RESUMEN

BACKGROUND: Perilla frutescens (Lamiaceae) is distributed in East Asia and is classified into var. frutescens and crispa. P. frutescens is multipurpose crop for human health because of a variety of secondary metabolites such as phenolic compound and essential oil. However, a lack of genetic information has hindered the development and utilization of Perilla genotypes. METHODS AND RESULTS: This study was performed to develop expressed sequence tag-simple sequence repeat (EST-SSR) markers from P. frutescens var. crispa (wild type) and Antisperill (a mutant cultivar) and used them to assess the genetic diversity of, and relationships among, 94 P. frutescens genotypes. We obtained 65 Gb of sequence data comprising 632,970 transcripts by de novo RNA-sequencing. Of the 14,780 common SSRs, 102 polymorphic EST-SSRs were selected using in silico polymerase chain reaction (PCR). Overall, successful amplification from 58 EST-SSRs markers revealed remarkable genetic diversity and relationships among 94 P. frutescens genotypes. In total, 268 alleles were identified, with an average of 4.62 alleles per locus (range 2-11 alleles/locus). The average polymorphism information content (PIC) value was 0.50 (range 0.04-0.86). In phylogenetic and population structure analyses, the genotypes formed two major groups: Group I (var. crispa) and Group II (var. frutescens). CONCLUSION: This results suggest that 58 novel EST-SSR markers derived from wild-type cultivar (var. crispa) and its mutant cultivar (Antisperill) have potential uses for population genetics and recombinant inbred line mapping analyses, which will provide comprehensive insights into the genetic diversity and relationship of P. frutescens.

Asunto(s)

Etiquetas de Secuencia Expresada , Repeticiones de Microsatélite/genética , Mutación , Perilla frutescens/genética , Polimorfismo Genético , Transcriptoma/genética , Alelos , Productos Agrícolas/genética , Sitios Genéticos , Genotipo , Filogenia , RNA-Seq/métodos

RESUMEN

Objective: To excavate the terpenoid synthesis and metabolism-related gene function and screen the interaction protein and fingerprint analysis of Antrodia cinnamomea mycelium, a cDNA library from A. cinnamomea mycelia was constructed and the EST sequences were analyzed. Methods: The cDNA library from the A. cinnamomea mycelium was constructed by the Gateway technique. A part of EST sequences about the bioinformatics, functional annotation and EST-SSR were analyzed. Results: The cDNA library of the A. cinnamomea mycelium was constructed successfully. The recombinant rate of the cDNA library was 95%, the titer of the library was 6.1 × 106 cfu/mL, the total cloning number was 1.2 × 107 cfu, the length of cDNA was between 300-2 000 bp with an average length of 1 000 bp. The clones were randomly sequenced and 65 valid ESTs were obtained. After being compared in the Genbank database, 45 ESTs had a definite annotation, and 18 ESTs were unnamed and hypothetical protein. The results with GO functional annotation showed that the ESTs involved the cell composition, transport, catalytic activity, regulation functions and etc. It contained 271 SSRs of all the ESTs in total. The nucleotide repeats in A. cinnamomea were abundant, among which dinucleotide and trinucleotide repeat units were more common accounting for 94.23%. Conclusion: The cDNA library from the A. cinnamomea mycelium and its ESTs related biological information were preliminarily identified, which will provide a theoretical foundation for research the mycelium genomics of A. cinnamomea.

RESUMEN

Simple sequence repeats (SSRs) or microsatellite markers derived from expressed sequence tags (ESTs) are routinely used for molecular assisted-selection breeding, comparative genomic analysis, and genetic diversity studies. In this study, we investigated 54,546 ESTs for the identification and development of SSR markers in Pogostemon cablin (Patchouli). In total, 1219 SSRs were identified from 1144 SSR-containing ESTs. Trinucleotides (80.8%) were the most abundant SSRs, followed by di- (10.8%), mono- (7.1%), and hexa-nucleotides (1.3%). The top six motifs were CCG/CGG (15.3%), AAG/CTT (15.0%), ACC/GGT (13.5%), AGG/CCT (12.4%), ATC/ATG (9.9%), and AG/CT (9.8%). On the basis of these SSR-containing ESTs, a total of 192 primer pairs were randomly designed and used for polymorphism analysis in 38 accessions collected from different geographical regions of Guangdong, China. Of the SSR markers, 45 were polymorphic and had allele variations from two to four. Furthermore, a transferability analysis of these primer pairs revealed a 10⁻40% cross-species transferability in 10 related species. This report is the first comprehensive study on the development and analysis of a large set of SSR markers in P. cablin. These markers have the potential to be used in quantitative trait loci mapping, genetic diversity studies, and the fingerprinting of cultivars of P. cablin.

