Abstract:A novel Toxoplasma gondii interspersed repeat element (TgIRE), present in most of the tachyzoite chromosomes, was characterised. Two regions on the TgIRE sequence showed high identity to two different T. gondii expressed sequence tag cDNAs of unknown function, which seems to be TgIRE pseudogenes. Two set of primers were designed, 2-2' and 2-3, that amplify products of 1.02 and 0.62 kb, respectively. T. gondii DNA from RH and Me49 strains was amplified with TgIRE 2-2' primers, and the respective 1.02 kb product… Show more
“…Interestingly, TgTARE1 belongs to the satellite DNA Sat350/Sat680 family already described to be near Toxoplasma telomeres by Bal31 digestion [37], and also detected in Neospora caninum [38]. Another Toxoplasma element already described to be present at the end of several chromosomes is TgIRE [12, 39]. This element was found to be part of every TgTASL, located contiguous to the TgTARE3 in Fragment C (Figure 2B, Additional file 3A).Figure 2
Internal structure of Telomeric-associated sequences in
Toxoplasma
.…”
BackgroundChromosome ends are composed of telomeric repeats and subtelomeric regions, which are patchworks of genes interspersed with repeated elements. Although chromosome ends display similar arrangements in different species, their sequences are highly divergent. In addition, these regions display a particular nucleosomal composition and bind specific factors, therefore producing a special kind of heterochromatin. Using data from currently available draft genomes we have characterized these putative Telomeric Associated Sequences in Toxoplasma gondii.ResultsAn all-vs-all pairwise comparison of T. gondii assembled chromosomes revealed the presence of conserved regions of ∼ 30 Kb located near the ends of 9 of the 14 chromosomes of the genome of the ME49 strain. Sequence similarity among these regions is ∼ 70%, and they are also highly conserved in the GT1 and VEG strains. However, they are unique to Toxoplasma with no detectable similarity in other Apicomplexan parasites. The internal structure of these sequences consists of 3 repetitive regions separated by high-complexity sequences without annotated genes, except for a gene from the Toxoplasma Specific Family. ChIP-qPCR experiments showed that nucleosomes associated to these sequences are enriched in histone H4 monomethylated at K20 (H4K20me1), and the histone variant H2A.X, suggesting that they are silenced sequences (heterochromatin). A detailed characterization of the base composition of these sequences, led us to identify a strong long-range compositional bias, which was similar to that observed in other genomic silenced fragments such as those containing centromeric sequences, and was negatively correlated to gene density.ConclusionsWe identified and characterized a region present in most Toxoplasma assembled chromosomes. Based on their location, sequence features, and nucleosomal markers we propose that these might be part of subtelomeric regions of T. gondii. The identified regions display a unique trinucleotide compositional bias, which is shared (despite the lack of any detectable sequence similarity) with other silenced sequences, such as those making up the chromosome centromeres. We also identified other genomic regions with this compositional bias (but no detectable sequence similarity) that might be functionally similar.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-21) contains supplementary material, which is available to authorized users.
