Limits...
Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus.

Gissi C, Pesole G, Cattaneo E, Tartari M - BMC Genomics (2006)

Bottom Line: The C. intestinalis htt transcript exhibits some peculiar features, such as spliced leader trans-splicing in the 98 nt-long 5' untranslated region (UTR), an alternative splicing in the coding region, eight alternative polyadenylation sites, and no similarities of both 5' and 3'UTRs compared to homologs of the cogeneric C. savignyi.On the contrary, the 3'-half of the gene is highly conserved in all chordates at the level of both gene structure and protein sequence.Between the two Ciona species, a fast evolutionary rate and/or an early divergence time is suggested by the absence of significant similarity between UTRs, protein divergence comparable to that observed between mammals and fishes, and different distribution of repetitive elements.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Milano, Italy. carmela.gissi@unimi.it <carmela.gissi@unimi.it>

ABSTRACT

Background: To gain insight into the evolutionary features of the huntingtin (htt) gene in Chordata, we have sequenced and characterized the full-length htt mRNA in the ascidian Ciona intestinalis, a basal chordate emerging as new invertebrate model organism. Moreover, taking advantage of the availability of genomic and EST sequences, the htt gene structure of a number of chordate species, including the cogeneric ascidian Ciona savignyi, and the vertebrates Xenopus and Gallus was reconstructed.

Results: The C. intestinalis htt transcript exhibits some peculiar features, such as spliced leader trans-splicing in the 98 nt-long 5' untranslated region (UTR), an alternative splicing in the coding region, eight alternative polyadenylation sites, and no similarities of both 5' and 3'UTRs compared to homologs of the cogeneric C. savignyi. The predicted protein is 2946 amino acids long, shorter than its vertebrate homologs, and lacks the polyQ and the polyP stretches found in the the N-terminal regions of mammalian homologs. The exon-intron organization of the htt gene is almost identical among vertebrates, and significantly conserved between Ciona and vertebrates, allowing us to hypothesize an ancestral chordate gene consisting of at least 40 coding exons.

Conclusion: During chordate diversification, events of gain/loss, sliding, phase changes, and expansion of introns occurred in both vertebrate and ascidian lineages predominantly in the 5'-half of the htt gene, where there is also evidence of lineage-specific evolutionary dynamics in vertebrates. On the contrary, the 3'-half of the gene is highly conserved in all chordates at the level of both gene structure and protein sequence. Between the two Ciona species, a fast evolutionary rate and/or an early divergence time is suggested by the absence of significant similarity between UTRs, protein divergence comparable to that observed between mammals and fishes, and different distribution of repetitive elements.

Show MeSH

Related in: MedlinePlus

Bayesian phylogenetic tree of huntingtin, reconstructed from protein sequences. Branch lengths are proportional to the number of substitutions per site. Numbers close to the nodes represent Bayesian posterior probabilities.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1636649&req=5

Figure 2: Bayesian phylogenetic tree of huntingtin, reconstructed from protein sequences. Branch lengths are proportional to the number of substitutions per site. Numbers close to the nodes represent Bayesian posterior probabilities.

Mentions: The percentage of amino acid (aa) differences between all pairs of the eleven analysed chordate proteins are reported in Table 2. The sequence divergence between C. intestinalis and C. savignyi is as high as 27.95%, although these species belong to the same genus. This value is surprisingly high, particularly compared to the pairwise aa differences observed among vertebrates. Indeed, the divergence between pufferfishes belonging to the same family of Tetraodontidae (Tetraodon and Fugu) is only 4.97%, and that between mammals of the same order (mouse and rat) is as low as 2.86% (Table 2). On the contrary, the distance observed between the two Ciona species is comparable to that observed between mammals and fishes. The evolutionary tree based on amino acid data confirms the high divergence between the two Ciona species, and suggests the existence of long branches for these species (Figure 2).


Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus.

Gissi C, Pesole G, Cattaneo E, Tartari M - BMC Genomics (2006)

Bayesian phylogenetic tree of huntingtin, reconstructed from protein sequences. Branch lengths are proportional to the number of substitutions per site. Numbers close to the nodes represent Bayesian posterior probabilities.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1636649&req=5

Figure 2: Bayesian phylogenetic tree of huntingtin, reconstructed from protein sequences. Branch lengths are proportional to the number of substitutions per site. Numbers close to the nodes represent Bayesian posterior probabilities.
Mentions: The percentage of amino acid (aa) differences between all pairs of the eleven analysed chordate proteins are reported in Table 2. The sequence divergence between C. intestinalis and C. savignyi is as high as 27.95%, although these species belong to the same genus. This value is surprisingly high, particularly compared to the pairwise aa differences observed among vertebrates. Indeed, the divergence between pufferfishes belonging to the same family of Tetraodontidae (Tetraodon and Fugu) is only 4.97%, and that between mammals of the same order (mouse and rat) is as low as 2.86% (Table 2). On the contrary, the distance observed between the two Ciona species is comparable to that observed between mammals and fishes. The evolutionary tree based on amino acid data confirms the high divergence between the two Ciona species, and suggests the existence of long branches for these species (Figure 2).

Bottom Line: The C. intestinalis htt transcript exhibits some peculiar features, such as spliced leader trans-splicing in the 98 nt-long 5' untranslated region (UTR), an alternative splicing in the coding region, eight alternative polyadenylation sites, and no similarities of both 5' and 3'UTRs compared to homologs of the cogeneric C. savignyi.On the contrary, the 3'-half of the gene is highly conserved in all chordates at the level of both gene structure and protein sequence.Between the two Ciona species, a fast evolutionary rate and/or an early divergence time is suggested by the absence of significant similarity between UTRs, protein divergence comparable to that observed between mammals and fishes, and different distribution of repetitive elements.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Milano, Italy. carmela.gissi@unimi.it <carmela.gissi@unimi.it>

ABSTRACT

Background: To gain insight into the evolutionary features of the huntingtin (htt) gene in Chordata, we have sequenced and characterized the full-length htt mRNA in the ascidian Ciona intestinalis, a basal chordate emerging as new invertebrate model organism. Moreover, taking advantage of the availability of genomic and EST sequences, the htt gene structure of a number of chordate species, including the cogeneric ascidian Ciona savignyi, and the vertebrates Xenopus and Gallus was reconstructed.

Results: The C. intestinalis htt transcript exhibits some peculiar features, such as spliced leader trans-splicing in the 98 nt-long 5' untranslated region (UTR), an alternative splicing in the coding region, eight alternative polyadenylation sites, and no similarities of both 5' and 3'UTRs compared to homologs of the cogeneric C. savignyi. The predicted protein is 2946 amino acids long, shorter than its vertebrate homologs, and lacks the polyQ and the polyP stretches found in the the N-terminal regions of mammalian homologs. The exon-intron organization of the htt gene is almost identical among vertebrates, and significantly conserved between Ciona and vertebrates, allowing us to hypothesize an ancestral chordate gene consisting of at least 40 coding exons.

Conclusion: During chordate diversification, events of gain/loss, sliding, phase changes, and expansion of introns occurred in both vertebrate and ascidian lineages predominantly in the 5'-half of the htt gene, where there is also evidence of lineage-specific evolutionary dynamics in vertebrates. On the contrary, the 3'-half of the gene is highly conserved in all chordates at the level of both gene structure and protein sequence. Between the two Ciona species, a fast evolutionary rate and/or an early divergence time is suggested by the absence of significant similarity between UTRs, protein divergence comparable to that observed between mammals and fishes, and different distribution of repetitive elements.

Show MeSH
Related in: MedlinePlus