Asunto(s)

Etiquetas de Secuencia Expresada , Marcadores Genéticos , Repeticiones de Microsatélite , Pogostemon/genética , Transcriptoma , Biología Computacional/métodos , ADN de Plantas , Perfilación de la Expresión Génica , Secuenciación de Nucleótidos de Alto Rendimiento , Anotación de Secuencia Molecular , Polimorfismo Genético

RESUMEN

Lead (Pb) is one of the most serious environmental pollutants. The aquatic fern Salvinia minima Baker is capable to hyper-accumulate Pb in their tissues. However, the molecular mechanisms involved in its Pb accumulation and tolerance capacity are not fully understood. In order to investigate the molecular mechanisms that are activated by S. minima in response to Pb, we constructed a suppression subtractive hybridization library (SSH) in response to an exposure to 40µM of Pb(NO3)2 for 12h. 365 lead-related differentially expressed sequences tags (ESTs) were isolated and sequenced. Among these ESTs, 143 unique cDNA (97 were registered at the GenBank and 46 ESTs were not registered, because they did not meet the GenBank conditions). Those ESTs were identified and classified into 3 groups according to Blast2GO. In terms of metabolic pathways, they were grouped into 29 KEGG pathways. Among the ESTs, we identified some that might be part of the mechanism that this fern may have to deal with this metal, including abiotic-stress-related transcription factors, some that might be involved in tolerance mechanisms such as ROS scavenging, membrane protection, and those of cell homeostasis recovery. To validate the SSH library, 4 genes were randomly selected from the library and analyzed by qRT-PCR. These 4 genes were transcriptionally up-regulated in response to lead in at least one of the two tested tissues (roots and leaves). The present library is one of the few genomics approaches to study the response to metal stress in an aquatic fern, representing novel molecular information and tools to understand the molecular physiology of its Pb tolerance and hyperaccumulation capacity. Further research is required to elucidate the functions of the lead-induced genes that remain classified as unknown, to perhaps reveal novel molecular mechanisms of Pb tolerance and accumulation capacity in aquatic plants.

Asunto(s)

Helechos/efectos de los fármacos , Plomo/toxicidad , Nitratos/toxicidad , Contaminantes Químicos del Agua/toxicidad , Secuencia de Bases , ADN Complementario/metabolismo , Etiquetas de Secuencia Expresada , Helechos/metabolismo , Regulación de la Expresión Génica de las Plantas , Biblioteca de Genes , Hojas de la Planta/efectos de los fármacos , Hojas de la Planta/metabolismo , Raíces de Plantas/efectos de los fármacos , Raíces de Plantas/metabolismo , Regulación hacia Arriba

