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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...sexual recombination, and indicates that aneuploidy is a relevant process in Leishmania’s survival and evolution. Chromosomal duplications were also shown to directly impact gene expression, in which chromosomes with extra copies were highly expressed compared with disomic counterparts, with the sole...
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Research: Clonal copy-number mosaicism in autoreactive T lymphocytes in diabetic NOD mice
- Maha Alriyami,
- Luc Marchand,
- Quan Li,
- Xiaoyu Du,
- Martin Olivier,
- and Constantin Polychronakos
Genome Res. December 2019 29: 1951-1961; Published in Advance November 6, 2019, doi:10.1101/gr.247882.118
...23 shows doubling of the peak in T cells.T cells involved in host defense have smaller copy number changesAs a normal host-defense control, we tested DNA from memory CD4+ T cells from the popliteal lymph nodes of 10 NOD mice (eight females and two males; 9–14 wk) infected with Leishmania major (L...
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Resource: Copy number variation of individual cattle genomes using next-generation sequencing
- Derek M. Bickhart,
- Yali Hou,
- Steven G. Schroeder,
- Can Alkan,
- Maria Francesca Cardone,
- Lakshmi K. Matukumalli,
- Jiuzhou Song,
- Robert D. Schnabel,
- Mario Ventura,
- Jeremy F. Taylor,
- Jose Fernando Garcia,
- Curtis P. Van Tassell,
- Tad S. Sonstegard,
- Evan E. Eichler,
- and George E. Liu
Genome Res. April 2012 22: 778-790; Published in Advance February 2, 2012, doi:10.1101/gr.133967.111
...et al. 1997). It is possible that reads from the PAR of chrYwere insteadmapped to chrX, thereby inflating RDvalueswithin that region of the chromosome. Copy number polymorphic genes Using the cattle RefSeq gene annotations, we identified copy number polymorphic genes and then assigned a CN estimate...
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Research: Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
- Tim Downing,
- Hideo Imamura,
- Saskia Decuypere,
- Taane G. Clark,
- Graham H. Coombs,
- James A. Cotton,
- James D. Hilley,
- Simonne de Doncker,
- Ilse Maes,
- Jeremy C. Mottram,
- Mike A. Quail,
- Suman Rijal,
- Mandy Sanders,
- Gabriele Schönian,
- Olivia Stark,
- Shyam Sundar,
- Manu Vanaerschot,
- Christiane Hertz-Fowler,
- Jean-Claude Dujardin,
- and Matthew Berriman
Genome Res. December 2011 21: 2143-2156; Published in Advance October 28, 2011, doi:10.1101/gr.123430.111
...population structure as well as selective processes induced by drug treatment. In contrast to the limited SNP variation among the 17 lines, extensive variation in chromosomal copy number was discovered. Aneuploidy is known to arise in Leishmania, but for only a small number of chromosomes and under...
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LETTER: Hemizygous subtelomeres of an African trypanosome chromosome may account for over 75% of chromosome length
- Sergio Callejas,
- Vanessa Leech,
- Christopher Reitter,
- and Sara Melville
Genome Res. September 2006 16: 1109-1118; Published in Advance August 9, 2006, doi:10.1101/gr.5147406
.... 1997 ; Melville et al. 1998 , 1999 , 2000 ). Chromosome size polymorphism is not unique to African trypanosomes: It has been observed in Plasmodium and Leishmania , where size variation of 10%–25% has been reported ( Janse 1993 ; Wincker et al. 1996 ), and in T. cruzi , where twofold variation has been...
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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
...( Bowman et al. 1998 ; Gardner et al. 1998 ) and one from Leishmania major ( Myler et al. 1999 ), and to a large contig from Trypanosoma cruzi ( Andersson et al. 1998 ) and a high throughput EST project in Toxoplasma gondii ( Ajioka et al. 1998 ). The characteristic feature of the chromosome structure of E...
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LETTER: Functional mapping of a trypanosome centromere by chromosome fragmentation identifies a 16-kb GC-rich transcriptional “strand-switch” domain as a major feature
- Samson O. Obado,
- Martin C. Taylor,
- Shane R. Wilkinson,
- Elizabeth V. Bromley,
- and John M. Kelly
Genome Res. January 2005 15: 36-43; doi:10.1101/gr.2895105
...( Nagaki et al. 2004 ). In parasitic protozoa, the nature of centromeres is a major gap in our understanding of chromosome structure and propagation. A putative centromere has been delineated to a 400-kb fragment of chromosome 5 of the trypanosomatid Leishmania ( Tamar and Papadopoulou 2001...
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ARTICLE: The Small Chromosomes of Trypanosoma brucei Involved in Antigenic Variation Are Constructed Around Repetitive Palindromes
- Bill Wickstead,
- Klaus Ersfeld,
- and Keith Gull
Genome Res. June 2004 14: 1014-1024; doi:10.1101/gr.2227704
.... In Leishmania , targeted deletions of a stable linear extrachromosome have implicated an ∼30-kb region in mitotic stability ( Dubessay et al. 2001 ). The reduced size and complexity of MCs compared with MBCs represents a considerable advantage in the search for elements involved in chromosome stability. Weiden...
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LETTER: A Random Sequencing Approach for the Analysis of the Trypanosoma cruzi Genome: General Structure, Large Gene and Repetitive DNA Families, and Gene Discovery
- Fernán Agüero,
- Ramiro E. Verdún,
- Alberto Carlos C. Frasch,
- and Daniel O. Sánchez
Genome Res. December 1, 2000 10: 1996-2005; Published in Advance November 21, 2000, doi:10.1101/gr.146300
...distribution of protein-coding genes. Proc. Natl. Acad. Sci. 96 : 2902 – 2906 . ↵ Network T.L.G. ( 1998 ) The complete chromosomal organization of the reference strain of the Leishmania project, L. major Friedlin. Parasitol. Today 14 : 301 – 303 . ↵ Nilsen T.W. ( 1995 ) Trans-splicing: An update. Mol. Biochem...
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Letter: Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences
- Elmar Schilling,
- Carol El Chartouni,
- and Michael Rehli
Genome Res. November 2009 19: 2028-2035; Published in Advance August 17, 2009, doi:10.1101/gr.095562.109
...hypermethylation inmyeloid leukemia.Cancer Res 66: 6118–6128. Gessner A, Blum H, Ro¨llinghoff M. 1993. Differential regulation of IL-9expression after infection with Leishmania major in susceptible and resistant mice. Immunobiology 189: 419–435. Heijmans BT, Kremer D, Tobi EW, Boomsma DI, Slagboom PE. 2007...

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