Population genetics geneting mapping and comparative genomics studies on greek fish species using neutral polymorphism markers genes and expressed DNA sequences (expressed sequence Tags-ESTs)

2012 ◽  
Author(s):  
Emmanouella Vogiatzi
Keyword(s):  
Population Genetics ◽  
Comparative Genomics ◽  
Fish Species ◽  
Dna Sequences ◽  
Expressed Sequence Tags ◽  
Expressed Sequence

scholarly journals Comparative Genomics in Switchgrass Using 61,585 High‐Quality Expressed Sequence Tags

2008 ◽  
Vol 1 (2) ◽  
Author(s):  
Christian M. Tobias ◽  
Gautam Sarath ◽  
Paul Twigg ◽  
Erika Lindquist ◽  
Jasmyn Pangilinan ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Expressed Sequence Tags ◽  
High Quality ◽  
Expressed Sequence

Rapid gene discovery in plant parasitic nematodes via Expressed Sequence Tags

Nematology ◽  
2000 ◽  
Vol 2 (7) ◽  
pp. 719-731 ◽  
Author(s):  
Pierre Abad ◽  
David Bird ◽  
John Jones ◽  
James McCarter
Keyword(s):  
Dna Sequences ◽  
Expressed Sequence Tags ◽  
Expression Profiling ◽  
Gene Discovery ◽  
Parasitic Nematodes ◽  
Cdna Clones ◽  
Plant Parasitic Nematodes ◽  
Expressed Sequence ◽  
Single Sequence ◽  
Plant Parasitic

AbstractProjects currently underway are generating thousands of publicly available DNA sequences representing numerous genes from plant parasitic nematodes. Use of these data has the potential to revolutionise gene discovery, as well as aiding in genome physical mapping and expression profiling experiments. This article introduces sequences called expressed sequence tags or ESTs, which are single-sequence reads from randomly-selected cDNA clones. We review the process used to create these sequences and outline the strengths and weaknesses of ESTs as research tools. Instructions on how to access and use EST data also are provided. Découverte rapide de gènes chez les nématodes parasites des plantes: le point sur l'utilisation des Etiquettes de Séquences Exprimées - Les projets actuellement en cours génèrent des milliers de séquences d'ADN, publiquement disponibles, représentant de nombreux gènes de nématodes parasites des plantes. L'utilisation de ces données pourrait révolutionner la découverte des gènes en facilitant aussi bien les expériences de cartographie physique que celles de profils d'expression. Cet article présente les séquences dérivées de clones d'ADNc sélectionnés au hasard, appelées étiquettes de séquences exprimées (ESTs). Nous exposons le processus utilisé pour les générer de même que les avantages et les inconvénients des ESTs comme outils de recherche. Les instructions concernant l'accès et l'utilisation des ESTs sont également fournies.

Expressed sequence tags for the chicken genome from a normalized 10-day-old white leghorn whole-embryo cDNA library. 3. DNA sequence analysis of genetic variation in commercial chicken populations

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 261-267 ◽  
Author(s):  
E J Smith ◽  
L Shi ◽  
G Smith
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Expressed Sequence Tags ◽  
Chicken Genome ◽  
Dna Sequence Analysis ◽  
Genetic Maps ◽  
Commercial Chicken ◽  
Genomic Regions ◽  
Expressed Sequence

Single nucleotide polymorphisms (SNPs) have emerged as a major class of DNA markers with the advantage of permitting the development of high-density genetic maps adequate for quantitative trait loci (QTL) identification by linkage-disequilibrium analysis. Here we describe results of a relatively high-depth survey of chicken broiler and layer populations for SNPs in targeted genomic regions of chicken expressed sequence tag (EST) sites. The sequences scanned, representing the composite sequence of 12 amplified fragments for a total of 6489 bp, were randomly distributed, occurring on six different chromosomes or linkage groups in the chicken genome. Although one of the genomic DNA sequences did not match the reference cDNA sequence, another contained an intron that separated two putative exons. The number of SNPs observed within each of the 12 EST-targeted genomic regions ranged from 0 to 10 for a total of 44 and a frequency of 0.7%. About 70% of the polymorphisms were shared between layer and broiler populations. The average heterozygosity within the populations ranged from 0.15 to 0.48, with the layer populations showing the higher heterozygosity. SNPs and oligonucleotides described will provide a resource for genetic analysis in commercial chicken populations. The data appear to indicate that the relative frequency of SNPs in the targeted regions scanned is higher than the frequency reported for any of the other regions scanned to date in other eukaryotic genomes. Additionally, the results suggest that the use of DNA pools may offer an efficient approach to SNP detection in chickens, as has been shown in other vertebrates.Key words: DNA sequence analysis, SNPs, expressed sequence tags, chicken.

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.

Tc8, a Tourist-like Transposon in Caenorhabditis elegans

Genetics ◽  
2001 ◽  
Vol 158 (3) ◽  
pp. 1081-1088 ◽  
Author(s):  
Quang Hien Le ◽  
Kime Turcotte ◽  
Thomas Bureau
Keyword(s):  
Caenorhabditis Elegans ◽  
Expressed Sequence Tags ◽  
Large Family ◽  
Insertion Sequences ◽  
Normal Plant ◽  
Nematode Caenorhabditis Elegans ◽  
Plant Genomes ◽  
Plant Genes ◽  
Expressed Sequence ◽  
Eukaryotic Genomes

Abstract Members of the Tourist family of miniature inverted-repeat transposable elements (MITEs) are very abundant among a wide variety of plants, are frequently found associated with normal plant genes, and thus are thought to be important players in the organization and evolution of plant genomes. In Arabidopsis, the recent discovery of a Tourist member harboring a putative transposase has shed new light on the mobility and evolution of MITEs. Here, we analyze a family of Tourist transposons endogenous to the genome of the nematode Caenorhabditis elegans (Bristol N2). One member of this large family is 7568 bp in length, harbors an ORF similar to the putative Tourist transposase from Arabidopsis, and is related to the IS5 family of bacterial insertion sequences (IS). Using database searches, we found expressed sequence tags (ESTs) similar to the putative Tourist transposases in plants, insects, and vertebrates. Taken together, our data suggest that Tourist-like and IS5-like transposons form a superfamily of potentially active elements ubiquitous to prokaryotic and eukaryotic genomes.

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