Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent

Smýkal, Petr; Kalendar, Ruslan; Ford, Rebecca; Macas, Jiří; Griga, Miroslav

doi:10.1038/hdy.2009.45

Cited by 55 publications

(47 citation statements)

References 48 publications

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“…The phylogenetic conservation of CvA among the family Trochidae, in addition to the distantly related Bivalvia (Gaffney et al, 2003), confirms that CvA is an ancient molluscan TE. Furthermore, the establishment of the close association between this MITE and DNA families in G. cineraria observed in this study supports the idea that CvA is a dispersal agent for microsatellites, through hitchhiking within TEs during transposition (Coates et al, 2009;Smý kal et al, 2009). These processes can also explain the formation and account for the abundance of multilocus DNA families in G. cineraria.…”

Section: Te Abundance and Microsatellite Proliferationsupporting

confidence: 64%

“…One suggestion is that TEs that carry microsatellite repeated regions may have behaved as microsatelliteinducing elements in the host genomes of the plants pea and barley and some insects (Ramsay et al, 1999;Wilder and Hollocher, 2001;Coates et al, 2009;Smý kal et al, 2009). Likewise, Gaffney et al (2003) proposed that CvA may be an ancient TE that has behaved as a source of satellite DNA in distantly related bivalves.…”

Section: Te Abundance and Microsatellite Proliferationmentioning

confidence: 99%

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Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

et al. 2010

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Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2 kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of these were novel, and could be grouped into DNA families based upon sequence similarities. Significant inter-specific variation in abundance of cryptic repetitive DNA and DNA families was observed. Repbase scans show that a large proportion of cryptic repetitive DNA was identified as transposable elements (TEs). We argue that a large number of TEs and their transpositional activity may be linked to differential rates of DNA multiplication and recombination. This is likely to be an important factor explaining inter-specific variation in genome stability and hence microsatellite marker development success rates. Gastropods also differed significantly in the type of TEs classes (autonomous vs non-autonomous) observed. We propose that dissimilar transpositional mechanisms differentiate the TE classes in terms of their propensity for transposition, fixation and/or silencing. Consequently, the phylogenetic conservation of non-autonomous TEs, such as CvA, suggests that dispersal of these elements may have behaved as microsatelliteinducing elements. Results seem to indicate that, compared to autonomous, non-autonomous TEs maybe have a more active role in genome rearrangement processes. The implications of the findings for genomic rearrangement, stability and marker development are discussed.

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Section: Te Abundance and Microsatellite Proliferationsupporting

confidence: 64%

Section: Te Abundance and Microsatellite Proliferationmentioning

confidence: 99%

Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

et al. 2010

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“…DNA sequence showed 90-91% homology to the DNA sequence from clone JICPSV-598E15, complete sequence of P. sativum. In addition, this DNA sequence was also similar to DNA sequence of BARE-1 gene in barley and RIRE-1 gene in rice (Smykal, 2009). BARE-1 gene in barley was resistant gene to powdery mildew caused by E. graminis f. sp.…”

Section: Dna Sequence Analysismentioning

confidence: 61%

Study of Powdery Mildew Resistance in seven Lines of Snow Pea, Pisumsativum

Chompupoung¹,

Kumphai²,

Sittigul³

et al. 2012

JAS

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Snow pea is one of the important crops grown on highland of Thailand. However, it is very susceptible to powdery mildew. Thus, resistant cultivar increases the production of this crop at a reduced costs. Seven pea lines/cultivars, namely P117, P185, P309, No.3, No.4, No.5 and Fang No.7, were evaluated for phenotypic powdery mildew resistance at Pang Da Royal Agricultural Station, Samoeng district, Chiang Mai during the period of November, 2007 -March, 2008. They were divided into 3 groups: highly resistant group (R) i.e. P117, P185 and P309, moderately resistant group (M) i.e. No.3, No.4 and 5, and susceptible group (S) i.e. Fang No.7. In addition, DNA marker for powdery mildew resistance, er, was tested using PCR technique with 3 primers, ScOPD10, OPU17 and OPO02. It was found that only ScOPD10 could yield an 850-bp marker specific to resistant group. DNA sequencing of this 850 bp marker showed 618-624 bases. The sequence was compared www.ccsenet.org/jas Journal of Agricultural Science Vol. 4, No. 5; 2012 ISSN 1916-9752 E-ISSN 1916 210 with databases in NCBI GenBank. After BLAST searches, the 618-624 base sequences had 90-91% homology to the DNA sequence from clone JICPSV-598E15, complete sequence of P. sativum.

