The Experts below are selected from a list of 18066 Experts worldwide ranked by ideXlab platform
Pierre Sourdille - One of the best experts on this subject based on the ideXlab platform.
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study of simple Sequence repeat ssr markers from wheat Expressed Sequence Tags ests
Theoretical and Applied Genetics, 2004Co-Authors: N Nicot, V Chiquet, B Gandon, L Amilhat, Fabrice Legeai, Philippe Leroy, M Bernard, Pierre SourdilleAbstract:The increasing availability of Expressed Sequence Tags (ESTs) in wheat (Triticum aestivum) and related cereals provides a valuable resource of non-anonymous DNA molecular markers. We examined 170,746 wheat ESTs from the public (International Triticeae EST Cooperative) and Genoplante databases, previously clustered in contigs, for the presence of di- to hexanucleotide simple Sequence repeats (SSRs). Analysis of 46,510 contigs identified 3,530 SSRs, which represented 7.5% of the total number of contigs. Only 74% of the Sequences allowed primer pairs to be designed, 70% led to an amplification product, mainly of a high quality (68%), and 53% exhibited polymorphism for at least one cultivar among the eight tested. Even though dinucleotide SSRs were less represented than trinucleotide SSRs (15.5% versus 66.5%, respectively), the former showed a much higher polymorphism level (83% versus 46%). The effect of the number and type of repeats is also discussed. The development of new EST-SSRs markers will have important implications for the genetic analysis and exploitation of the genetic resources of wheat and related species and will provide a more direct estimate of functional diversity.
Ximing Guo - One of the best experts on this subject based on the ideXlab platform.
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Expressed Sequence Tags from the zhikong scallop chlamys farreri discovery and annotation of host defense genes
Fish & Shellfish Immunology, 2009Co-Authors: Lingling Wang, Linsheng Song, Jianmin Zhao, Limei Qiu, Huan Zhang, Ximing GuoAbstract:A high-quality cDNA library was constructed from whole body tissues of the zhikong scallop, Chlamys farreri, challenged by Listonella anguillarum. A total of 5720 clones were Sequenced, yielding 5123 Expressed Sequence Tags (ESTs). Among the 3326 unique genes identified, 2289 (69%) genes had no significant (E-value < 1e-5) matches to known Sequences in public databases and 194 (6%) matched proteins of unknown functions. The remaining 843 (25%) genes that exhibited homology with genes of known functions, showed broad involvement in metabolic processes (31%), cell structure and motility (20%), gene and protein expression (12%), cell signaling and cell communication (8%), cell division (4%), and notably, 25% of those genes were related to immune function. They included stress response genes, complement-like genes, proteinase and proteinase inhibitors, immune recognition receptors and immune effectors. The EST collection obtained in this study provides a useful resource for gene discovery and especially for the identification of host-defense genes and systems in scallops and other molluscs. (C) 2009 Elsevier Ltd. All rights reserved.
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development of Expressed Sequence Tags from the bay scallop argopecten irradians irradians
Marine Biotechnology, 2006Co-Authors: Linsheng Song, Jianhai Xiang, Ximing GuoAbstract:The bay scallop, Argopecten irradians irradians, introduced from North America, has become one of the most important aquaculture species in China. Inan effort to identify scallop genes involved in host defense, a high-quality cDNA library was constructed from whole body tissues of the bay scallop. A total of 5828 successful sequencing reactions yielded 4995 Expressed Sequence Tags (ESTs) longer than 100 bp. Cluster and assembly analyses of the ESTs identified 637 contigs (consisting of 2853 Sequences) and 2142 singletons, totaling 2779 unique Sequences. Basic Local Alignment Search Tool (BLAST) analysis showed that the majority (73%) of the unique Sequences had no significant homology (E-value >= 0.005) to Sequences in GenBank. Among the 748 Sequences with significant GenBank matches, 160 (21.4%) were for genes related to metabolism, 131 (17.5%) for cell/organism defense, 124 (16.6%) for gene/protein expression, 83 (11.1%) for cell structure/motility, 70 (9.4%) for cell signaling/communication, 17 (2.3%) for cell division, and 163 (21.8%) matched to genes of unknown functions. The list of host-defense genes included many genes with known and important roles in innate defense such as lectins, defensins, proteases, protease inhibitors, heat shock proteins, antioxidants, and Toll-like receptors. The study provides a significant number of ESTs for gene discovery and candidate genes for studying host defense in scallops and other molluscs.
