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LETTER: Evolution of protein domain promiscuity in eukaryotes
- Malay Kumar Basu,
- Liran Carmel,
- Igor B. Rogozin,
- and Eugene V. Koonin
Genome Res. March 2008 18: 449-461; Published in Advance January 29, 2008, doi:10.1101/gr.6943508
...crucial roles in interaction networks, particularly those that contribute to signal transduction. A systematic comparative-genomic analysis of promiscuous domains in eukaryotes is described. Two quantitative measures of domain promiscuity are introduced and applied to the analysis of 28 genomes of diverse...
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Research: Genomic analysis of the causative agents of coccidiosis in domestic chickens
- Adam J. Reid,
- Damer P. Blake,
- Hifzur R. Ansari,
- Karen Billington,
- Hilary P. Browne,
- Josephine Bryant,
- Matt Dunn,
- Stacy S. Hung,
- Fumiya Kawahara,
- Diego Miranda-Saavedra,
- Tareq B. Malas,
- Tobias Mourier,
- Hardeep Naghra,
- Mridul Nair,
- Thomas D. Otto,
- Neil D. Rawlings,
- Pierre Rivailler,
- Alejandro Sanchez-Flores,
- Mandy Sanders,
- Chandra Subramaniam,
- Yea-Ling Tay,
- Yong Woo,
- Xikun Wu,
- Bart Barrell,
- Paul H. Dear,
- Christian Doerig,
- Arthur Gruber,
- Alasdair C. Ivens,
- John Parkinson,
- Marie-Adèle Rajandream,
- Martin W. Shirley,
- Kiew-Lian Wan,
- Matthew Berriman,
- Fiona M. Tomley,
- and Arnab Pain
Genome Res. October 2014 24: 1676-1685; Published in Advance July 11, 2014, doi:10.1101/gr.168955.113
...). Comparative genomics of the Coccidia and wider Apicomplexa Eight thousand, six hundred and three protein-coding genes are predicted in the E. tenella assembly, significantlymore than the 7286 found in the related coccidian T. gondii (Supplemental Table S1), despite T. gondii having a nuclear that is ;20% (10...
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LETTER: Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database
- Li Li,
- Brian P. Brunk,
- Jessica C. Kissinger,
- Deana Pape,
- Keliang Tang,
- Robert H. Cole,
- John Martin,
- Todd Wylie,
- Mike Dante,
- Steven J. Fogarty,
- Daniel K. Howe,
- Paul Liberator,
- Carmen Diaz,
- Jennifer Anderson,
- Michael White,
- Maria E. Jerome,
- Emily A. Johnson,
- Jay A. Radke,
- Christian J. Stoeckert, Jr.,
- Robert H. Waterston,
- Sandra W. Clifton,
- David S. Roos,
- and L. David Sibley
Genome Res. March 1, 2003 13: 443-454; doi:10.1101/gr.693203
...Maria E Jerome Fogarty DK Howe Daniel K Howe Diaz, C Johnson, E.A Fogarty, S.J Waterston, Robert H White Roos Jennifer Howe Daniel K. Brian Brunk genome;13/3/443 1549-5469 10.1101/gr.693203 1088-9051 Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene...
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LETTER: Three distinct modes of intron dynamics in the evolution of eukaryotes
- Liran Carmel,
- Yuri I. Wolf,
- Igor B. Rogozin,
- and Eugene V. Koonin
Genome Res. July 2007 17: 1034-1044; Published in Advance May 10, 2007, doi:10.1101/gr.6438607
.... Wolf, Y.I Rogozin, IB L Carmel 10.1101/gr.6438607 1088-9051 genome;gr.6438607 Three distinct modes of intron dynamics in the evolution of eukaryotes Three distinct modes of intron dynamics in the evolution of eukaryotes Liran Carmel , Yuri I. Wolf , Igor B. Rogozin , and Eugene V. Koonin 1 National...
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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
..., China, and the United States (n = 72) in the largest comparative genomics study to date. We applied rigorous filters to exclude mixed infections and analyzed a data set from 141 isolates from the zoonotic groups IIa (n = 119) and IId (n = 22). Based on 28,047 high-quality, biallelic genomic SNPs, we...
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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
...Ajioka, James W Marra, Marco Brian Brunk Manger, I 1549-5469 genome;8/1/18 1088-9051 10.1101/gr.8.1.18 Gene Discovery by EST Sequencing in Toxoplasma gondiiReveals Sequences Restricted to the Apicomplexa Gene Discovery by EST Sequencing in Toxoplasma gondii Reveals Sequences Restricted...
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LETTER: Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases
- Marius K. Lemberg and
- Matthew Freeman
Genome Res. November 2007 17: 1634-1646; Published in Advance October 15, 2007, doi:10.1101/gr.6425307
...is low. We have combined BLAST-based database mining with functional and structural data to generate a comprehensive genomic analysis of eukaryotic rhomboid-like proteins. We show that robust membrane topology models are necessary to classify active rhomboid proteases unambiguously, and we define rules...
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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
...across the eukaryotic tree of life, with protists displaying extreme examples. Apicomplexan and dinoflagellate protists have evolved highly reduced mitochondrial sequences, mtDNA, consisting of only three cytochrome genes and fragmented rRNA genes. Here, we report the independent evolution of fragmented...
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Research: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements
- Luisa Berná,
- Pablo Marquez,
- Andrés Cabrera,
- Gonzalo Greif,
- María E. Francia,
- and Carlos Robello
Genome Res. May 2021 31: 823-833; Published in Advance April 27, 2021, doi:10.1101/gr.262832.120
...of synteny, encouraging rethinking the as basis of the comparative unique biology of these pathogens.The Apicomplexa comprise a large phylum of parasitic alveolates of medical and veterinary importance, causing deadly diseases such as malaria, cryptosporidiosis, neosporosis, and toxoplasmosis, among others...
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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
...to specific Apicomplexa orders (Li et al. 2003a; Martens et al. 2008), or even individual species (Brayton et al. 2007). The availability of genomic data sets for 15 species offers an opportunity to build on these initial studies and undertake more systematic analyses to explore genetic diversity within...

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