scholarly journals Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library inPerilla frutescens(L.)

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Eun Soo Seong ◽  
Ji Hye Yoo ◽  
Jae Hoo Choi ◽  
Chang Heum Kim ◽  
Mi Ran Jeon ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Medicinal Plant ◽  
Cdna Library ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Expressed Sequence Tags ◽  
Full Length ◽  
Full Length Cdna ◽  
Expressed Sequence ◽  
Simple Sequence

Perilla frutescensis valuable as a medicinal plant as well as a natural medicine and functional food. However, comparative genomics analyses ofP. frutescensare limited due to a lack of gene annotations and characterization. A full-length cDNA library fromP. frutescensleaves was constructed to identify functional gene clusters and probable EST-SSR markers via analysis of 1,056 expressed sequence tags. Unigene assembly was performed using basic local alignment search tool (BLAST) homology searches and annotated Gene Ontology (GO). A total of 18 simple sequence repeats (SSRs) were designed as primer pairs. This study is the first to report comparative genomics and EST-SSR markers fromP. frutescenswill help gene discovery and provide an important source for functional genomics and molecular genetic research in this interesting medicinal plant.

scholarly journals Generation and Analysis of Expressed Sequence Tags (ESTs) from Muscle Full-Length cDNA Library of Wujin Pig

2014 ◽  
Vol 13 (2) ◽  
pp. 378-386
Author(s):  
Su-mei ZHAO ◽  
Yong-gang LIU ◽  
Hong-bing PAN ◽  
Xi ZHANG ◽  
Chang-rong GE ◽  
...  
Keyword(s):  
Cdna Library ◽  
Expressed Sequence Tags ◽  
Full Length ◽  
Full Length Cdna ◽  
Expressed Sequence

Construction of Full-Length cDNA Library and Development of EST-Derived Simple Sequence Repeat (EST-SSR) Markers in Senecio scandens

2014 ◽  
Vol 52 (11-12) ◽  
pp. 494-508 ◽  
Author(s):  
Gang Qian ◽  
Junjiao Ping ◽  
Jian Lu ◽  
Zhen Zhang ◽  
Lei Wang ◽  
...  
Keyword(s):  
Cdna Library ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Full Length ◽  
Sequence Repeat ◽  
Full Length Cdna ◽  
Simple Sequence

scholarly journals Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags

2004 ◽  
Vol 79 (4) ◽  
pp. 227-232 ◽  
Author(s):  
Yasunari Ogihara ◽  
Keiichi Mochida ◽  
Kanako Kawaura ◽  
Koji Murai ◽  
Motoaki Seki ◽  
...  
Keyword(s):  
Cdna Library ◽  
Expressed Sequence Tags ◽  
Hexaploid Wheat ◽  
Large Scale ◽  
Full Length ◽  
Full Length Cdna ◽  
Expressed Sequence

scholarly journals Short note: Development of Six EST-SSR Markers in Larch

2011 ◽  
Vol 60 (1-6) ◽  
pp. 161-163 ◽  
Author(s):  
X. Yang ◽  
X. Sun ◽  
S. Zhang
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Expressed Sequence Tags ◽  
Short Note ◽  
Biological Applications ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Six simple sequence repeats (SSR) markers were developed from expressed sequence tags (ESTs) in the genus Larix. Based on evaluation with 49 L. kaempferi genotypes, the number of alleles per locus ranged from two to four, and the expected (He) and observed (Ho) heterozygosity values were 0.225−0.694 and 0.201−0.656, respectively. The inbreeding coffcient (FIS) for all loci were less than zero except that LAReSSR85 was 0.4383. All the six EST-SSR markers were transferable to L. gmelini, L. olgensis var Koreana, L. principisrupprechtii and L. olgensis. BlastX analysis showed that five of the EST-SSRs were homologous to known genes. The six EST-SSR markers developed here can be valuable for biological applications in Larix.

scholarly journals Construction of a full-length cDNA library and analysis of expressed sequence tags in white jute (Corchorus capsularis L.)

2015 ◽  
Vol 14 (23) ◽  
pp. 1928-1935 ◽  
Author(s):  
Tao Aifen ◽  
Li Xiaozhen ◽  
Qi Jianmin ◽  
Fang Pingping ◽  
Lin Lihui ◽  
...  
Keyword(s):  
Cdna Library ◽  
Expressed Sequence Tags ◽  
Full Length ◽  
Full Length Cdna ◽  
Corchorus Capsularis ◽  
Expressed Sequence

Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 985-998 ◽  
Author(s):  
Siva P Kumpatla ◽  
Snehasis Mukhopadhyay
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Expressed Sequence Tags ◽  
Rapid Development ◽  
Dinucleotide Repeats ◽  
High Throughput Analysis ◽  
Species Markers ◽  
Nucleotide Repeats ◽  
Expressed Sequence ◽  
Simple Sequence

Simple sequence repeat (SSR) markers are widely used in many plant and animal genomes due to their abundance, hypervariability, and suitability for high-throughput analysis. Development of SSR markers using molecular methods is time consuming, laborious, and expensive. Use of computational approaches to mine ever-increasing sequences such as expressed sequence tags (ESTs) in public databases permits rapid and economical discovery of SSRs. Most of such efforts to date focused on mining SSRs from monocotyledonous ESTs. In this study, we have computationally mined and examined the abundance of SSRs in more than 1.54 million ESTs belonging to 55 dico tyledonous species. The frequency of ESTs containing SSRs among species ranged from 2.65% to 16.82%. Dinucleotide repeats were found to be the most abundant followed by tri- or mono-nucleotide repeats. The motifs A/T, AG/GA/CT/TC, and AAG/AGA/GAA/CTT/TTC/TCT were the predominant mono-, di-, and tri-nucleotide SSRs, respectively. Most of the mononucleotide SSRs contained 15–25 repeats, whereas the majority of the di- and tri-nucleotide SSRs contained 5–10 repeats. The comprehensive SSR survey data presented here demonstrates the potential of in silico mining of ESTs for rapid development of SSR markers for genetic analysis and applications in dicotyledonous crops.Key words: simple sequence repeats, expressed sequence tags, SSRs, ESTs, bioinformatics, mining, survey, dicotyledonous species, markers.

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