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RESEARCH: Gene Discovery by EST Sequencing in Toxoplasma gondiiReveals Sequences Restricted to the Apicomplexa
- James W. Ajioka,
- John C. Boothroyd,
- Brian P. Brunk,
- Adrian Hehl,
- Ledeana Hillier,
- Ian D. Manger,
- Marco Marra,
- G. Christian Overton,
- David S. Roos,
- Kiew-Lian Wan,
- Robert Waterston,
- and L. David Sibley
Genome Res. January 1, 1998 8: 18-28; doi:10.1101/gr.8.1.18
...Gene Discovery by EST Sequencing in Toxoplasma gondii Reveals Sequences Restricted to the Apicomplexa James W. Ajioka 1 , John C. Boothroyd 2 , Brian P. Brunk 3 , Adrian Hehl 2 , Ledeana Hillier 4 , Ian D. Manger 2 , Marco...
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LETTER: Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization
- King-Hwa Ling,
- Marie-Adele Rajandream,
- Pierre Rivailler,
- Alasdair Ivens,
- Soon-Joo Yap,
- Alda M.B.N. Madeira,
- Karen Mungall,
- Karen Billington,
- Wai-Yan Yee,
- Alan T. Bankier,
- Fionnadh Carroll,
- Alan M. Durham,
- Nicholas Peters,
- Shu-San Loo,
- Mohd Noor Mat Isa,
- Jeniffer Novaes,
- Michael Quail,
- Rozita Rosli,
- Mariana Nor Shamsudin,
- Tiago J.P. Sobreira,
- Adrian R. Tivey,
- Siew-Fun Wai,
- Sarah White,
- Xikun Wu,
- Arnaud Kerhornou,
- Damer Blake,
- Rahmah Mohamed,
- Martin Shirley,
- Arthur Gruber,
- Matthew Berriman,
- Fiona Tomley,
- Paul H. Dear,
- and Kiew-Lian Wan
Genome Res. March 2007 17: 311-319; Published in Advance February 6, 2007, doi:10.1101/gr.5823007
...-segments, and are more abundant in intergenic sequence than within introns or exons. This motif appears so far to be unique to the Apicomplexa. Segmental duplications The chromosome contains many segmental duplications ( Fig. 1 ), mostly within the P-segments and often containing predicted genes. Duplications within...
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REPORT: Gene Survey of the Pathogenic Protozoan Trypanosoma cruzi
- Betina M. Porcel,
- Anh-Nhi Tran,
- Martti Tammi,
- Zoltan Nyarady,
- Maria Rydåker,
- Turan P. Urmenyi,
- Edson Rondinelli,
- Ulf Pettersson,
- Bj̈orn Andersson,
- and Lena Åslund
Genome Res. August 1, 2000 10: 1103-1107; doi:10.1101/gr.10.8.1103
...REFERENCES ↵ Ajioka J.W. , Boothroyd J.C. , Brunk B.P. , Hehl A. , Hillier L. , Manger I.D. , Marra M. , Overton G.C. , Roos D.S. , Wan K.-L. , et al. ( 1998 ) Gene discovery by EST sequencing in Toxoplasma gondii reveals sequences restricted to the Apicomplexa. Genome Res. 8 : 18 – 28 . ↵ Altschul S...
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Letter: The origins of apicomplexan sequence innovation
- James Wasmuth,
- Jennifer Daub,
- José Manuel Peregrín-Alvarez,
- Constance A.M. Finney,
- and John Parkinson
Genome Res. July 2009 19: 1202-1213; Published in Advance April 10, 2009, doi:10.1101/gr.083386.108
...conservation between the Apicomplexa and other taxa, a series of BLAST searches were performed against the following databases (selected tomaximize sequence and taxonomic coverage): COGENT for complete s, UniProt for nonredundant proteins, and PartiGeneDB for partial s. In total, 87,736 apicomplexan sequences...
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Research: A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia
- Sivaranjani Namasivayam,
- Rodrigo P. Baptista,
- Wenyuan Xiao,
- Erica M. Hall,
- Joseph S. Doggett,
- Karin Troell,
- and Jessica C. Kissinger
Genome Res. May 2021 31: 852-865; Published in Advance April 27, 2021, doi:10.1101/gr.266403.120
..., lanes 2–4; Hikosaka et al. 2013).View larger version: In this window In a new window Figure 1. Sequence evidence of fragmented mtDNA and full-length protein-encoding genes. (A, D–F) Each row of colored blocks represents individual, annotated T. gondii (A) mtDNA-specific PCR amplicons; (D) EST reads; (E...
