aurel, additional, Bell, Neil M, additional, Isaac, Tom H, additional, Dethlefsen, Mark, additional, Chana, Jasmin, additional, Ibbotson, Lindsey A, additional, Palmer, Rebecca N, additional, Bush, James, additional, Dunning, Alexander J, additional, Love, David M, additional, Pachoumi, Olympia, additional, Kelly, Douglas J, additional, Shibahara, Aya, additional, Wu, Mei, additional, Sosna, Maciej, additional, Dear, Paul H, additional, Tolle, Fabian, additional, Petrini, Edoardo, additional, Amasio, Michele, additional, Shelford, Leigh R, additional, Saavedra, Monica S, additional, Sheridan, Eoin, additional, Kuleshova, Jekaterina, additional, Podd, Gareth J, additional, Balmforth, Barnaby W, additional, and Frayling, Cameron A, additional

Published
2019
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24. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary

Author

Rabeder Gernot, O'Brien Stephen J, Bray Sarah CE, Briggs Adrian W, Dear Paul H, Spriggs Helen, Soibelzon Leopoldo, Stiller Mathias, Kolokotronis Sergios-Orestis, Malaspinas Anna-Sapfo, Noçon Aline, Unger Tina, Krause Johannes, Matheus Paul, Cooper Alan, Slatkin Montgomery, Pääbo Svante, and Hofreiter Michael

Subjects
Evolution, QH359-425
Abstract

Abstract Background Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods. Results We present a fully resolved phylogeny for ursids based on ten complete mitochondrial genome sequences from all eight living and two recently extinct bear species, the European cave bear (Ursus spelaeus) and the American giant short-faced bear (Arctodus simus). The mitogenomic data yield a well-resolved topology for ursids, with the sloth bear at the basal position within the genus Ursus. The sun bear is the sister taxon to both the American and Asian black bears, and this clade is the sister clade of cave bear, brown bear and polar bear confirming a recent study on bear mitochondrial genomes. Conclusion Sequences from extinct bears represent the third and fourth Pleistocene species for which complete mitochondrial genomes have been sequenced. Moreover, the cave bear specimen demonstrates that mitogenomic studies can be applied to Pleistocene fossils that have not been preserved in permafrost, and therefore have a broad application within ancient DNA research. Molecular dating of the mtDNA divergence times suggests a rapid radiation of bears in both the Old and New Worlds around 5 million years ago, at the Miocene-Pliocene boundary. This coincides with major global changes, such as the Messinian crisis and the first opening of the Bering Strait, and suggests a global influence of such events on species radiations.

Published
2008
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29. Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

Author

Hamilton, Eileen P, primary, Kapusta, Aurélie, additional, Huvos, Piroska E, additional, Bidwell, Shelby L, additional, Zafar, Nikhat, additional, Tang, Haibao, additional, Hadjithomas, Michalis, additional, Krishnakumar, Vivek, additional, Badger, Jonathan H, additional, Caler, Elisabet V, additional, Russ, Carsten, additional, Zeng, Qiandong, additional, Fan, Lin, additional, Levin, Joshua Z, additional, Shea, Terrance, additional, Young, Sarah K, additional, Hegarty, Ryan, additional, Daza, Riza, additional, Gujja, Sharvari, additional, Wortman, Jennifer R, additional, Birren, Bruce W, additional, Nusbaum, Chad, additional, Thomas, Jainy, additional, Carey, Clayton M, additional, Pritham, Ellen J, additional, Feschotte, Cédric, additional, Noto, Tomoko, additional, Mochizuki, Kazufumi, additional, Papazyan, Romeo, additional, Taverna, Sean D, additional, Dear, Paul H, additional, Cassidy-Hanley, Donna M, additional, Xiong, Jie, additional, Miao, Wei, additional, Orias, Eduardo, additional, and Coyne, Robert S, additional

Published
2016
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30. Author response: Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

