Using Bioinpormcotics Methods to Develop EST-SSR Makers from Sheep’s ESTs

Zhang, Wenxiang; ZunBao, Wang; Zhao, Zhangwu; XianCun, Zeng; Wu, Hongbin; Peng, Yu

doi:10.3923/javaa.2010.2759.2762

Cited by 4 publications

(4 citation statements)

References 7 publications

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“…AC/GT was the second most abundant repeat and accounted for 38.40% of dimeric repeats. This dimeric SSR distribution was different than what had been previously found in catfish (Serapion et al, 2004), zebrafish (Zhang et al, 2010), sheep (Zhang et al, 2010), and cattle (Yan et al, 2008). A previous study indicated that the AT/TA repeats in genic and non-genic sequences in vertebrate genomes (including G. gallus) are less common than AC/GT repeats (Toth et al, 2000).…”

Section: Figure 12contrasting

confidence: 81%

Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus)

Bakhtiarizadeh

Arefnejad²,

Ebrahimie

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Many years of domestication and breeding have given rise to the wide range of chicken breeds that exist today; however, an increasing number of local chicken breeds are under threat of extinction. A comprehensive characterization of chicken markers (especially type I markers) is needed to monitor and conserve genetic diversity in this species. The explosion of genomics and functional genomics information in recent years has opened new possibilities for the generation of molecular markers. We analyzed a large number of expressed sequence tags (ESTs) to test the possibility of using EST-derived microsatellite markers for investigating the Gallus gallus genome. Chromosomal locations for the majority of these SSRs were predicted. Of the 31,576 unigenes assembled from the 544,150 redundant EST sequences, 1757 Functional genome analysis for efficient EST-SSRs in chicken SSR markers were discovered on 1544 ESTs, using the SSRLocator software, with an average density of 28.7 kb per SSR. The dimer motifs were the most frequent (46.38%), followed by trimeric (38.58%), tetrameric (10.19%), pentameric (4.5%), and hexameric (<1%) markers. Different from the case for cattle and sheep, AT/TA was the most abundant dimeric repeat, accounting for 41.71% of all dimeric repeats in the chicken ESTs. The EST-SSR distribution was not uniform among the chromosomes; the majority of the EST-SSRs were located on chromosomes GGA2 and GGA10. We found that most of the EST-SSRs are involved in positive regulation of cellular and metabolic processes. This is the first time that EST sequences have been mined to find chicken microsatellites. On average, 3.8% of the G. gallus UniGene sequences could be exploited for development of EST-SSRs, indicating a good source for molecular markers as well as for functional genome analysis.

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Section: Figure 12contrasting

confidence: 81%

Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus)

Bakhtiarizadeh

Arefnejad²,

Ebrahimie

et al. 2012

Genet. Mol. Res.

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“…GT repeats were the most common in dimeric repeats as expected from previous studies on vertebrates (Toth et al, 2000) but in contrast to the other reports for cattle (Yan et al, 2008), sheep (Zhang et al, 2010), and chicken (Bakhtiarizadeh et al, 2012a). This is unlikely to be true in plants that the AT/TA repeats have the highest frequency.…”

Section: Discussioncontrasting

confidence: 58%

Application of Efficient Express Sequence Tags Information for Classification and Functional Study of Simple Sequence Repeats in Cattle Testis Tissue

Manavipour

Ehsani

Masoudi

2020

Trop. Anim. Sci. J.

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Genomic markers play an important role in tracing the flow of genetic causality of observable signals in animals and plants. In farm animals, the participation of male animals in the gene pool of subsequent generations are much higher than female animals and testes are the most important organs of the male reproductive system. This study was conducted to investigate simple sequence repeats (SSR) within the expressed sequence tags (ESTs) in order to classify the Bos taurus testis tissue's genes for their relationship and specificity with related reproductive domains. A total of 48,549 publicly available EST sequences from cattle testis tissue downloaded from GenBank database, out of which, 10,237 sequences that their library made from testis tissue were extracted and specialized as the studied sequences using several searching tools and software. Across these selective sequences, 2,039 contigs, 5,097 singletons, and 153 SSRs were detected. EST-SSRs were subsequently evaluated using GenBank and categorized based on their functions in biological systems of dairy cattle. Investigation of these motifs showed that the identified EST-SSRs can be classified into 48 types that GT in dinucleotides and GCC in trinucleotides had the highest frequency. Annotation and gene ontology analysis revealed a relationship among 54 domains with the observed SSRs. Localization and characterization of such markers can help tracing the production of amino acids coded by identified repeats as shown in this study.

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“…Analysis of SSR densities in the human genome revealed that dinucleotide (AC/GT and AT/AT) and trinucleotide (AAC/GTT, AAT/ATT, AAG/CTT and AGG/CCT) repeats were the most common in humans 32 . AC/GT repeats were also reported to be the most common dinucleotide repeat in other organisms, including fish 35 and sheep 36 . CG-rich SSR motifs are very rare in the transcriptome of the M .…”

Section: Resultsmentioning

confidence: 98%

Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis

Chang

Ee-Uli

et al. 2019

Sci Rep

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Macaca fascicularis , also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild cynomolgus macaque populations in Malaysia has not been thoroughly elucidated. In this study, we developed genic-simple sequence repeat (genic-SSR) markers from an in-house transcriptome dataset generated from the Malaysian cynomolgus macaque via RNA sequencing, and applied these markers on 26 cynomolgus macaque individuals. A collection of 14,751 genic-SSRs were identified, where 13,709 were perfect SSRs. Dinucleotide repeats were the most common repeat motifs with a frequency of 65.05%, followed by trinucleotide repeats (20.55%). Subsequently, we designed 300 pairs of primers based on perfect di- and trinucleotide SSRs, in which 105 SSRs were associated with functional genes. A subset of 30 SSR markers were randomly selected and validated, yielding 19 polymorphic markers with an average polymorphism information content value of 0.431. The development of genic-SSR markers in this study is indeed timely to provide useful markers for functional and population genetic studies of the cynomolgus macaque and other related non-human primate species.

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Using Bioinpormcotics Methods to Develop EST-SSR Makers from Sheep’s ESTs

Cited by 4 publications

References 7 publications

Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus)

Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus)

Application of Efficient Express Sequence Tags Information for Classification and Functional Study of Simple Sequence Repeats in Cattle Testis Tissue

Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis

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