RESUMEN

Of the two commercially cultivated coffee (Coffea) species, C. arabica (arabica) is highly susceptible and C. canephora (robusta) is highly resistant to the insect pest Xylotrechus quadripes (Coleoptera: Cerambycidae), commonly known as coffee white stem borer (CWSB). We constructed a forward-subtracted cDNA library by Suppression Subtractive Hybridization (SSH) from robusta bark tissue for profiling genes induced by CWSB infestation. Among the 265 unigenes of the SSH EST library, 7 unigenes (5 contigs and 2 singletons) matching different pectin-degrading enzymes were discovered. These ESTs matched one pectate lyase, three polygalacturonases, and one pectin acetylesterase gene. Quantitative real-time PCR (qRT-PCR) revealed that CWSB infestation strongly induces the pectate lyase gene at 72 h. Complete cDNA sequence of the pectate lyase gene was obtained through 3' and 5' RACE reactions. It was a 1595 bp long sequence that included full CDS and both UTRs. Against C. canephora genome sequences in Coffee Genome Hub database ( http://coffee-genome.org/ ), it had 22 matches to different pectate lyase genes mapped on 9 of the 11 pseudochromosomes, the top match being Cc07_g00190 Pectate lyase. In NCBI database, it matched pectate lyase sequences of several plants. Apart from C. canephora, the closest pectate lyase matches were from Sesamum indicum and Nicotiana tabacum. The pectinolytic enzymes discovered here are thought to play a role in the production of oligogalacturonides (OGs) which act as Damage-Associated Molecular Pattern (DAMP) signals eliciting innate immunity in plants. The pectate lyase gene, induced by CWSB infestation, along with other endogenous pectinolytic enzymes and CWSB-specific elicitors, may be involved in triggering basal defense responses to protect the CWSB-damaged tissue against pathogens, as well as to contain CWSB in robusta.

RESUMEN

PREMISE OF THE STUDY: Sacred lotus (Nelumbo nucifera) is a perennial aquatic herbaceous plant of ecological, ornamental, and economic importance. MicroRNAs (miRNAs) play an important role in plant development. However, reports of miRNAs and their role in sacred lotus have been limited. METHODS: Using the homology search of known miRNAs with genome and transcriptome contig sequences, we employed a pipeline to identify miRNAs in N. nucifera. We also predicted the targets of these miRNAs. RESULTS: We found 106 conserved miRNAs in N. nucifera, and 456 of their miRNA targets were annotated. Quantitative real-time PCR (qRT-PCR) analysis revealed the different expression levels of the 10 selected conserved miRNAs in tissues of young leaves, stems, and flowers of N. nucifera. Negative correlation of expression level between five miRNAs and their target genes was also revealed. DISCUSSION: Combining bioinformatics and experiment analysis, we identified the miRNAs in N. nucifera. The results can be used as a workbench for further investigation of the roles of miRNAs in N. nucifera.

RESUMEN

The venomics of Gloydius intermedius were investigated using expressed sequence tags (ESTs) analyses, 2D gel-electrophoresis combined with MALDI-TOF/TOF, and LC-MS/MS. A total of 1920 ESTs from the venom gland cDNA library were sequenced; 74% of them belonged to toxin-families. The four most abundant families among the toxin transcripts were: serine protease (SP, 36.2%), bradykinin potentiating peptide (25.3%), l-amino acid oxidase (LAAO, 13.1%), and phospholipase A2 (PLA2, 9.9%). Moreover, the full sequences of four PLA2s, eight SPs, cysteine-rich secretory protein (CRISP), C-type-lectin-like-protein (CTLP), hyaluronidase, metalloproteinase, and nerve growth factor were deduced from the cDNA sequences. Excluding the CRISP and hyaluronidase, most of the G. intermedius venom proteins bear 92-99% sequence identities to those of other pitviper venoms. The most abundant components are PLA2s (37%), SPs (20%) and LAAO (6%), while metalloproteinase, CTLP, and other components each account for <3% of the total venom proteins. The abundance of Gintexin (a crotoxin-like neurotoxin) and low levels of hemorrhagic metalloproteases, disintegrins and CTLPs highlight the great venom differences between G. intermedius and other hemorrhagic pitvipers. The bimorphism of hemorrhagic and neurotoxic venoms among Gloydius is confirmed; our results shed more lights on the co-evolution of both neurotoxicity and hypotension in some viperid venoms.

