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1.  Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software 
BMC Genomics  2014;15(1):1045.
Background
RNA-seq studies have an important role for both large-scale analysis of gene expression and for transcriptome reconstruction. However, the lack of software specifically developed for the analysis of the transcriptome structure in lower eukaryotes, has so far limited the comparative studies among different species and strains.
Results
In order to fill this gap, an innovative software called ORA (Overlapped Reads Assembler) was developed. This software allows a simple and reliable analysis of the transcriptome structure in organisms with a low number of introns. It can also determine the size and the position of the untranslated regions (UTR) and of polycistronic transcripts. As a case study, we analyzed the transcriptional landscape of six S. cerevisiae strains in two different key steps of the fermentation process. This comparative analysis revealed differences in the UTR regions of transcripts. By extending the transcriptome analysis to yeast species belonging to the Saccharomyces genus, it was possible to examine the conservation level of unknown non-coding RNAs and their putative functional role.
Conclusions
By comparing the results obtained using ORA with previous studies and with the transcriptome structure determined with other software, it was proven that ORA has a remarkable reliability. The results obtained from the training set made it possible to detect the presence of transcripts with variable UTRs between S. cerevisiae strains. Finally, we propose a regulatory role for some non-coding transcripts conserved within the Saccharomyces genus and localized in the antisense strand to genes involved in meiosis and cell wall biosynthesis.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-1045) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-1045
PMCID: PMC4302112  PMID: 25441755
Saccharomyces cerevisiae; Saccharomyces sensu-stricto; Transcriptome assembly software; Transcriptome variability; UTR; Non-coding RNA; Cell wall; Reproductive process in single-celled organism
2.  Whole-Genome Sequence of Streptococcus macedonicus Strain 33MO, Isolated from Curd of Morlacco Cheese in the Veneto Region (Italy) 
Genome Announcements  2014;2(4):e00746-14.
A genetic characterization of Streptococcus macedonicus is important to better understand the characteristics of this lactic acid bacterium, frequently detected in fermented food bacteria communities. This report presents the draft genome sequence description of strain 33MO, the first publicly available genome sequence of an Italian S. macedonicus isolate.
doi:10.1128/genomeA.00746-14
PMCID: PMC4125769  PMID: 25103758
3.  Genome Sequences of Four Italian Streptococcus thermophilus Strains of Dairy Origin 
Genome Announcements  2014;2(2):e00126-14.
This report describes the genome sequences of four Streptococcus thermophilus strains, namely, TH982, TH985, TH1477, and 1F8CT, isolated from different dairy environments from the Campania and the Veneto regions in Italy. These data are aimed at increasing the genomic information available on this species, which is of paramount importance for the dairy industry.
doi:10.1128/genomeA.00126-14
PMCID: PMC3953188  PMID: 24625867
4.  Genome Sequence of Lactobacillus fabifermentans Strain T30PCM01, Isolated from Fermenting Grape Marc 
Genome Announcements  2014;2(1):e00060-14.
Here, we report the draft genome assembly of Lactobacillus fabifermentans strain T30PCM01 isolated from grape marc. Its genome is the largest (3.58 Mbp) among Lactobacillus species and reveals an enormous potential for carbohydrate utilization and transcriptional regulation.
doi:10.1128/genomeA.00060-14
PMCID: PMC3931359  PMID: 24558238
5.  Genome Sequences of Streptococcus thermophilus Strains MTH17CL396 and M17PTZA496 from Fontina, an Italian PDO Cheese 
Genome Announcements  2014;2(1):e00067-14.
Here is presented the whole-genome sequences of Streptococcus thermophilus strains MTH17CL396 and M17PTZA496, isolated from fontina protected designation of origin (PDO) cheese in the Valle d’Aosta Region (Italy). S. thermophilus is a lactic acid bacterium widely present in dairy products, and these are the first publicly available genome sequences of S. thermophilus strains isolated from cheese.
doi:10.1128/genomeA.00067-14
PMCID: PMC3924375  PMID: 24526643
6.  Whole-Genome Sequences of Streptococcus thermophilus Strains TH1435 and TH1436, Isolated from Raw Goat Milk 
Genome Announcements  2014;2(1):e01129-13.
We report the genome sequences of two Streptococcus thermophilus strains, TH1435 and TH1436, isolated from raw goat milk devoted to the production of artisanal cheese in the Friuli-Venezia Giulia region in Italy. The genome sequences of these two quickly acidifying strains are the first available genome sequences of S. thermophilus strains isolated in Italy.
doi:10.1128/genomeA.01129-13
PMCID: PMC3894273  PMID: 24435859
7.  Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates 
Background
Abyssal microorganisms have evolved particular features that enable them to grow in their extreme habitat. Genes belonging to specific functional categories are known to be particularly susceptible to high-pressure; therefore, they should show some evidence of positive selection. To verify this hypothesis we computed the amino acid substitution rates between two deep-sea microorganisms, Photobacterium profundum SS9 and Shewanella benthica KT99, and their respective shallow water relatives.
Results
A statistical analysis of all the orthologs, led to the identification of positive selected (PS) genes, which were then used to evaluate adaptation strategies. We were able to establish "Motility" and "Transport" as two classes significantly enriched with PS genes. The prevalence of transporters led us to analyze variable amino acids (PS sites) by mapping them according to their membrane topology, the results showed a higher frequency of substitutions in the extra-cellular compartment. A similar analysis was performed on soluble proteins, mapping the PS sites on the 3D structure, revealing a prevalence of substitutions on the protein surface. Finally, the presence of some flagellar proteins in the Vibrionaceae PS list confirms the importance of bacterial motility as a SS9 specific adaptation strategy.
Conclusion
The approach presented in this paper is suitable for identifying molecular adaptations to particular environmental conditions. The statistical method takes into account differences in the ratio between non-synonymous to synonymous substitutions, thus allowing the detection of the genes that underwent positive selection. We found that positive selection in deep-sea adapted bacteria targets a wide range of functions, for example solute transport, protein translocation, DNA synthesis and motility. From these data clearly emerges an involvement of the transport and metabolism processes in the deep-sea adaptation strategy of both bathytypes considered, whereas the adaptation of other biological processes seems to be specific to either one or the other. An important role is hypothesized for five PS genes belonging to the transport category that had been previously identified as differentially expressed in microarray experiments. Strikingly, structural mapping of PS sites performed independently on membrane and soluble proteins revealed that residues under positive selection tend to occur in specific protein regions.
doi:10.1186/1471-2148-8-313
PMCID: PMC2600651  PMID: 19014525

Results 1-7 (7)