SoyTEdb: a comprehensive database of transposable elements in the soybean genome

<p>Abstract</p> <p>Background</p> <p>Transposable elements are the most abundant components of all characterized genomes of higher eukaryotes. It has been documented that these elements not only contribute to the shaping and reshaping of their host genomes, but also play significant roles in regulating gene expression, altering gene function, and creating new genes. Thus, complete identification of transposable elements in sequenced genomes and construction of comprehensive transposable element databases are essential for accurate annotation of genes and other genomic components, for investigation of potential functional interaction between transposable elements and genes, and for study of genome evolution. The recent availability of the soybean genome sequence has provided an unprecedented opportunity for discovery, and structural and functional characterization of transposable elements in this economically important legume crop.</p> <p>Description</p> <p>Using a combination of structure-based and homology-based approaches, a total of 32,552 retrotransposons (Class I) and 6,029 DNA transposons (Class II) with clear boundaries and insertion sites were structurally annotated and clearly categorized, and a soybean transposable element database, SoyTEdb, was established. These transposable elements have been anchored in and integrated with the soybean physical map and genetic map, and are browsable and visualizable at any scale along the 20 soybean chromosomes, along with predicted genes and other sequence annotations. BLAST search and other infrastracture tools were implemented to facilitate annotation of transposable elements or fragments from soybean and other related legume species. The majority (> 95%) of these elements (particularly a few hundred low-copy-number families) are first described in this study.</p> <p>Conclusion</p> <p>SoyTEdb provides resources and information related to transposable elements in the soybean genome, representing the most comprehensive and the largest manually curated transposable element database for any individual plant genome completely sequenced to date. Transposable elements previously identified in legumes, the third largest family of flowering plants, are relatively scarce. Thus this database will facilitate structural, evolutionary, functional, and epigenetic analyses of transposable elements in soybean and other legume species.</p

A new novel mutation in FBN1 causes autosomal dominant Marfan syndrome in a Chinese family

Purpose: Screening of mutations in the fibrillin-1 (FBN1) gene in a Chinese family with autosomal dominant Marfan syndrome (MFS). Methods: It has been reported that FBN1 mutations account for approximately 90% of Autosomal Dominant MFS. FBN1 mutations were analyzed in a Chinese family of 36 members including 13 MFS patients. The genomic DNAs from blood leukocytes of the patients and their relatives were isolated and the entire coding region of FBN1 was amplified by PCR. The sequence of FBN1 was dertermined with an ABI 3100 Genetic Analyzer. Results: A previously unreported the missense mutation G214S (caused by a 640 A -&gt; G heterozygous change) in FBN1 was identified in the Chinese family. The mutation was associated with the disease phenotype in patients, but not detected in their relatives or in the 100 normal controls. Conclusions: This is the first report of molecular characterization of FBN1 in the MFS family of Chinese origin. Our results expand the spectrum of FBN1 mutations causing MFS and further confirm the role of FBN1 in the pathogenesis of MFS. Direct sequencing of the mutation in FBN1 may be used for diagnosis of MFS.http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000301238300001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701Biochemistry &amp; Molecular BiologyOphthalmologySCI(E)PubMed10ARTICLE10-1181-861

TARE1, a Mutated Copia-Like LTR Retrotransposon Followed by Recent Massive Amplification in Tomato.

Long terminal repeat retrotransposons (LTR-RTs) are the major DNA components in flowering plants. Most LTR-RTs contain dinucleotides ‘TG’ and ‘CA’ at the ends of the two LTRs. Here we report the structure, evolution, and propensity of a tomato atypical retrotransposon element (TARE1) with both LTRs starting as ‘TA’. This family is also characterized by high copy numbers (354 copies), short LTR size (194 bp), extremely low ratio of solo LTRs to intact elements (0.05:1), recent insertion (most within 0.75~1.75 million years, Mys), and enrichment in pericentromeric region. The majority (83%) of the TARE1 elements are shared between S. lycopersicum and its wild relative S. pimpinellifolium, but none of them are found in potato. In the present study, we used shared LTR-RTs as molecular markers and estimated the divergence time between S. lycopersicum and S. pimpinellifolium to be TARE1 elements, together with two closely related families, TARE2and TGRE1, have formed a sub-lineage belonging to a Copia-like Ale lineage. Although TARE1and TARE2 shared similar structural characteristics, the timing, scale, and activity of their amplification were found to be substantially different. We further propose a model wherein a single mutation from ‘G’ to ‘A’ in 3′ LTR followed by amplification is responsible for the origin ofTARE1, thus providing evidence that the proliferation of a spontaneous mutation can be mediated by the amplification of LTR-RTs at the level of RNA

Preservation of (−)-Epigallocatechin-3-gallate Antioxidant Properties Loaded in Heat Treated β-Lactoglobulin Nanoparticles

(−)-Epigallocatechin-3-gallate (EGCG) was loaded in heat treated β-lactoglobulin (β-Lg) for the preservation of antioxidant activity. The effects of pH (2.5–7.0), the heating temperature of β-Lg (30–85 °C), the molar ratio of β-Lg to EGCG (1:2–1:32), and the β-Lg concentration (1–10 mg/mL) on the properties of β-Lg–EGCG complexes were studied. All four factors significantly influenced the particle size, the ζ-potential, and the entrapment efficiency of EGCG and EGCG loading in β-Lg particles. A stable and clear solution system could be obtained at pH 6.4–7.0. The highest protection of EGCG antioxidant activity was obtained with β-Lg heated at 85 °C and the molar ratio of 1:2 (β-Lg: EGCG). β-Lg–EGCG complexes were found to have the same secondary structure as native β-Lg

The Tomato Hoffman's Anthocyaninless Gene Encodes a bHLH Transcription Factor Involved in Anthocyanin Biosynthesis That Is Developmentally Regulated and Induced by Low Temperatures.

