Characterization of chromosome-specific genomic DNA from hexaploid oat

Genome ◽  
2012 ◽  
Vol 55 (4) ◽  
pp. 265-268 ◽  
Author(s):  
Xiaomei Luo ◽  
Charlene P. Wight ◽  
Yonghong Zhou ◽  
Nicholas A. Tinker
Keyword(s):  
Avena Sativa ◽  
Orthologous Genes ◽  
Specific Sequence ◽  
Coding Regions ◽  
Repeat Sequences ◽  
Genome Complexity ◽  
Chromosome Isolation ◽  
Sequence Elements ◽  
Genome Complexity Reduction

We have sequenced, assembled, and characterized a set of complexity-reduced genomic clones derived from a chromosome 18D-specific library from hexaploid oat ( Avena sativa L.). Sequences from 314 clones were assembled into 99 contigs of identical or nearly identical sequence. The Censor tool was used to identify similarity to known and characterized repeat sequences in RepBase. Eight repeat classes were scattered throughout 50 contigs, with most repeats belonging to seven transposon and retrotransposon classes. After accounting for known repeats, additional matches to orthologous genes from other species were identified in 24 regions of 22 contigs, and an additional 47 regions matched genomic sequences from oat and other related species. These results provide information about the types and density of transposable elements in the oat genome, as well as the potential for identifying unique or chromosome-specific sequence elements in oat. Overall, these results predict a low success rate in identifying chromosome-specific coding regions in oat through chromosome isolation and genome complexity reduction.

scholarly journals Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine

2021 ◽  
Vol 7 (3) ◽  
pp. 47
Author(s):  
Marios Lange ◽  
Rodiola Begolli ◽  
Antonis Giakountis
Keyword(s):  
Disease Onset ◽  
Cancer Genome ◽  
Driver Mutations ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Coding Regions ◽  
Functional Variants ◽  
Coding Variants ◽  
Clinical Potential

The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them.

scholarly journals Genetic and Molecular Characterization of the Maizerp3Rust Resistance Locus

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 381-394 ◽  
Author(s):  
Craig A Webb ◽  
Todd E Richter ◽  
Nicholas C Collins ◽  
Marie Nicolas ◽  
Harold N Trick ◽  
...  
Keyword(s):  
Family Members ◽  
Crossing Over ◽  
Resistance Locus ◽  
Leucine Rich Repeat ◽  
Bac Contig ◽  
Puccinia Sorghi ◽  
Coding Regions ◽  
Complex Locus ◽  
Sequence Identities

AbstractIn maize, the Rp3 gene confers resistance to common rust caused by Puccinia sorghi. Flanking marker analysis of rust-susceptible rp3 variants suggested that most of them arose via unequal crossing over, indicating that rp3 is a complex locus like rp1. The PIC13 probe identifies a nucleotide binding site-leucine-rich repeat (NBS-LRR) gene family that maps to the complex. Rp3 variants show losses of PIC13 family members relative to the resistant parents when probed with PIC13, indicating that the Rp3 gene is a member of this family. Gel blots and sequence analysis suggest that at least 9 family members are at the locus in most Rp3-carrying lines and that at least 5 of these are transcribed in the Rp3-A haplotype. The coding regions of 14 family members, isolated from three different Rp3-carrying haplotypes, had DNA sequence identities from 93 to 99%. Partial sequencing of clones of a BAC contig spanning the rp3 locus in the maize inbred line B73 identified five different PIC13 paralogues in a region of ∼140 kb.

scholarly journals Identification and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family

2006 ◽  
Vol 394 (3) ◽  
pp. 575-579 ◽  
Author(s):  
Sergey V. Novoselov ◽  
Deame Hua ◽  
Alexey V. Lobanov ◽  
Vadim N. Gladyshev
Keyword(s):  
Mammalian Cells ◽  
Insertion Sequence ◽  
Phylogenetic Analyses ◽  
Dependent Manner ◽  
Putative Active Site ◽  
A Genome ◽  
Sequence Elements ◽  
Identification And Characterization ◽  
Insertion Sequence Elements

Sec (selenocysteine) is a rare amino acid in proteins. It is co-translationally inserted into proteins at UGA codons with the help of SECIS (Sec insertion sequence) elements. A full set of selenoproteins within a genome, known as the selenoproteome, is highly variable in different organisms. However, most of the known eukaryotic selenoproteins are represented in the mammalian selenoproteome. In addition, many of these selenoproteins have cysteine orthologues. Here, we describe a new selenoprotein, designated Fep15, which is distantly related to members of the 15 kDa selenoprotein (Sep15) family. Fep15 is absent in mammals, can be detected only in fish and is present in these organisms only in the selenoprotein form. In contrast with other members of the Sep15 family, which contain a putative active site composed of Sec and cysteine, Fep15 has only Sec. When transiently expressed in mammalian cells, Fep15 incorporated Sec in an SECIS- and SBP2 (SECIS-binding protein 2)-dependent manner and was targeted to the endoplasmic reticulum by its N-terminal signal peptide. Phylogenetic analyses of Sep15 family members suggest that Fep15 evolved by gene duplication.

scholarly journals Characterization of Duck Microsatellite Repeat Sequences

2001 ◽  
Vol 35 (4) ◽  
pp. 217-219 ◽  
Author(s):  
Hideaki TAKAHASHI ◽  
Masahiro SATOH ◽  
Mitsuru MINEZAWA ◽  
Tresnawati PURWADARIA ◽  
Hardi PRASETYO
Keyword(s):  
Microsatellite Repeat ◽  
Repeat Sequences

scholarly journals Comparative characterization of starch biopolymers extracted from cereals using two different techniques

2020 ◽  
pp. 21-26
Author(s):  
Marisa Rivera-Arredondo ◽  
Mario Alberto Rodríguez-Ángeles ◽  
Verónica de Jesús Morales-Félix ◽  
Marina Gaytán-Ruelas
Keyword(s):  
Oryza Sativa ◽  
Avena Sativa ◽  
Chemical Characteristics ◽  
Crystalline Region ◽  
Environmental Legislation ◽  
Ecological Awareness ◽  
Comparative Characterization ◽  
Naoh Treatment

In the field of research and consequent elaboration of biopolymers it has been growing in the last decade, either due to the hardening of the environmental legislation of each country or due to ecological awareness, in any case the term biopolymer is quite broad, these being used as material premium in medicines, food supplements and of course in the production of bioplastics. Since the topic of interest is the comparative characterization of biopolymers using starch extracted from two different cereals, oats and rice, using the alkaline technique with NaOH treatment and the milling technique, assuming that the starch extracted from the Oryza sativa cereal presents chemical characteristics, geometric and mechanical superior in both techniques used unlike the polymers made with Avena sativa starch. These results suggest that the starch quality of each cereal is relevant for the production of biopolymers [1]. The commercially significant properties of starch, such as its mechanical strength and flexibility, depend on the strength and character of the crystalline region, which depends on the ratio of amylose and amylopectin.

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