“…Interestingly, TgTARE1 belongs to the satellite DNA Sat350/Sat680 family already described to be near Toxoplasma telomeres by Bal31 digestion [37], and also detected in Neospora caninum [38]. Another Toxoplasma element already described to be present at the end of several chromosomes is TgIRE [12, 39]. This element was found to be part of every TgTASL, located contiguous to the TgTARE3 in Fragment C (Figure 2B, Additional file 3A).Figure 2
Internal structure of Telomeric-associated sequences in
Toxoplasma
.…”
BackgroundChromosome ends are composed of telomeric repeats and subtelomeric regions, which are patchworks of genes interspersed with repeated elements. Although chromosome ends display similar arrangements in different species, their sequences are highly divergent. In addition, these regions display a particular nucleosomal composition and bind specific factors, therefore producing a special kind of heterochromatin. Using data from currently available draft genomes we have characterized these putative Telomeric Associated Sequences in Toxoplasma gondii.ResultsAn all-vs-all pairwise comparison of T. gondii assembled chromosomes revealed the presence of conserved regions of ∼ 30 Kb located near the ends of 9 of the 14 chromosomes of the genome of the ME49 strain. Sequence similarity among these regions is ∼ 70%, and they are also highly conserved in the GT1 and VEG strains. However, they are unique to Toxoplasma with no detectable similarity in other Apicomplexan parasites. The internal structure of these sequences consists of 3 repetitive regions separated by high-complexity sequences without annotated genes, except for a gene from the Toxoplasma Specific Family. ChIP-qPCR experiments showed that nucleosomes associated to these sequences are enriched in histone H4 monomethylated at K20 (H4K20me1), and the histone variant H2A.X, suggesting that they are silenced sequences (heterochromatin). A detailed characterization of the base composition of these sequences, led us to identify a strong long-range compositional bias, which was similar to that observed in other genomic silenced fragments such as those containing centromeric sequences, and was negatively correlated to gene density.ConclusionsWe identified and characterized a region present in most Toxoplasma assembled chromosomes. Based on their location, sequence features, and nucleosomal markers we propose that these might be part of subtelomeric regions of T. gondii. The identified regions display a unique trinucleotide compositional bias, which is shared (despite the lack of any detectable sequence similarity) with other silenced sequences, such as those making up the chromosome centromeres. We also identified other genomic regions with this compositional bias (but no detectable sequence similarity) that might be functionally similar.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-21) contains supplementary material, which is available to authorized users.
“…Regardless, similar to tandem gene arrays discussed in Figure 6, it appears that even noncoding repeats like the B1 gene and the 529-bp repeat can also change in number irrespective of whether there is sexual recombination. Although the 529-bp repeat and B1 gene are found in a single locus, other tandem repeats like TgIRE and SAT350 are found across multiple subtelomeric genomic locations (Echeverria et al 2000;Clemente et al 2004). We mapped these sequences across the genome in all of our sequenced T. gondii strains and again found different results depending on the queried locus.…”
Section: Long-read Assembly Adds New Sequences To the T Gondii Reference Genomementioning
in the protist pathogen Toxoplasma gondii and related tissue coccidia A novel fragmented mitochondrial genome Genome Res. May , 2021 31: 823-833 Luisa Berná, Pablo Marquez, Andrés Cabrera, et al. rearrangements reveals misassembly, karyotype differences, and chromosomal Reevaluation of the Toxoplasma gondii and Neospora caninum genomes P
A family of repetitive DNA elements of approximately 350 bp-Sat350-that are members of Toxoplasma gondii satellite DNA was further analyzed. Sequence analysis identified at least three distinct repeat types within this family, called types A, B, and C. B repeats were divided into the subtypes B1 and B2. A search for internal repetitions within this family permitted the identification of conserved regions and the design of PCR primers that amplify almost all these repetitive elements. These primers amplified the expected 350-bp repeats and a novel 680-bp repetitive element (Sat680) related to this family. Two additional tandemly repeated high-order structures corresponding to this satellite DNA family were found by searching the Toxoplasma genome database with these sequences. These studies were confirmed by sequence analysis and identified: (1). an arrangement of AB1CB2 350-bp repeats and (2). an arrangement of two 350-bp-like repeats, resulting in a 680-bp monomer. Sequence comparison and phylogenetic analysis indicated that both high-order structures may have originated from the same ancestral 350-bp repeat. PCR amplification, sequence analysis and Southern blot showed that similar high-order structures were also found in the Toxoplasma-sister taxon Neospora caninum. The Toxoplasma genome database (http://ToxoDB.org ) permitted the assembly of a contig harboring Sat350 elements at one end and a long nonrepetitive DNA sequence flanking this satellite DNA. The region bordering the Sat350 repeats contained two differentially expressed sequence-related regions and interstitial telomeric sequences.
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