Anthocyanin pigments play many roles in plants, including providing protection against biotic and abiotic stresses. Many of the genes that mediate anthocyanin accumulation have been identified through studies of flowers and fruits; however, the mechanisms of genes involved in anthocyanin regulation in seedlings under low-temperature stimulus are less well understood. Genetic characterization of a tomato inbred line, FMTT271, which showed no anthocyanin pigmentation, revealed a mutation in a bHLH transcription factor (TF) gene, which corresponds to the ah (Hoffman's anthocyaninless) locus, and so the gene in FMTT271 at that locus was named ah. Overexpression of the wild type allele of AH in FMTT271 resulted in greater anthocyanin accumulation and increased expression of several genes in the anthocyanin biosynthetic pathway. The expression of AH and anthocyanin accumulation in seedlings was shown to be developmentally regulated and induced by low-temperature stress. Additionally, transcriptome analyses of hypocotyls and leaves from the near-isogenic lines seedlings revealed that AH not only influences the expression of anthocyanin biosynthetic genes, but also genes associated with responses to abiotic stress. Furthermore, the ah mutation was shown to cause accumulation of reactive oxidative species and the constitutive activation of defense responses under cold conditions. These results suggest that AH regulates anthocyanin biosynthesis, thereby playing a protective role, and that this function is particularly important in young seedlings that are particularly vulnerable to abiotic stresses

Identification and Characterization of microRNA during Bemisia tabaci Infestations in Solanum lycopersicum and Solanum habrochaites

MicroRNAs (miRNAs) are a class of small non-coding RNAs that can regulate target gene expression during many plant growth and development processes. In recent years, several studies identified the miRNAs involved in fruit development, leaf development, and abiotic responses in tomato. However, little is known about the miRNAs that respond to insect attack. Here, miRNAs were identified by high-throughput sequencing at different stages after infections by the whitefly Bemisia tabaci in Solanum lycopersicum and Solanum habrochaites, which are susceptible and resistant to whitefly, respectively. A total of 44 known miRNA families were identified, and 33 were shared between the two species. Among these, 13 miRNA families were newly reported in tomato. After strict filtering, some novel miRNAs were also discovered. The global expression patterns of the miRNAs exhibited were different between the two species, reflecting their different responses and resistance levels to whitefly attack. Some of the predicted target genes of differentially expressed miRNAs may be involved in responding to, and defending against, diseases and insects. Thus, plant miRNAs are important in the responses to, and resistance against, insects and provide a useful resource for further investigations into the mechanism of miRNA-mediated plant–insect interactions. Keywords: Solanum lycopersicum, Solanum habrochaites, Bemisia tabaci, miRNAs, whitefly infection, high-throughput sequencin

Insertions/deletions-associated nucleotide polymorphism in Arabidopsis thaliana

Although high levels of within-species variation are commonly observed, a general mechanism for the origin of such variation is still lacking. Insertions and deletions (indels) are a widespread feature of genomes and we hypothesize that there might be an association between indels and patterns of nucleotide polymorphism. Here, we investigate flanking sequences around 18 indels (>100bp) among a large number of accessions of the plant, Arabidopsis thaliana. We found two distinct haplotypes, i.e. a nucleotide dimorphism, present around each of these indels and dimorphic haplotypes always corresponded to the indel-present/-absent patterns. In addition, the peaks of nucleotide diversity between the two divergent alleles were closely associated with these indels. Thus, there exists a close association between indels and dimorphisms. Further analysis suggests that indel-associated substitutions could be an important component of genetic variation shaping nucleotide polymorphism in Arabidopsis. Finally, we suggest a mechanism by which indels might generate these highly divergent haplotypes. This study provides evidence that nucleotide dimorphisms, which are frequently regarded as evidence of frequency-dependent selection, could be explained simply by structural variation in the genome

Identification of Quantitative Trait Loci for Fruit Weight, Soluble Solids Content, and Plant Morphology Using an Introgression Line Population of Solanum pennellii in a Fresh Market Tomato Inbred Line

Introgression lines are convenient populations for the identification, fine-mapping, and functional analysis of genes that are responsible for variations in traits, particularly quantitative trait genes. An introgression line population of Solanum pennellii LA0716 in a fresh market tomato inbred line 1052 was developed by our group. This population was composed of 214 lines. In the present study, five quantitative trait loci (QTLs) for fruit weight, two QTLs for soluble solids content (SSC), three QTLs for plant height, and one QTL for leaf size were identified using this introgression line population. Among these, fw3a and fw4a for fruit weight, ssc7a for SSC, h4t2a, h4t3a, and h4t7a for plant height, and lz12a for leaf size were determined to be novel loci. These results serve as a foundation for fine-mapping and functional analysis of genes underlying these QTLs