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Herpes Simplex Virus Type 2 free pdf ebook was written by Debra Hoffman on January 02, 2004 consist of 12 page(s). You're reading the first 10 out of 12 pages of this docs, please download or login to readmore.
Vous vous interdisez d'y diffuser des messages dont les propos sont contraires a la loi (lire l'article 4 des CGU) ou dont le contenu reproduirait sans autorisation une oeuvre protegee par la propriete intellectuelle (tels qu'articles de presse, message d'un tiers). For mono-, di- and trinucleotide repeats, the repeat numbers decreased with the increase of re- peats iterations, implicating that the formation ten- dency of SSRs might be from low iterations to high iterations. The high iterations SSRs might have sub- jected to strong selected pressure and survived to perform different functions. The analysis suggested that the repeats formation may be an essential evolu- tionary driving force for the HSV-1 genome, and the results might be helpful for studying the genome structure, repeats genesis and genome evolution of HSV-1.
All these thresholds have made mor e important contribu - tions in the history of exploring the genome repeat se- quences. Microsatellite length might be an important factor in affecting mutation rate in HSV-1 genome. Here, a relatively low threshold is adopted to study the repeat sequences in the HSV-1 genome, and the analysis may provide new insight into roles of repeat sequences in genome origination, organization and evo- lution. The count of SSRs reduces fast with the increase of iterations, and this indicated that it is relatively hard to form repeats with high iterations and long-unit, and these repeats seem to be more instability in HSV-1 genome.
The count of repeats with different iterations in different repeat motifs of the HSV-1 genome. However, tetra-, penta- and hexanucleotide repeats were not seriously analyzed in the paper, on account of the low content, compared to mono-, di- and trinucleotide repeats.
Sequences The HSV-1 genome sequence was selected for analysis of relationship between repeat sequence and molecular evolution in the level of genome-wide. Short Repeats and Genome Evo lutio n The number of repeats with two iterations w as 21,665 in the entire genome, accounting for 68.33% of the total repeats, and they absolutely predominate in the HSV-1 genome (Table 2).
The genome se- quence with FASTA format was downloaded from the NCBI, and its accession number is NC_001806.1. Addi- tionally, ten genes were randomly selected from the HSV-1 genome in order to make a survey whether the repeats distributed evenly among different fragments. The two iterations repeats should be subjected to weaker selective pressure in the HSV-1 evolutionary process. High per- centage of two times repeats suggested that two times repeats may be the basis of forming repeats with high iterations in the HSV-1 genome. Repeats Extraction A program called IMEx (imperfect microsatellite extrac- tor) was selected, which can be used to extract perfect microsatellites [14].
The genome of HSV-1 is prone to form shorter repeat sequences, and these re- peats may provide a molecular bias for fast adapting to environmental change in the HSV-1 genome. All thresholds of repeat iterations were set to 2 for mono-, di-, tri-, tetra-, penta- and hex- anucleotide repeats in this paper.

All repeat motifs in the sequence that selected randomly from HVS-1 genome were painted in different c olor d epe ndi n g on d i fferent it er at ion s. Long Repeats of Low Frequency The exceptions were that there were only two pentanu- cleotide repeats found with six iterations and one hexa- nucleotide repeat with more than 12 iterations. The ob- servation of low frequency of longer, complicated re- peats possibly result from those repeat sequences are faced with stronger selection pressure than short simple repeats. Percentage of repetitive sequences in the entire ge- nome and ten randomly selected genes of HSV-1. In the long evolutionary history, the occurrence of long repeat sequences may be lost resulting from harmful or lethal to genome, this may make the genome unable to observe growing longer very quickly. Therefore, considerable parts of the short repeats (approximately 96%) were neglected in previous studies (Ta b l e 2 ).
The repeat con- tent is the highest in gene RS1 and the lowest in UL9 gene; it varies from 60% to 70% among the ten genes selected randomly from the HSV-1 genome. The remains of long repeat sequences may be benefit to the genomes and have sur- vived from selection pressure to maintain different re- ported functions [6].
These num- bers showed that the percentages of repeats were quite high in both genome and genes of HSV-1, and the re- peats were widespread in fragments of the genome with little preference. Obviously, simple repeats are the main components of the genome and they may play important roles in HSV-1. This mechanism may explain the observation of the mi- crosatellite polymorphisms deriving mainly from vari- ability in length rather than in the primary sequence [24] and an experimental variant of citrus exocortis viroid (CEVd) expanding its genome with a 96 nucleotide re- peat sequences [25].
The significantly high content of repeat sequences in the genome indicated that the occurrence of repeats is not random but an essential feature. This is possibly an evidence for the repeat prone mechanism with relation to genome ex- panding. Therefore, there may be a mechanism existed to make the genome prone to keep repeat sequences in the process of replication.
In the long evolutionary history of the HSV-1 genome, the occur- rence repeats should be ever more or less than 66.12%, but maybe it holds at this level to f ace selection pressure and adapt to the environment.
SSRs were distributed relatively equally throughout the genome and presented a mosaic-shaped; and repeats were quite high in both genome and genes of HSV-1. RESULTS AND DISCUSSION When detecting a sequence for microsatellite, definition of the minimum number of repeat iterations is an impor- tant empirical criterion. The Variation Trend of Repeats The two iterations repeats were found to be the most abundant accounting for 68.33% of the total repeats (Ta- ble 2). Simple repeats are the main components of the genome and they may play important roles in HSV-1.
In most previous studies, the minimum number of iterations were set to 6, 3, 3, 3, 3 and 3 for mono-, di-, tri, tetra-, penta- and hexanucleo- tide repeats respectively [15,16], or a repeat spanned a minimum of 12 nt [6,9,17] or longer [11]. In detail, the main elements of SSRs with two iterations include about 62.67% of mononucleotide, and more than 90% of di-, tri-, tetra-, penta-, and hexanuc- leotide repeats, respectively. HSV-1 genome tends to form a lot of two iterations re-peats, which may be the basis of forming high repetitive sequences, and it also tends to form more simple repeats than complicated repeats in the genome. Theoretically, however, as long as the iteration is more than once, the motif should be called a repeat sequence.