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Resource: Precision environmental health monitoring by longitudinal exposome and multi-omics profiling
- Peng Gao,
- Xiaotao Shen,
- Xinyue Zhang,
- Chao Jiang,
- Sai Zhang,
- Xin Zhou,
- Sophia Miryam Schüssler-Fiorenza Rose,
- and Michael Snyder
Genome Res. June 2022 32: 1199-1214; Published in Advance June 6, 2022, doi:10.1101/gr.276521.121
...classification and abundance were determined using a customized lowest common ancestor (LCA) algorithm (Jiang et al. 2018, 2021). The raw and processed sequencing data used in this study were previously published and deposited to the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) under...
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LETTER: Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates and intron number
- Scott William Roy and
- Daniel L. Hartl
Genome Res. June 2006 16: 750-756; Published in Advance May 15, 2006, doi:10.1101/gr.4845406
...and the valine (encoded by GTA) restored. A BLASTN search of dbEST yielded no hits, thus this conjecture could not be confirmed. Expression level For each species, we determined the number of expressed sequence tags (ESTs) from that species matching each gene from each ortholog pair (Table 2 ). Direct...
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LETTER: Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii
- Asis Khan,
- Ulrike Böhme,
- Krystyna A. Kelly,
- Ellen Adlem,
- Karen Brooks,
- Mark Simmonds,
- Karen Mungall,
- Michael A. Quail,
- Claire Arrowsmith,
- Tracey Chillingworth,
- Carol Churcher,
- David Harris,
- Matthew Collins,
- Nigel Fosker,
- Audrey Fraser,
- Zahra Hance,
- Kay Jagels,
- Sharon Moule,
- Lee Murphy,
- Susan O'Neil,
- Marie-Adele Rajandream,
- David Saunders,
- Kathy Seeger,
- Sally Whitehead,
- Thomas Mayr,
- Xuenan Xuan,
- Junichi Watanabe,
- Yutaka Suzuki,
- Hiroyuki Wakaguri,
- Sumio Sugano,
- Chihiro Sugimoto,
- Ian Paulsen,
- Aaron J. Mackey,
- David S. Roos,
- Neil Hall,
- Matthew Berriman,
- Bart Barrell,
- L. David Sibley,
- and James W. Ajioka
Genome Res. September 2006 16: 1119-1125; Published in Advance August 10, 2006, doi:10.1101/gr.5318106
...linkage disequilibria . Infect. Genet. Evol. 4 : 107 – 114 . Li L. , Brunk B.P. , Kissinger J.C. , Pape D. , Tang K. , Cole R.H. , Martin J. , Wylie T. , Dante M. , Fogarty S.J. , et al. ( 2003 ) Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database...
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REPORT: Sequence and Analysis of Chromosome I of the Amitochondriate Intracellular Parasite Encephalitozoon cuniculi (Microspora)
- Pierre Peyret,
- Michael D. Katinka,
- Simone Duprat,
- Francis Duffieux,
- Valérie Barbe,
- Martin Barbazanges,
- Jean Weissenbach,
- William Saurin,
- and Christian P. Vivarès
Genome Res. February 1, 2001 11: 198-207; doi:10.1101/gr.164301
.... , Overton G.C. , Roos D.S. , Wan , et al. ( 1998 ) Gene discovery by EST sequencing in Toxoplasma gondii reveals sequences restricted to the Apicomplexa. Genome Res. 8 : 18 – 28 . ↵ Beauvais B. , Sarfati C. , Challier S. , Derouin F. ( 1994 ) In vitro model to assess effect of antimicrobial agents...
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LETTER: Data-Mining Approaches Reveal Hidden Families of Proteases in the Genome of Malaria Parasite
- Yimin Wu,
- Xiangyun Wang,
- Xia Liu,
- and Yufeng Wang
Genome Res. April 1, 2003 13: 601-616; doi:10.1101/gr.913403
..., intron loss, and horizontal gene transfer are proposed to be important modes in the evolution of aspartic proteases in the parasite genus Apicomplexa , including P. falciparum ( Jean et al. 2001 ). The proteases encoded by or destined to parasite organelles are of particular interest because organelles...

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