Analysis of Expressed Sequence Tags (EST) in Date Palm

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.

Download Full-text

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

AoB Plants ◽

10.1093/aobpla/plaa064 ◽

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.

Download Full-text

In silico prediction of conserved microRNAs and their targets from the Asian rice gall midge (Orseolia oryzae) expressed sequence tags

Gene Reports ◽

10.1016/j.genrep.2021.101032 ◽

2021 ◽

Vol 23 ◽

pp. 101032

Author(s):

Isha Atray ◽

J.S. Bentur ◽

Suresh Nair

Keyword(s):

Expressed Sequence Tags ◽

In Silico ◽

Gall Midge ◽

In Silico Prediction ◽

Orseolia Oryzae ◽

Asian Rice ◽

Rice Gall Midge ◽

Expressed Sequence

Download Full-text

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

Genome ◽

10.1139/g04-088 ◽

2005 ◽

Vol 48 (1) ◽

pp. 12-17 ◽

Cited By ~ 14

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.

Download Full-text

Molecular diversity and evolutionary trends of cysteine-rich peptides from the venom glands of Chinese spider Heteropoda venatoria

Scientific Reports ◽

10.1038/s41598-021-82668-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jie Luo ◽

Yiying Ding ◽

Zhihao Peng ◽

Kezhi Chen ◽

Xuewen Zhang ◽

...

Keyword(s):

Expressed Sequence Tags ◽

Molecular Diversity ◽

Insect Pests ◽

Phylogenetic Analyses ◽

Spider Venom ◽

Evolutionary Trends ◽

The Family ◽

Venom Glands ◽

Venom Evolution ◽

Expressed Sequence

AbstractHeteropoda venatoria in the family Sparassidae is highly valued in pantropical countries because the species feed on domestic insect pests. Unlike most other species of Araneomorphae, H. venatoria uses the great speed and strong chelicerae (mouthparts) with toxin glands to capture the insects instead of its web. Therefore, H. venatoria provides unique opportunities for venom evolution research. The venom of H. venatoria was explored by matrix-assisted laser desorption/ionization tandem time-of-flight and analyzing expressed sequence tags. The 154 sequences coding cysteine-rich peptides (CRPs) revealed 24 families based on the phylogenetic analyses of precursors and cysteine frameworks in the putative mature regions. Intriguingly, four kinds of motifs are first described in spider venom. Furthermore, combining the diverse CRPs of H. venatoria with previous spider venom peptidomics data, the structures of precursors and the patterns of cysteine frameworks were analyzed. This work revealed the dynamic evolutionary trends of venom CRPs in H. venatoria: the precursor has evolved an extended mature peptide with more cysteines, and a diminished or even vanished propeptides between the signal and mature peptides; and the CRPs evolved by multiple duplications of an ancestral ICK gene as well as recruitments of non-toxin genes.

Download Full-text