Asunto(s)

Venenos de Crotálidos/química , Proteoma , Proteínas de Reptiles/química , Transcriptoma , Secuencia de Aminoácidos , Animales , Cromatografía Liquida , Crotoxina/química , Electroforesis en Gel Bidimensional , Electroforesis en Gel de Poliacrilamida , Etiquetas de Secuencia Expresada , Perfilación de la Expresión Génica , Hialuronoglucosaminidasa/química , L-Aminoácido Oxidasa/química , Metaloproteasas/química , Datos de Secuencia Molecular , Factor de Crecimiento Nervioso/química , Fosfolipasas A2/química , Isoformas de Proteínas/química , Proteómica , Proteínas de Reptiles/análisis , Alineación de Secuencia , Análisis de Secuencia de Proteína , Serina Proteasas/química , Espectrometría de Masas en Tándem , Viperidae

RESUMEN

Low temperature is a major abiotic stress that seriously limits mangrove productivity and distribution, the molecular mechanisms of cold tolerance involved in mangroves are still poorly understood at present. It was used to identify the potential cold-related genes in Kandelia obovata (K. obovata) by suppression subtractive hybridization. 334 cold-related expressed sequence tags (ESTs) out of 670 clones were isolated and sequenced. Among these ESTs, 143 unique cDNAs were identified and classified into ten groups, such as metabolism, energy, cell rescue and defense, transcription and photosynthesis according to NCBI blast. Based on bioinformatics analysis, these ESTs were mainly related to response to stimulus and metabolic process, and were included to 72 KEGG pathways. Two selected genes (e.g., aquaporin gene and zinc family protein gene) from the library were further analyzed by quantitative real-time PCR analysis. Both the two genes were found to be transcriptionally up-regulated under cold stress, which partly approve the construction of the subtractive cDNA library. The diversity of the putative functions of these genes indicated that cold stress resulted in a complex response in K. obovata. Further investigation on the functions and potential pathways of these genes will facilitate the understanding of the molecular adaptations to cold tolerance in mangrove plants.

Asunto(s)

Etiquetas de Secuencia Expresada , Regulación de la Expresión Génica de las Plantas , Proteínas de Plantas/genética , Rhizophoraceae/genética , Técnicas de Hibridación Sustractiva , Secuencia de Aminoácidos , Secuencia de Bases , Frío/efectos adversos , Datos de Secuencia Molecular , Filogenia , Hojas de la Planta/genética , Hojas de la Planta/metabolismo , Proteínas de Plantas/metabolismo , Alineación de Secuencia , Estrés Fisiológico/genética

RESUMEN

Scorpion venom consists of a complex mixture of molecules including biologically active compounds. Because of their high potency and selectivity, toxins have medical applicability. In the last decades, scorpion toxins have thus gained considerable interest among scientist in the fields of pharmacology, biophysics and neurobiology. Identification of scorpion venom peptides and toxins can be achieved based on transcriptome approaches. We constructed the first cDNA library and Expressed Sequence Tag (EST) study to explore the transcriptomic composition of the telson from the southern African scorpion Hottentotta conspersus, belonging to the family Buthidae. We obtained 21 new venom-related sequences (8 contigs and 16 singlets) from a total of 98 ESTs analyzed, including putative neurotoxins (chloride, potassium, sodium and calcium channel toxins), bradykinin-potentiating peptides and other venom peptides without established function. These novel toxin-related sequences might serve as basis for further research both of pharmaceutical and phylogenetic nature.

Asunto(s)

Proteínas de Artrópodos/metabolismo , Neurotoxinas/metabolismo , Venenos de Escorpión/metabolismo , Escorpiones/metabolismo , África Austral , Secuencia de Aminoácidos , Animales , Proteínas de Artrópodos/química , Proteínas de Artrópodos/genética , Proteínas de Artrópodos/toxicidad , Biología Computacional , Etiquetas de Secuencia Expresada , Biblioteca de Genes , Moduladores del Transporte de Membrana/análisis , Moduladores del Transporte de Membrana/química , Moduladores del Transporte de Membrana/metabolismo , Moduladores del Transporte de Membrana/toxicidad , Datos de Secuencia Molecular , Familia de Multigenes , Neurotoxinas/química , Neurotoxinas/genética , Neurotoxinas/toxicidad , Péptidos/química , Péptidos/genética , Péptidos/metabolismo , Péptidos/toxicidad , Filogenia , Proteómica , Receptores de Bradiquinina/agonistas , Venenos de Escorpión/química , Venenos de Escorpión/genética , Venenos de Escorpión/toxicidad , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Transcriptoma