Author

Hamilton, Eileen P, primary, Kapusta, Aurélie, additional, Huvos, Piroska E, additional, Bidwell, Shelby L, additional, Zafar, Nikhat, additional, Tang, Haibao, additional, Hadjithomas, Michalis, additional, Krishnakumar, Vivek, additional, Badger, Jonathan H, additional, Caler, Elisabet V, additional, Russ, Carsten, additional, Zeng, Qiandong, additional, Fan, Lin, additional, Levin, Joshua Z, additional, Shea, Terrance, additional, Young, Sarah K, additional, Hegarty, Ryan, additional, Daza, Riza, additional, Gujja, Sharvari, additional, Wortman, Jennifer R, additional, Birren, Bruce W, additional, Nusbaum, Chad, additional, Thomas, Jainy, additional, Carey, Clayton M, additional, Pritham, Ellen J, additional, Feschotte, Cédric, additional, Noto, Tomoko, additional, Mochizuki, Kazufumi, additional, Papazyan, Romeo, additional, Taverna, Sean D, additional, Dear, Paul H, additional, Cassidy-Hanley, Donna M, additional, Xiong, Jie, additional, Miao, Wei, additional, Orias, Eduardo, additional, and Coyne, Robert S, additional

Published
2016
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31. Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum

Author

Bankier, Alan T., Spriggs, Helen F., Fartmann, Berthold, Konfortov, Bernard A., Madera, Martin, Vogel, Christine, Teichmann, Sarah A., Ivens, Al, and Dear, Paul H.

Subjects
Coccidia -- Genetic aspects, Chromosome mapping -- Genetic aspects, Genetic research -- Analysis, Genomes -- Physiological aspects, Genomes -- Research, Health
Abstract

Research has been conducted on apicomplexan Cryptosporidium parvum. The authors describe the physical genome mapping of the lowa isolate and chromosome 6 seqiencing and analysis.

Published
2003

32. Numts help to reconstruct the demographic history of the ocellated lizard (Lacerta lepida) in a secondary contact zone

Author

Miraldo, Andreia, Hewitt, Godfrey M, Dear, Paul H., Paulo, Octavio S., Emerson, Brent C., and Fundação para a Ciência e a Tecnologia (Portugal)

Subjects
Secondary contact zone, Refugia, Heteroplasmy, Numts
Abstract

In northwestern Iberia, two largely allopatric Lacerta lepida mitochondrial lineages occur, L5 occurring to the south of Douro River and L3 to the north, with a zone of putative secondary contact in the region of the Douro River valley. Cytochrome b sequence chromatograms with polymorphisms at nucleotide sites diagnostic for the two lineages were detected in individuals in the region of the Douro River and further north within the range of L3. We show that these polymorphisms are caused by the presence of four different numts (I-IV) co-occurring with the L3 genome, together with low levels of heteroplasmy. Two of the numts (I and II) are similar to the mitochondrial genome of L5 but are quite divergent from the mitochondrial genome of L3 where they occur. We show that these numts are derived from the mitochondrial genome of L5 and were incorporated in L3 through hybridization at the time of secondary contact between the lineages. The additional incidence of these numts to the north of the putative contact zone is consistent with an earlier postglacial northward range expansion of L5, preceding that of L3. We show that genetic exchange between the lineages responsible for the origin of these numts in L3 after secondary contact occurred prior to, or coincident with, the northward expansion of L3. This study shows that, in the context of phylogeographic analysis, numts can provide evidence for past demographic events and can be useful tools for the reconstruction of complex evolutionary histories., This work was supported by a grant from FCT, Portugal (POCI/BIA‐BDE/59288/2004). A. M. was supported by a PhD grant from FCT (SFRH/BD/16996/2004).

