scholarly journals Expressed Sequence Tags as a Tool for Phylogenetic Analysis of Placental Mammal Evolution

PLoS ONE ◽  
2007 ◽  
Vol 2 (8) ◽  
pp. e775 ◽  
Author(s):  
Morgan Kullberg ◽  
Björn Hallström ◽  
Ulfur Arnason ◽  
Axel Janke
Keyword(s):  
Phylogenetic Analysis ◽  
Expressed Sequence Tags ◽  
Placental Mammal ◽  
Mammal Evolution ◽  
Expressed Sequence

scholarly journals Expressed Sequence Tags (ESTs) and Phylogenetic Analysis of Floral Genes from a Paleoherb Species, Asarum caudigerum

2006 ◽  
Vol 98 (1) ◽  
pp. 157-163 ◽  
Author(s):  
YINHE ZHAO ◽  
GUOYING WANG ◽  
JINPENG ZHANG ◽  
JUNBO YANG ◽  
SHANG PENG ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Expressed Sequence Tags ◽  
Expressed Sequence

Identification of FXYD protein genes in a teleost: tissue-specific expression and response to salinity change

2008 ◽  
Vol 294 (4) ◽  
pp. R1367-R1378 ◽  
Author(s):  
Christian Kølbæk Tipsmark
Keyword(s):  
Skeletal Muscle ◽  
Phylogenetic Analysis ◽  
Atlantic Salmon ◽  
Expressed Sequence Tags ◽  
Cell Types ◽  
Salinity Change ◽  
Specific Expression ◽  
Conserved Domain ◽  
Discrete Manner ◽  
Expressed Sequence

It is increasingly clear that alterations in Na+-K+-ATPase kinetics to fit the demands in specialized cell types is vital for the enzyme to execute its different physiological roles in diverse tissues. In addition to tissue-dependent expression of isoforms of the conventional subunits, α and β, auxiliary FXYD proteins appear to be essential regulatory components. The present study identified genes belonging to this family in Atlantic salmon by analysis of expressed sequence tags. Based on the conserved domain of these small membrane proteins, eight expressed FXYD isoforms were identified. Phylogenetic analysis suggests that six isoforms are homologues to the previously identified FXYD2, FXYD5, FXYD6, FXYD7, FXYD8, and FXYD9, while two additional isoforms were found (FXYD11 and FXYD12). Using quantitative PCR, tissue-dependent expression of the different isoforms was analyzed in gill, kidney, intestine, heart, muscle, brain, and liver. Two isoforms were expressed in several tissues (FXYD5 and FXYD9), while six isoforms were distributed in a discrete manner. In excitable tissues, two isoforms were highly expressed in brain (FXYD6 and FXYD7) and one in skeletal muscle (FXYD8). In osmoregulatory tissues, one isoform was expressed predominantly in gill (FXYD11), one in kidney (FXYD2), and one equally in kidney and intestine (FXYD12). Expression of several FXYD genes in kidney and gill differed between fresh water and seawater salmon, suggesting significance during osmoregulatory adaptations. In addition to identifying novel FXYD isoforms, these studies are the first to show the tissue dependence in their expression and modulation by salinity in any teleosts.

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.

scholarly journals VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽  
2020 ◽  
Vol 12 (6) ◽  
Author(s):  
Morad M Mokhtar ◽  
Ebtissam H A Hussein ◽  
Salah El-Din S El-Assal ◽  
Mohamed A M Atia
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Expressed Sequence Tags ◽  
Genetic Linkage ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Microrna Target ◽  
Genetic Linkage Maps ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 12-17 ◽  
Author(s):  
L D Chaves ◽  
J A Rowe ◽  
K M Reed
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Meleagris Gallopavo ◽  
Whole Genome Sequence ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Important Species ◽  
Expressed Sequence

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

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