Abstract
A pseudogene, designated as "ps(5.8S+ITS-2)", paralogous to the 5.8S gene and internal transcribed spacer (ITS)-2 of the nuclear ribosomal DNA (rDNA), has been recently found in many triatomine species distributed throughout North America, Central America and northern South America. Among characteristics used as criteria for pseudogene verification, secondary structures and free energy are highlighted, showing a lower fit between minimum free energy, partition function and centroid structures, although in given cases the fit only appeared to be slightly lower. The unique characteristics of "ps(5.8S+ITS-2)" as a processed or retrotransposed pseudogenic unit of the ghost type are reviewed, with emphasis on its potential functionality compared to the functionality of genes and spacers of the normal rDNA operon. Besides the technical problem of the risk for erroneous sequence results, the usefulness of "ps(5.8S+ITS-2)" for specimen classification, phylogenetic analyses and systematic/taxonomic studies should be highlighted, based on consistence and retention index values, which in pseudogenic sequence trees were higher than in functional sequence trees. Additionally, intraindividual, interpopulational and interspecific differences in pseudogene amount and the fact that it is a pseudogene in the nuclear rDNA suggests a potential relationships with fitness, behaviour and adaptability of triatomine vectors and consequently its potential utility in Chagas disease epidemiology and control.
Highlights
A pseudogene, designated as “ps(5.8S+ITS-2)”, paralogous to the 5.8S gene and internal transcribed spacer (ITS)-2 of the nuclear ribosomal DNA, has been recently found in many triatomine species distributed throughout North America, Central America and northern South America
Pseudogenes are of particular interest to biologists since they can interfere with gene centric studies [such as de novo gene prediction and polymerase chain reaction (PCR) amplification] and to evolutionary biologists because of the possibility to study their age and mutational rates and tendencies (Rouchka & Cha 2009)
This means that the “ps(5.8S+ITS-2)” pseudogene has followed an evolution enabling it to cover a geographical distribution throughout North America, Central America and northern South America [see Carcavallo et al Fig. 2: secondary structure mountain plots of height vs. position for the functional and pseudogenic sequences of the 5.8S gene of representative Triatominae taxa: A: functional conserved gene in Triatomini; B: pseudogenic sequence in Triatoma dimidiata dimidiata from Guatemala; C: pseudogenic sequence in T. dimidiata capitata from Colombia; D: pseudogenic sequence in T. sp. aff. dimidiata sensu (Bargues et al 2008) from Yucatan, Mexico; E: pseudogenic sequence in Triatoma phyllosoma phyllosoma from Mexico; F: pseudogenic sequence in Triatoma sanguisuga from the United States of America
Summary
The coexistence of two different 5.8S+ITS-2 sequences within the same triatomine specimen, one corresponding to the normal functional rdna operon and another paralogous one corresponding to the pseudogenic, was confirmed by (i) double signal in the sequencing chromatograms (Fig. 1), (ii) cloning and subsequent clone sequencing, (iii) different specific primer sequencing for each functional and paralogous sequences and (iv) relative quantification by real-time PCR (Bargues et al 2014). In the 5.8S gene, criteria for pseudogene identification included length variability, lower guaninecytosine content, mutations regarding the functional uniform sequence and relatively high base substitutions in evolutionary conserved sites (Table I). At ITS-2 level, criteria were the shorter sequence and large proportion of insertions and deletions (indels) (Table I) (Bargues et al 2014). DNA secondary structures - The tendency of complementary strands of DNA to form double helices is well known since long time ago. Single stranded nucleic acid sequences contain many complementary regions that have the potential to form double helices when the molecule folds back on itself. The resulting pattern of double helical stretches interspersed with loops is what is called the secondary structure of an RNA or DNA. Tertiary interactions are weaker than secondary structure and, RNA folding is regarded as a hierarchical process in which second-
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