Published
2012

33. Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus

Author

Vu, Giang T. H., primary, Schmutzer, Thomas, additional, Bull, Fabian, additional, Cao, Hieu X., additional, Fuchs, Jörg, additional, Tran, Trung D., additional, Jovtchev, Gabriele, additional, Pistrick, Klaus, additional, Stein, Nils, additional, Pecinka, Ales, additional, Neumann, Pavel, additional, Novak, Petr, additional, Macas, Jiri, additional, Dear, Paul H., additional, Blattner, Frank R., additional, Scholz, Uwe, additional, and Schubert, Ingo, additional

Published
2015
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34. Genomic analysis of the causative agents of coccidiosis in domestic chickens

Author

Reid, Adam J., Blake, Damer P., Ansari, Hifzur R., Billington, Karen, Browne, Hilary P., Bryant, Josephine, Dunn, Matt, Hung, Stacy S., Kawahara, Fumiya, Miranda-Saavedra, Diego, Malas, Tareq B., Mourier, Tobias, Naghra, Hardeep, Nair, Mridul, Otto, Thomas D., Rawlings, Neil D., Rivailler, Pierre, Sanchez-Flores, Alejandro, Sanders, Mandy, Subramaniam, Chandra, Tay, Yea-Ling, Woo, Yong, Wu, Xikun, Barrell, Bart, Dear, Paul H., Doerig, Christian, Gruber, Arthur, Ivens, Alasdair C., Parkinson, John, Rajandream, Marie-Adèle, Shirley, Martin W., Wan, Kiew-Lian, Berriman, Matthew, Tomley, Fiona M., Pain, Arnab, Reid, Adam J., Blake, Damer P., Ansari, Hifzur R., Billington, Karen, Browne, Hilary P., Bryant, Josephine, Dunn, Matt, Hung, Stacy S., Kawahara, Fumiya, Miranda-Saavedra, Diego, Malas, Tareq B., Mourier, Tobias, Naghra, Hardeep, Nair, Mridul, Otto, Thomas D., Rawlings, Neil D., Rivailler, Pierre, Sanchez-Flores, Alejandro, Sanders, Mandy, Subramaniam, Chandra, Tay, Yea-Ling, Woo, Yong, Wu, Xikun, Barrell, Bart, Dear, Paul H., Doerig, Christian, Gruber, Arthur, Ivens, Alasdair C., Parkinson, John, Rajandream, Marie-Adèle, Shirley, Martin W., Wan, Kiew-Lian, Berriman, Matthew, Tomley, Fiona M., and Pain, Arnab

Abstract

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.

Published
2014

35. Genomic analysis of the causative agents of coccidiosis in domestic chickens

Author

Reid, Adam J., primary, Blake, Damer P., additional, Ansari, Hifzur R., additional, Billington, Karen, additional, Browne, Hilary P., additional, Bryant, Josephine, additional, Dunn, Matt, additional, Hung, Stacy S., additional, Kawahara, Fumiya, additional, Miranda-Saavedra, Diego, additional, Malas, Tareq B., additional, Mourier, Tobias, additional, Naghra, Hardeep, additional, Nair, Mridul, additional, Otto, Thomas D., additional, Rawlings, Neil D., additional, Rivailler, Pierre, additional, Sanchez-Flores, Alejandro, additional, Sanders, Mandy, additional, Subramaniam, Chandra, additional, Tay, Yea-Ling, additional, Woo, Yong, additional, Wu, Xikun, additional, Barrell, Bart, additional, Dear, Paul H., additional, Doerig, Christian, additional, Gruber, Arthur, additional, Ivens, Alasdair C., additional, Parkinson, John, additional, Rajandream, Marie-Adèle, additional, Shirley, Martin W., additional, Wan, Kiew-Lian, additional, Berriman, Matthew, additional, Tomley, Fiona M., additional, and Pain, Arnab, additional

Published
2014
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36. Numts help to reconstruct the demographic history of the ocellated lizard (Lacerta lepida) in a secondary contact zone

Author

Fundação para a Ciência e a Tecnologia (Portugal), Miraldo, Andreia, Hewitt, Godfrey M, Dear, Paul H., Paulo, Octávio S., Emerson, Brent C., Fundação para a Ciência e a Tecnologia (Portugal), Miraldo, Andreia, Hewitt, Godfrey M, Dear, Paul H., Paulo, Octávio S., and Emerson, Brent C.