B O Zhang - One of the best experts on this subject based on the ideXlab platform.
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fifteen polymorphic simple Sequence repeat markers from Expressed Sequence Tags of liriodendron tulipifera
Molecular Ecology Notes, 2006Co-Authors: Meng Xu, Huogen Li, B O ZhangAbstract:We developed and evaluated simple Sequence repeat (SSR) markers derived from Expressed Sequence Tags (ESTs) of Liriodendron tulipifera . Characteristics of 15 EST-SSR loci were investigated using 33 L. tulipifera individuals. The number of alleles per locus ranged from two to five. The expected and observed heterozygosities ranged from 0.216 to 0.751 and from 0.182 to 0.97, respectively. These loci were further tested for their cross-species transferability to Liriodendron Chinense . Because of their high level of polymorphism and transferability, our 15 single-locus EST-SSR markers will be valuable tools for research on mating system, population genetics and systemic evolution of Liriodendron .
Kermit Ritland - One of the best experts on this subject based on the ideXlab platform.
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robust simple Sequence repeat markers for spruce picea spp from Expressed Sequence Tags
Theoretical and Applied Genetics, 2004Co-Authors: Dainis Rungis, Yanik Berube, Jun Zhang, Steven G Ralph, Carol Ritland, Brian E Ellis, Carl J Douglas, Jorg Bohlmann, Kermit RitlandAbstract:Traditionally, simple Sequence repeat (SSR) markers have been developed from libraries of genomic DNA. However, the large, repetitive nature of conifer genomes makes development of robust, single-copy SSR markers from genomic DNA difficult. Expressed Sequence Tags (ESTs), or Sequences of messenger RNA, offer the opportunity to exploit single, low-copy, conserved Sequence motifs for SSR development. From a 20,275-unigene spruce EST set, we identified 44 candidate EST-SSR markers. Of these, 25 amplified and were polymorphic in white, Sitka, and black spruce; 20 amplified in all 23 spruce species tested; the remaining five amplified in all except one species. In addition, 101 previously described spruce SSRs (mostly developed from genomic DNA), were tested. Of these, 17 amplified across white, Sitka, and black spruce. The 25 EST-SSRs had approximately 9% less heterozygosity than the 17 genomic-derived SSRs (mean H=0.65 vs 0.72), but appeared to have less null alleles, as evidenced by much lower apparent inbreeding (mean F=0.046 vs 0.126). These robust SSRs are of particular use in comparative studies, and as the EST-SSRs are within the Expressed portion of the genome, they are more likely to be associated with a particular gene of interest, improving their utility for quantitative trait loci mapping and allowing detection of selective sweeps at specific genes.
Michael J Sharkey - One of the best experts on this subject based on the ideXlab platform.
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Expressed Sequence Tags reveal Proctotrupomorpha (minus Chalcidoidea) as sister to Aculeata (Hymenoptera: Insecta)
Molecular Phylogenetics and Evolution, 2010Co-Authors: Barbara J Sharanowski, S. Randal Voss, Ryan J. Yoder, John A. Walker, Barbara Robbertse, Michael J SharkeyAbstract:Hymenoptera is one of the most diverse groups of animals on the planet and have vital importance for ecosystem function as pollinators and parasitoids. Higher-level relationships among Hymenoptera have been notoriously difficult to resolve with both morphological and traditional molecular approaches. Here we examined the utility of Expressed Sequence Tags for resolving relationships among hymenopteran superfamilies. Transcripts were assembled for 6 disparate Hymenopteran taxa with additional Sequences added from public databases for a final dataset of 24 genes for 16 taxa and over 10 kb of Sequence data. The concatenated dataset recovered a robust and well-supported topology demonstrating the monophyly of Holometabola, Hymenoptera, Apocrita, Aculeata, Ichneumonoidea, and a sister relationship between the two most closely related proctotrupomorphs in the dataset (Cynipoidea + Proctotrupoidea). The data strongly supported a sister relationship between Aculeata and Proctotrupomorpha, contrary to previously proposed hypotheses. Additionally there was strong evidence indicating Ichneumonoidea as sister to Aculeata + Proctotrupomorpha. These relationships were robust to missing data, nucleotide composition biases, low taxonomic sampling, and conflicting signal across gene trees. There was also strong evidence indicating that Chalcidoidea is not contained within Proctotrupomorpha.