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“…The areas of localization of retrotransposons such as LINE were also found to be frequently involved in recombination and polymorphisms associated for CNV markers [15][16][17][18]. LINE RTE (BovB) and BovB SINE related repeats are most common among dispersed repeats in bovine genome.…”

Section: Introductionmentioning

confidence: 99%

Multi-Locus Genotyping of Cattle Genomes on the Bases of the Region Homology to Retrotransposons

Glazko¹,

Kosovskii²,

Kovalchuk³

et al. 2015

S-h. biol.

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A b s t r a c tIntensification in livestock has led to necessity of developing methods which allows to estimate animal genomic breeding values (GBV). In this, an approach was based on identifying association of animal production traits' variability to polymorphism in different genome elements, from microsatellite loci to millions of single nucleotide polymorphisms (SNPs), in genome-wide sequencing. Despite numerous accumulated data, the development of relatively simple, fast and affordable to interpretation methods of polyloci genotyping (genome scan) for assessing breed «gene pool standard» or genomic selection is still actual. The mobile genetic elements, being high polymorphic genomic sites, can serve as anchors in a multi-locus genotyping. The species-specific retrotransposons such as L1_BT LINE which present in the bovine genome with high frequency and the endogenous retrovirus ENV1_BT are of particular interest. In this regard, the aim of this work was the comparative analysis of polymorphism in genomic DNA fragments flanked by inverted repeats of nucleotide sequences homologous to fragments of these retrotransposons in genomes of specialized dairy Ayrshire and Black and White Holstein breeds and the Kalmyk beef breed. A recombination between L1_BT LINE and ENV1_BT we reported earlier turned out to be conservative in studied breeds. This apparently indicated it to be old in appearance. Since the genetic relationships identified from distribution patterns and length polymorphisms of DNA flanked by ENV1_BT inverted repeats differed significantly between specialized dairy breeds and local meat breed but were low variable within the breeds, this allowed to conclude about its relatively low transposition activity. The PIC values (polymorphic information content) for spectra produced in PCR with the endogenous retrovirus ERV1_BT fragment as a primer ranged from 0.075 to 0.089 for studied breeds. Distribution of inverted repeats homologous to L1_BT was different in character and varied among breeds and within breeds, the PIC values were substantially higher and ranged from 0.062 to 0.260. Thus, the use of multi-locus genotyping of transposable elements is effective for the purposes of animal genetics and breeding but their application depends on transposition activity. Our data showed that the ENV1_BT inverted repeats seem to be convenient marker in genetic differentiation among breeds and revealing «gene pool standard», whereas more transposable L1_BT elements are more relevant in indicating individual variability within a breed.Keywords: multi-locus genotyping, retrotransposons, inverted repeats, genomic scanning, breed, cattle.In recent years, a possible inclusion of genomic selection in traditional cattle breeding programs attracts the increasing attention [1][2][3][4]. To identify the genomic targets of artificial selection associated with desirable manifestation of productivity traits in beef and dairy cattle breeds, the genomic maps of single number polymorphisms (SNP) including 705243 such sites distribut...

show abstract

Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent

Cited by 55 publications

References 48 publications

Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

Study of Powdery Mildew Resistance in seven Lines of Snow Pea, Pisumsativum

Multi-Locus Genotyping of Cattle Genomes on the Bases of the Region Homology to Retrotransposons

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