RESUMEN

The endogenous small non-coding functional microRNAs (miRNAs) are short in size, range from ~21 to 24 nucleotides in length, play a pivotal role in gene expression in plants and animals by silencing genes either by destructing or blocking of translation of homologous mRNA. Although various high-throughput, time consuming and expensive techniques like forward genetics and direct cloning are employed to detect miRNAs in plants but comparative genomics complemented with novel bioinformatic tools pave the way for efficient and cost-effective identification of miRNAs through homologous sequence search with previously known miRNAs. In this study, an attempt was made to identify and characterize conserved miRNAs in garlic expressed sequence tags (ESTs) through computational means. For identification of novel miRNAs in garlic, a total 3227 known mature miRNAs of plant kingdom Viridiplantae were searched for homology against 21,637 EST sequences resulting in identification of 6 potential miRNA candidates belonging to 6 different miRNA families. The psRNATarget server predicted 33 potential target genes and their probable functions for the six identified miRNA families in garlic. Most of the garlic miRNA target genes seem to encode transcription factors as well as genes involved in stress response, metabolism, plant growth and development. The results from the present study will shed more light on the understanding of molecular mechanisms of miRNA in garlic which may aid in the development of novel and precise techniques to understand some post-transcriptional gene silencing mechanism in response to stress tolerance.

Asunto(s)

Etiquetas de Secuencia Expresada , Ajo/genética , Genes de Plantas , MicroARNs/genética , Secuencia de Bases , Biología Computacional/métodos , Secuencia Conservada , Ajo/metabolismo , Regulación de la Expresión Génica de las Plantas , Anotación de Secuencia Molecular , Datos de Secuencia Molecular , Filogenia

RESUMEN

To successful molecular breeding, identification and functional characterization of breeding related genes and development of molecular breeding techniques using DNA markers are essential. Although the development of a useful marker is difficult in the aspect of time, cost and effort, many markers are being developed to be used in molecular breeding and developed markers have been used in many fields. Single nucleotide polymorphisms (SNPs) markers were widely used for genomic research and breeding, but has hardly been validated for screening functional genes in olive flounder. We identified single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) database in olive flounder; out of a total 4,327 ESTs, 693 contigs and 514 SNPs were detected in total EST, and these substitutions include 297 transitions and 217 transversions. As a result, 144 SNP markers were developed on the basis of 514 SNP to selection of useful gene region, and then applied to each of eight wild and culture olive flounder (total 16 samples). In our experimental result, only 32 markers had detected polymorphism in sample, also identified 21 transitions and 11 transversions, whereas indel was not detected in polymorphic SNPs. Heterozygosity of wild and cultured olive flounder using the 32 SNP markers is 0.34 and 0.29, respectively. In conclusion, we identified SNP and polymorphism in olive flounder using newly designed marker, it supports that developed markers are suitable for SNP detection and diversity analysis in olive flounder. The outcome of this study can be basic data for researches for immunity gene and characteristic with SNP.

RESUMEN

The thymus is the central lymphoid organ for the development of bone marrow-derived precursor cells into mature T-cells. Understanding the molecular mechanism of thymic involution and regeneration is critical to develop methods to normalize or improve host immunity from the decreased immune function caused by thymic involution. In this study, the regenerating thymus cDNA library was constructed in the rat from a model of thymic involution and regeneration induced by cyclophosphamide. Expressed sequence tags (ESTs) were obtained by partial sequencing of 700 randomly selected insert-containing clones. A total of 630 ESTs were analyzed, of which 486 ESTs (78%) matched to known genes and 125 ESTs (19%) matched to other ESTs (unknown genes). The 19 ESTs (3%) did not match with any known sequences. The ESTs were grouped into six main functional categories: metabolism (44%), signaling components (20%), membrane transport (7%), cytoskeleton (2%), cell division (2%) and defense (2%). As a result of RT-PCR analysis, expression of putative gene 01, putative E2IG2 gene, musculin and osteoactivin significantly increased in rat thymus during regeneration. The putative gene 01 showed complete homology with mitochondrial ribosomal protein S4 by homology search and multiple alignment of amino acid. These results provide the extensive molecular information on thymus regeneration and will be useful source to identify various genes which may play an important role in the thymus regeneration as well as to clone novel genes. Furthermore, the availability of these data will serve as a basis for further research to understand the molecular mechanism of thymus regeneration.