Abstract

In northwestern Iberia, two largely allopatric Lacerta lepida mitochondrial lineages occur, L5 occurring to the south of Douro River and L3 to the north, with a zone of putative secondary contact in the region of the Douro River valley. Cytochrome b sequence chromatograms with polymorphisms at nucleotide sites diagnostic for the two lineages were detected in individuals in the region of the Douro River and further north within the range of L3. We show that these polymorphisms are caused by the presence of four different numts (I-IV) co-occurring with the L3 genome, together with low levels of heteroplasmy. Two of the numts (I and II) are similar to the mitochondrial genome of L5 but are quite divergent from the mitochondrial genome of L3 where they occur. We show that these numts are derived from the mitochondrial genome of L5 and were incorporated in L3 through hybridization at the time of secondary contact between the lineages. The additional incidence of these numts to the north of the putative contact zone is consistent with an earlier postglacial northward range expansion of L5, preceding that of L3. We show that genetic exchange between the lineages responsible for the origin of these numts in L3 after secondary contact occurred prior to, or coincident with, the northward expansion of L3. This study shows that, in the context of phylogeographic analysis, numts can provide evidence for past demographic events and can be useful tools for the reconstruction of complex evolutionary histories.

Published
2012

38. Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization.

Author

Ling , King Hwa, Rajandream, Marie Adèle, Rivailler, Pierre, Ivens, Alasdair C., Yap, Soon J., Madeira, Alda Maria Backx Noronha, Mungall, Karen L., Billington, Karen J., Yee, Wai Y., Bankier, Alan T., Carroll, Fionnadh, Durham, Alan Mitchell, Peters, Nick T., Loo, Shu S., Isa, M. N M, Novaes, Jeniffer, Quail, Michael A., Rosli, Rozita, Shamsudin, Mariana Nor, Sobreira, Tiago José Pascoal, Tivey, Adrian R., Wai, Siew F., White, Sarah E., Wu, Xikun, Kerhornou, Arnaud X., Blake, Damer P., Mohamed, Rahmah I., Shirley, Martin W., Gruber, Arthur, Berriman, Matthew, Tomley, Fiona M Fiona, Dear, Paul H., Wan, Kiew Lian, Ling , King Hwa, Rajandream, Marie Adèle, Rivailler, Pierre, Ivens, Alasdair C., Yap, Soon J., Madeira, Alda Maria Backx Noronha, Mungall, Karen L., Billington, Karen J., Yee, Wai Y., Bankier, Alan T., Carroll, Fionnadh, Durham, Alan Mitchell, Peters, Nick T., Loo, Shu S., Isa, M. N M, Novaes, Jeniffer, Quail, Michael A., Rosli, Rozita, Shamsudin, Mariana Nor, Sobreira, Tiago José Pascoal, Tivey, Adrian R., Wai, Siew F., White, Sarah E., Wu, Xikun, Kerhornou, Arnaud X., Blake, Damer P., Mohamed, Rahmah I., Shirley, Martin W., Gruber, Arthur, Berriman, Matthew, Tomley, Fiona M Fiona, Dear, Paul H., and Wan, Kiew Lian

Abstract

Eimeria tenella is an intracellular protozoan parasite that infects the intestinal tracts of domestic fowl and causes coccidiosis, a serious and sometimes lethal enteritis. Eimeria falls in the same phylum (Apicomplexa) as several human and animal parasites such as Cryptosporidium, Toxoplasma, and the malaria parasite, Plasmodium. Here we report the sequencing and analysis of the first chromosome of E. tenella, a chromosome believed to carry loci associated with drug resistance and known to differ between virulent and attenuated strains of the parasite. The chromosome - which appears to be representative of the genome - is gene-dense and rich in simple-sequence repeats, many of which appear to give rise to repetitive amino acid tracts in the predicted proteins. Most striking is the segmentation of the chromosome into repeat-rich regions peppered with transposon-like elements and telomere-like repeats, alternating with repeat-free regions. Predicted genes differ in character between the two types of segment, and the repeat-rich regions appear to be associated with strain-to-strain variation.

