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Research: Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists
- Marcin P. Sajek,
- Danielle Y. Bilodeau,
- Michael A. Beer,
- Emma Horton,
- Yukiko Miyamoto,
- Katrina B. Velle,
- Lars Eckmann,
- Lillian Fritz-Laylin,
- Olivia S. Rissland,
- and Neelanjan Mukherjee
Genome Res. October 2024 34: 1570-1581; Published in Advance September 26, 2024, doi:10.1101/gr.279526.124
..., the poly(A) signal is an AAUAAA hexamer, but we recently found that the deeply branching eukaryote Giardia lamblia uses a distinct hexamer (AGURAA) and lacks any known auxiliary elements. Our discovery prompted us to explore the evolutionary dynamics of poly(A) signals and auxiliary elements...
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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
...eukaryotic species were extracted from the RefSeq database (National Center for Biotechnology Information, NIH) unless another database is specified (Supplemental Table S1). The species used in this study with abbreviations are as follows (also see Supplemental Table S1): Giardia lamblia (Gl), Trypanosoma...
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LETTER: Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion
- Nuno L. Barbosa-Morais,
- Maria Carmo-Fonseca,
- and Samuel Aparício
Genome Res. January 2006 16: 66-77; Published in Advance December 12, 2005, doi:10.1101/gr.3936206
...-celled parasite Giardia lamblia ( Nixon et al. 2002 ) and its close relative Carpendiemona membranifera ( Simpson et al. 2002 ), and a core spliceosomal protein gene ( Prp8 ) is remarkably conserved between metazoans and the deep-branching protist Trichomonas vaginalis ( Fast and Doolittle 1999 ). Our finding...
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Research: Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs
- Adrian A. Valli,
- Bruno A.C.M. Santos,
- Silvia Hnatova,
- Andrew R. Bassett,
- Attila Molnar,
- Betty Y. Chung,
- and David C. Baulcombe
Genome Res. April 2016 26: 519-529; Published in Advance March 11, 2016, doi:10.1101/gr.199703.115
...independently in plant and animal lineages (Axtell et al. 2011). Most information about miRNAs is frommulticellular organisms, although they are also present in unicellular organisms, including the green alga Chlamydomonas reinhardtii (Molnár et al. 2007; Zhao et al. 2007), protozoans Giardia lamblia (Saraiya...
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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
...the Sarcocystidae were multiple instances of the annexin domain (PF00191). The domain has been implicated with a range of functions. In the diplomonad parasite Giardia lamblia, it is thought to regulate cytoskeletal dynamics during cyst transition (Bauer et al. 1999). From the coccidian EST libraries, annexin...
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ARTICLE: Sixty Alleles of the ALS7 Open Reading Frame in Candida albicans: ALS7 Is a Hypermutable Contingency Locus
- Ningxin Zhang,
- Annette L. Harrex,
- Barbara R. Holland,
- Lauren E. Fenton,
- Richard D. Cannon,
- and Jan Schmid
Genome Res. September 2003 13: 2005-2017; doi:10.1101/gr.1024903
...such as Plasmodium, Trypanosoma , and Giardia , such a repertoire of proteins is considered important not only for adhesion but also for evasion of host defenses ( Nash 1997 ; Ramasamy 1998 ; Barry and McCulloch 2001 ). High mutation rates in the genes encoding these proteins are a crucial part of generating...
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ARTICLE: Phylogenetic Analysis of Ribonuclease H Domains Suggests a Late, Chimeric Origin of LTR Retrotransposable Elements and Retroviruses
- Harmit S. Malik and
- Thomas H. Eickbush
Genome Res. July 1, 2001 11: 1187-1197; doi:10.1101/gr.185101
.... Indeed, the diplomonad Giardia lamblia appears to be the outgroup not only to other eukaryotic but also to all retroelement-encoded RNH domains. Is this (acquisition of an RNH domain from an early eukaryote) yet another example of replacement of a preexisting RNH domains, as hypothesized for retroviruses...
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LETTER: Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
- Schraga Schwartz,
- João Silva,
- David Burstein,
- Tal Pupko,
- Eduardo Eyras,
- and Gil Ast
Genome Res. January 2008 18: 88-103; Published in Advance November 21, 2007, doi:10.1101/gr.6818908
...signals at the root of the eukaryotic tree, based on a maximum parsimony reconstruction applied to the 5′ss and the BS. Evolution of the PPT The evolution of the PPT splicing signal and its functional importance in eukaryotes have been poorly addressed by previous studies. By using comparative genomics...
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LETTER: Mystery of Intron Gain
- Alexei Fedorov,
- Scott Roy,
- Larisa Fedorova,
- and Walter Gilbert
Genome Res. October 2003 13: 2236-2241; Published in Advance January 1, 2003, doi:10.1101/gr.1029803
...., Morrison, H.G., McArthur, A.G., Sogin, M.L., Loftus, B.J., and Samuelson, J. 2002 . A spliceosomal intron in Giardia lamblia . Proc. Natl. Acad. Sci. 99 : 3701 -3705. ↵ Ostertag, E.M. and Kazazian, H.H. 2001 . Biology of mammalian L1 retrotransposons. Annu. Rev. Genet. 35 : 501 -538. ↵ Palmer, J...
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LETTER: The Largest Subunit of Human RNA Polymerase III Is Closely Related to the Largest Subunit of Yeast and Trypanosome RNA Polymerase III
- Setareh Sepehri and
- Nouria Hernandez
Genome Res. October 1, 1997 7: 1006-1019; doi:10.1101/gr.7.10.1006
...) and Trypanosoma brucei ( Evers et al. 1989 ; Smith et al. 1989b ). In addition, the largest subunit of RNA polymerase III has been cloned from Plasmodium falciparum ( Li et al. 1991 ) and Giardia lamblia ( Lanzendoerfer et al. 1992 ), but unlike the largest subunit of RNA polymerase II, for which the human...

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