Asunto(s)

Animales , Ratas , División Celular , Células Clonales , Ciclofosfamida , Citoesqueleto , Etiquetas de Secuencia Expresada , Expresión Génica , Biblioteca de Genes , Membranas , Metabolismo , Regeneración , Proteínas Ribosómicas , Linfocitos T , Timo

RESUMEN

Dicrocoeliosis caused by Dicrocoelium dendriticum is an important liver disease, which affects ruminants all around the world. Despite the significant economic losses caused by this trematode, molecular knowledge is very scarce. In fact, there is no information in the expressed sequence tag (EST) database about the parasite. Furthermore, the immunological diagnosis of dicrocoeliosis remains unsatisfactory, and there aren't available recombinant proteins that could be tested in the diagnosis. For this reason a cDNA library was constructed with mRNA extracted from D. dendriticum adults for first time. A random preliminary screening of 230 phage plaques from the library resulted in the identification of 173 new EST. The deduced proteins expressed by these genes have been described as possible vaccine targets in other trematodes, and/or as relevant diagnosis antigens. Then, our goal was to identify D. dentriticum diagnosis genes to be used as recombinant antigens in the specific immunological diagnosis of the trematodoses. A D. dendriticum cDNA encoding an 8-kDa recombinant protein has been cloned, expressed in Escherichia coli and evaluated in dicrocoeliosis diagnosis using both Western Blot and enzyme-linked immunosorbent assay (ELISA). The recombinant expression molecule has demonstrated its value as a diagnosis antigen of dicrocoeliosis, able to discriminate between positive and controls on day 30 post infection. This is the first research conducted for identification and characterization of D. dendriticum ESTs, which can serve as a starting point for future research on immunodiagnosis and immunoprofilaxis of dicrocoeliosis.

Asunto(s)

Antígenos Helmínticos/genética , Dicroceliasis/diagnóstico , Dicrocoelium/genética , Etiquetas de Secuencia Expresada , Biblioteca de Genes , Secuencia de Aminoácidos , Animales , Antígenos Helmínticos/química , Antígenos Helmínticos/inmunología , Clonación Molecular , Biología Computacional , Reacciones Cruzadas , ADN Complementario/química , ADN de Helmintos/química , Dicroceliasis/parasitología , Dicrocoelium/inmunología , Dicrocoelium/aislamiento & purificación , Expresión Génica , Sueros Inmunes/inmunología , Hígado/parasitología , Masculino , Datos de Secuencia Molecular , ARN de Helminto/genética , ARN de Helminto/aislamiento & purificación , Proteínas Recombinantes/genética , Proteínas Recombinantes/inmunología , Sensibilidad y Especificidad , Alineación de Secuencia , Ovinos , Enfermedades de las Ovejas/sangre , Enfermedades de las Ovejas/diagnóstico , Enfermedades de las Ovejas/parasitología

RESUMEN

PREMISE OF THE STUDY: We developed and tested primers for 218 nuclear loci for studying population genetics, phylogeography, and genome evolution in bryophytes. • METHODS AND RESULTS: We aligned expressed sequence tags (ESTs) from Ceratodon purpureus to the Physcomitrella patens genome sequence, and designed primers that are homologous to conserved exons but span introns in the P. patens genome. We tested these primers on four isolates from New York, USA; Otavalo, Ecuador; and two laboratory isolates from Austria (WT4 and GG1). The median genome-wide nucleotide diversity was 0.008 substitutions/site, but the range was large (0-0.14), illustrating the among-locus heterogeneity in the species. • CONCLUSIONS: These loci provide a valuable resource for finely resolved, genome-wide population genetic and species-level phylogenetic analyses of C. purpureus and its relatives.