Published
2007

41. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary

Author

Krause, Johannes, primary, Unger, Tina, additional, Noçon, Aline, additional, Malaspinas, Anna-Sapfo, additional, Kolokotronis, Sergios-Orestis, additional, Stiller, Mathias, additional, Soibelzon, Leopoldo, additional, Spriggs, Helen, additional, Dear, Paul H, additional, Briggs, Adrian W, additional, Bray, Sarah CE, additional, O'Brien, Stephen J, additional, Rabeder, Gernot, additional, Matheus, Paul, additional, Cooper, Alan, additional, Slatkin, Montgomery, additional, Pääbo, Svante, additional, and Hofreiter, Michael, additional

Published
2008
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42. Real-Time PCRs and Fingerprinting Assays for the Detection and Characterization ofSalmonellaGenomic Island-1 Encoding Multidrug Resistance: Application to 445 European Isolates ofSalmonella, Escherichia coli, Shigella, andProteus

Author

Amar, Corinne F.L., primary, Arnold, Catherine, additional, Bankier, Alan, additional, Dear, Paul H., additional, Guerra, Beatriz, additional, Hopkins, Katie L., additional, Liebana, Ernesto, additional, Mevius, Dik J., additional, and Threlfall, E. John, additional

Published
2008
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45. Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization

Author

Ling, King-Hwa, primary, Rajandream, Marie-Adele, additional, Rivailler, Pierre, additional, Ivens, Alasdair, additional, Yap, Soon-Joo, additional, Madeira, Alda M.B.N., additional, Mungall, Karen, additional, Billington, Karen, additional, Yee, Wai-Yan, additional, Bankier, Alan T., additional, Carroll, Fionnadh, additional, Durham, Alan M., additional, Peters, Nicholas, additional, Loo, Shu-San, additional, Mat Isa, Mohd Noor, additional, Novaes, Jeniffer, additional, Quail, Michael, additional, Rosli, Rozita, additional, Nor Shamsudin, Mariana, additional, Sobreira, Tiago J.P., additional, Tivey, Adrian R., additional, Wai, Siew-Fun, additional, White, Sarah, additional, Wu, Xikun, additional, Kerhornou, Arnaud, additional, Blake, Damer, additional, Mohamed, Rahmah, additional, Shirley, Martin, additional, Gruber, Arthur, additional, Berriman, Matthew, additional, Tomley, Fiona, additional, Dear, Paul H., additional, and Wan, Kiew-Lian, additional

Published
2007
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47. Multiplex amplification of ancient DNA

Author

Römpler, Holger, primary, Dear, Paul H, additional, Krause, Johannes, additional, Meyer, Matthias, additional, Rohland, Nadin, additional, Schöneberg, Torsten, additional, Spriggs, Helen, additional, Stiller, Mathias, additional, and Hofreiter, Michael, additional

Published
2006
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50. Corrigendum: The genome of Cryptosporidium hominis

Author

Xu, Ping, Widmer, Giovanni, Wang, Yingping, Ozaki, Luiz S., Alves, Joao M., Serrano, Myrna G., Puiu, Daniela, Manque, Patricio, Akiyoshi, Donna, Mackey, Aaron J., Pearson, William R., Dear, Paul H., Bankier, Alan T., Peterson, Darrell L., Abrahamsen, Mitchell S., Kapur, Vivek, Tzipori, Saul, and Buck, Gregory A.

Abstract

Author(s): Ping Xu; Giovanni Widmer; Yingping Wang; Luiz S. Ozaki; Joao M. Alves; Myrna G. Serrano; Daniela Puiu; Patricio Manque; Donna Akiyoshi; Aaron J. Mackey; William R. Pearson; Paul H. [...]

Published
2004
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