Formation of repeat may be essential for evolution of HSV-1 genome, and the results might be helpful for studying the genome structure, repeats genesis and evolution of HSV-1. Whata€™s more important, the formation of repeats with high iterations isna€™t only one step in evolution. In addition, the mononucleotide repeats make up 80.56% of the total repeats, and repeat numbers also found to decrease with the increase of length of repeat unit.
Therefore, many shorter repeats were neglected and a large number of useful in- formation were not excavated in their studies. These data clearly showed that the HSV-1 genome tends to form a lot of two iterations repeats, which may be the basis of forming high repetitive sequences, and it also tends to form more simple repeats than complicated re- peats in the genome.
ACKNO WLEDGEMENTS This work was supported by the Special project for biodiversity 2012, 2013 of the Chinese ministry of environ mental protection and Ministry of Science and Technology torch plan [12C26214304703]. Here, set- ting the threshold value of all kinds of repeat iterations to 2, the results suggested that it significantly increased the amount of simple repeats, and the results also have more significance of evolution.
From Table 2, we can also summarized that mono- nucleotide repeats seldom exceeded 10 bp in length, and di-, tri-, and tetranucleotide repeats rarely exceeded 12 bp, penta- and hexanucleotide repeats scarcely ever ex- ceeded 20 bp. Expansions of slippage replication trend to get long of the SSRs, on the contrary, point mutations lead to shorten the long SSRs. Repeat Content in Panoramic Scope In order to give a snapshot of various repeats in the entire genome, a fragment was randomly selected from the HSV-1 genome, in which repeats were painted in differ- ent color depending on difference of iterations (Figure 1). One opinion thought that microsatellite repeat length is an equilibrium results from a balance between length and point mutations [21,22].
The figure showed that SSRs were distributed relatively equally throughout the genome and presented a mosaic- shaped.
Moreover, the longer SSRs (such as pentanuc- leotide, hexanucleotide repeatsa€¦) are more abundant in short and long terminal repeats (TRL and TRS), com- pared with unique long (UL) and unique short regions (US) (data not shown).
The observations are consistent with many previous studies about microsatellites, where they demonstrated that the SSRs distribution is not ran- dom in the genome. Previously, many reports have revealed that a large number of SSRs are located in transcribed regions of genomes, including expressed sequence tags (ESTs) and protein-coding genes [18]. For example, it has been found that: 10% of identified SSRs in primate [9], 15% in rabbit [19] located in the open reading frames (ORFs) or protein-coding genes.
In protein-coding regions of all known proteins, 14% proved to contain repeated se- quences, with a three times higher abundance of repeats in eukaryotes as in prokaryotes [20].
However, w e found 31,705 repetitive sequences in the HSV-1 genome under the criterion of setting the minimum number of iterations to 2 for mono- ~hexanucleotide repeats (Table 1, Sup- plementary Table 1). The 31,705 repeat tracts are 100,674 bp in nucleotide length covering 66.12% of the full genome (Table 1, Supplementary Table 2).

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