RESUMEN

The common carp (Cyprinus carpio) is an important aquaculture fish worldwide but only limited single nucleotide polymorphism (SNP) markers are characterized from expressed sequence tags (ESTs) in this species. In this study, 1487 putative SNPs were bioinformatically mined from 14,066 online ESTs mainly from the European common carp, with the occurrence rate of about one SNP every 173 bp. One hundred and twenty-one of these SNPs were selected for validation using PCR fragment sequencing, and 48 out of 81 primers could amplify the expected fragments in the Chinese common carp genome. Only 26 (21.5%) putative SNPs were validated, however, 508 new SNPs and 68 indels were identified. The ratios of transitions to transversions were 1.77 for exon SNPs and 1.05 for intron SNPs. All the 23 SNPs selected for population tests were polymorphic, with the observed heterozygosity (Ho) ranging from 0.053 to 0.526 (mean 0.262), polymorphism information content (PIC) from 0.095 to 0.357 (mean 0.246), and 21 SNPs were in Hardy-Weinberg equilibrium. These results suggest that different common carp populations with geographic isolation have significant genetic variation at the SNP level, and these new EST-SNP markers are readily available for genetics and breeding studies in common carp.

Asunto(s)

Carpas/genética , Etiquetas de Secuencia Expresada , Polimorfismo de Nucleótido Simple , Animales

RESUMEN

The sea hare Aplysia is a powerful model organism for studying the structure and function of the nervous system. Recently, the genomic characterization of Aplysia has been facilitated: A large scale EST sequences was acquired by sequencing cDNA libraries from A. californica and a parallel EST database of the closely related species A. kurodai was reported. These EST databases provide useful tools for both molecular biology and bioinformatics. In our previous report, we demonstrated the utility of the database by screening the candidate genes for the synaptic plasticity and the behavioral sensitization using the microarray containing A. kurodai ESTs. In this addendum, we have expanded our study to show that the protein domain repertoire and the abundance of regulatory genes displayed a linear relationship with the evolution of the complex brains in different lineages. This distinct set of protein domains may play critical roles in evolution of the nervous systems.

RESUMEN

To accelerate the molecular analysis of specifically induced antibacterial peptide against pathogen (E. coli), cDNA library prepared from the larvae fatbody of Bombyx mori was examined by the expressed sequence tag (EST) analysis. In a total of 722 clones, 653 clones were unique genes. Of 653 unique genes, 43.2% (282/653 ESTs) was identified as characterized genes, 38.1% (249/653 ESTs) as uncharacterized genes, and 18.7% (122/653 ESTs) as novel ESTs. According to the functional categorization of the characterized genes, 36.2% (102/282 ESTs) was antibacterial proteins. The highest expressed peptides, 78.4% of all the expressed antibacterial proteins (80/102 ESTs), belonged to the cecropin family. The antibacterial effect of selected clones representing novel ESTs based on a phylogenetic analysis was examined against various bacterial strains. None of the clones showed significant inhibitory effect to the bacteria tested. These results suggested that most of the novel molecules induced by E. coli may not act as immune-induced antibacterial peptides in the fatbody.

Asunto(s)

Humanos , Bacterias , Bombyx , Células Clonales , Etiquetas de Secuencia Expresada , Biblioteca de Genes , Larva , Péptidos

RESUMEN

Objective To analyze the simple sequence repeat(SSR)information in expressed sequence tag(EST)resource of Saruma henryi and lay a solid foundation for the development of EST-SSR markers in this species.Methods ESTs of S.henryi were downloaded from GenBank and used to perform the contig assembly using Sequencher 4.8.Uni-ESTs were obtained and screened for SSR-containing unigenes using SciRoKo 3.4.The distributing frequency of the EST-SSRs and the basic characteristics of motifs were analyzed.Results A total of 10 274 ESTs of S.henryi were retrieved and were assembled into 6 643 non-redundant Uni-ESTs with a total length of 5.11?106 bp.In all,the data mining yielded 1 408 SSR loci,which corresponded to 1 232 Uni-ESTs(18.55%).On average,EST-SSRs spanned 22.30 bp,and occurred every 3.63 kb in length.In S.henryi,mononucleotide repeats predominated with an occurrence frequency of 12.24%.Dinucleotide repeats followed with a frequency of 5.01%.The most frequent one was A/T among all the repeat motifs,then followed by AG/CT.Conclusion SSRs in ESTs of S.henryi display a relatively high level of occurrence frequency and show abundance of types.