@article {14098,
	title = {Sequence diversity and evolution of multigene families in Trypanosoma cruzi},
	journal = {Molecular and Biochemical Parasitology},
	volume = {157},
	year = {2008},
	month = {2008/01//},
	pages = {65 - 72},
	abstract = {Several copies of genes belonging to three multigene families present in the genome of Trypanosoma cruzi were sequenced and comparatively analyzed across six different strains of the parasite belonging to the T. cruzi I lineage (Colombiana, Silvio X10 and Dm28c), the T. cruzi II lineage (Esmeraldo and JG) and a hybrid strain (CL Brener). For all three gene families analyzed, our results support the division in T. cruzi I and II lineages. Furthermore, in agreement with its hybrid nature, sequences derived from the CL Brener clone clustered together with T. cruzi II sequences as well as with a third group of sequences. Paralogous sequences encoding Amastin, an amastigote surface glycoprotein and TcAG48, an antigenic RNA binding protein, which are clustered in the parasite genome, present higher intragenomic variability in T. cruzi II and CL Brener strains, when compared to T. cruzi I strains. Paralogous sequences derived from the TcADC gene family, which encode various isoforms of adenylyl cyclases and are dispersed throughout the T. cruzi genome, exhibit similar degree of variability in all strains, except in the CL Brener strain, in which the sequences were more divergent. Several factors including mutation rates and gene conversion mechanisms, acting differently within the T. cruzi population, may contribute to create such distinct levels of sequence diversity in multigene families that are clustered in the T. cruzi genome.},
	keywords = {Amastin, Gene conversion, Genetic diversity, Multigene families, Trypanosoma cruzi},
	isbn = {0166-6851},
	doi = {16/j.molbiopara.2007.10.002},
	url = {http://www.sciencedirect.com/science/article/pii/S0166685107002769},
	author = {Cerqueira,Gustavo C. and Bartholomeu,Daniella C. and DaRocha,Wanderson D. and Hou,Lihua and Freitas-Silva,Danielle M. and Machado,Carlos Renato and El-Sayed, Najib M. and Teixeira,Santuza M.R.}
}
@article {14068,
	title = {Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements},
	journal = {Molecular and Biochemical Parasitology},
	volume = {145},
	year = {2006},
	month = {2006/02//},
	pages = {158 - 170},
	abstract = {The ingi and L1Tc non-LTR retrotransposons - which constitute the ingi clade - are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5{\textquoteright}-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.},
	keywords = {Degenerate retroelement, Evolution, Ingi, L1Tc, Leishmania major, Non-LTR retrotransposon, Retroposon, Trypanosoma brucei, Trypanosoma cruzi},
	isbn = {0166-6851},
	doi = {16/j.molbiopara.2005.09.017},
	url = {http://www.sciencedirect.com/science/article/pii/S0166685105002963},
	author = {Bringaud,Fr{\'e}d{\'e}ric and Ghedin,Elodie and Blandin,Ga{\"e}lle and Bartholomeu,Daniella C. and Caler,Elisabet and Levin,Mariano J. and Baltz,Th{\'e}o and El-Sayed, Najib M.}
}
@article {14091,
	title = {Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi},
	journal = {Molecular and Biochemical Parasitology},
	volume = {124},
	year = {2002},
	month = {2002/09/10/},
	pages = {73 - 78},
	abstract = {As observed for most eukaryotic cells, trypanosomatids contains non-LTR retrotransposons randomly inserted in the nuclear genome. Autonomous retroelements which, code for their own transposition, have been characterized in Trypanosoma brucei (ingi) and Trypanosoma cruzi (L1Tc), whereas non-autonomous retroelements have only been characterized in T. brucei (RIME). Here, we have characterized in the genome of Trypanosoma cruzi four complete copies of a non-autonomous non-LTR retrotransposon, called NARTc. This 0.26 kb NARTc element has the characteristics of non-LTR retrotransposons: the presence a poly(dA) tail and of a short flanking duplicated motif. Analysis of the Genome Survey Sequence databases indicated that the Trypanosoma cruzi haploid genome contains about 140 NARTc copies and about twice as many L1Tc copies. Interestingly, the NARTc and L1Tc retroelements share, with the Trypanosoma brucei ingi and RIME retrotransposons, a common sequence (the first 45 bp with 91\% identity), whereas the remaining sequences are very divergent. This suggests that these four trypanosome non-LTR retrotransposons were derived from the same common ancester and the sequence of their 5{\textquoteright}-extremity may have a functional role. In addition, the genome of Leishmania major contains the same conserved motif present in the trypanosome retroelements, whicle no transposable elements have been detected so far in Leishmania sp.},
	keywords = {Ingi, L1Tc, Non-LTR retrotransposon, RIME, Trypanosoma brucei, Trypanosoma cruzi},
	isbn = {0166-6851},
	doi = {16/S0166-6851(02)00167-6},
	url = {http://www.sciencedirect.com/science/article/pii/S0166685102001676},
	author = {Bringaud,Fr{\'e}d{\'e}ric and Garc{\'\i}a-P{\'e}rez,Jos{\'e} Luis and Heras,Sara R. and Ghedin,Elodie and El-Sayed, Najib M. and Andersson,Bj{\"o}rn and Baltz,Th{\'e}o and Lopez,Manuel C.}
}
