Amplification of Orthologous Genes Using Degenerate Primers

2010 ◽  
pp. 175-185
Author(s):  
Samya Chakravorty ◽  
Jim O. Vigoreaux
Keyword(s):  
Orthologous Genes ◽  
Degenerate Primers

INTERACTION OF MIRNA WITH MRNA OF ORTHOLOGOUS GENES INVOLVED IN THE DEVELOPMENT OF NEURODEGENERATIVE AND ONCOLOGICAL DISEASES

2018 ◽  
Author(s):  
O. YURIKOVA ◽  
◽  
S. ATAMBAYEVA ◽  
R. NIYAZOVA ◽  
A. IVASHCHENKO ◽  
...  
Keyword(s):  
Orthologous Genes ◽  
Oncological Diseases

CONSERVATISM OF MIRNA BINDING SITE IN MRNA OF IGFBP3 GENE AND ITS ORTHOLOGOUS GENES

2018 ◽  
Author(s):  
D. AISINA ◽  
◽  
R. NIYAZOVA ◽  
S. ATAMBAYEVA ◽  
A. IVASHCHENKO ◽  
...  
Keyword(s):  
Binding Site ◽  
Mirna Binding Site ◽  
Orthologous Genes

scholarly journals Dating the primigenial C4-CYP21 duplication in primates.

Genetics ◽  
1993 ◽  
Vol 134 (1) ◽  
pp. 331-339 ◽  
Author(s):  
Y Horiuchi ◽  
H Kawaguchi ◽  
F Figueroa ◽  
C O'hUigin ◽  
J Klein
Keyword(s):  
World Monkey ◽  
Orthologous Genes ◽  
Pigtail Macaque ◽  
Single Chromosome ◽  
Old World ◽  
Histocompatibility Complex ◽  
Cyp21 Gene ◽  
Multiple Copies ◽  
Fourth Component ◽  
Flanking Regions

Abstract C4 and CYP21 are two adjacent, but functionally unrelated genes residing in the middle of the mammalian major histocompatibility complex (Mhc). The C4 gene codes for the fourth component of the complement cascade, whereas the CYP21 gene specifies an enzyme (cytochrome P450c21) of the glucocorticoid and mineralocorticoid pathways. The genes occur frequently in multiple copies on a single chromosome arranged in the order C4 ... CYP21 ... C4 ... CYP21. The unit of duplication (a module) is the C4-CYP21 gene pair. We sequenced the flanking regions of the C4-CYP21 modules and the intermodular regions of the chimpanzee, gorilla, and orangutan, as well as the intermodular region of an Old World monkey, the pigtail macaque. By aligning the sequences, we could identify the duplication breakpoints in these species. The breakpoint turned out to be at exactly the same position as that found previously in humans. The sequences flanking paralogous genes in the same species were found to be more similar to one another than sequences flanking orthologous genes in different species. We interpret these results as indicating that the original (primigenial) duplication occurred before the separation of apes from Old World monkeys more than 23 million years ago. The nature of the sequence at the breakpoint suggests that the duplication occurred by nonhomologous recombination. Since then, the C4-CYP21 haplotypes have been expanding and contracting by homologous crossing over which has homogenized the sequences in each species.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Genome Assembly of the Canadian Two-row Malting Barley Cultivar AAC Synergy

2021 ◽  
Author(s):  
Wayne Xu ◽  
James R Tucker ◽  
Wubishet A Bekele ◽  
Frank M You ◽  
Yong-Bi Fu ◽  
...  
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
Barley Cultivar ◽  
Malting Barley ◽  
Orthologous Genes ◽  
Hordeum Vulgare L ◽  
Chromosome Conformation ◽  
Mate Pair ◽  
Genome Assemblies ◽  
First Time

Abstract Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cultivar AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, N50 of 2.32 Mb and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single-copy orthologous genes). After removal of small scaffolds (< 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with the updated version of six-row Morex and recently released two-row Golden Promise genome assemblies.

The expansin EXP1 gene in the elongation zone is induced during soybean embryonic axis germination and differentially expressed in response to ABA and PEG treatments

2020 ◽  
pp. 1-9
Author(s):  
Nidia H. Montechiarini ◽  
Luciana Delgado ◽  
Eligio N. Morandi ◽  
Néstor J. Carrillo ◽  
Carlos O. Gosparini
Keyword(s):  
Cell Wall ◽  
Seed Germination ◽  
Water Availability ◽  
Expression Profiles ◽  
Soybean Seed ◽  
Embryonic Axis ◽  
Growth Potential ◽  
Elongation Zone ◽  
Degenerate Primers ◽  
Embryonic Axes

Abstract During soybean seed germination, the expansive growth potential of the embryonic axes is driven by water uptake while cell wall loosening occurs in cells from the elongation zone (EZ). Expansins are regarded as primary promoters of cell wall remodelling in all plant expansion processes, with the expression profiles of the soybean expansins supporting their cell or tissue specificity. Therefore, we used embryonic axes isolated from whole seed and focused on the EZ to study seed germination. Using a suite of degenerate primers, we amplified an abundantly expressed expansin gene at the EZ during soybean embryonic axis germination, which was identified as EXP1 by in silico analyses. Expression studies showed that EXP1 was induced under germination conditions in distilled water and down-regulated by abscisic acid (ABA), which inhibits soybean germination by physiologically restraining expansion. Moreover, we also identified a time window of ABA responsiveness within the first 6 h of incubation in water, after which ABA lost control of both EXP1 expression and embryonic axis germination, thus confirming the early role of EXP1 in the EZ during this process. By contrast, EXP1 levels in the EZ increased even when germination was impaired by osmotically limiting the water availability required to develop the embryonic axes’ growth potential. We propose that these higher EXP1 levels are involved in the fast germination of soybean embryonic axes as soon as water availability is re-established. Taken together, our results show strong EXP1 expression in the EZ and postulate EXP1 as a target candidate for soybean seed germination control.

scholarly journals Arabidopsis LEC1 and LEC2 Orthologous Genes Are Key Regulators of Somatic Embryogenesis in Cassava

2019 ◽  
Vol 10 ◽  
Author(s):  
Alejandro Brand ◽  
Mauricio Quimbaya ◽  
Joe Tohme ◽  
Paul Chavarriaga-Aguirre
Keyword(s):  
Somatic Embryogenesis ◽  
Orthologous Genes

scholarly journals Characterization of a beta-actin mRNA zipcode-binding protein.

1997 ◽  
Vol 17 (4) ◽  
pp. 2158-2165 ◽  
Author(s):  
A F Ross ◽  
Y Oleynikov ◽  
E H Kislauskis ◽  
K L Taneja ◽  
R H Singer
Keyword(s):  
Nuclear Export ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Affinity Purification ◽  
Nuclear Export Signal ◽  
Degenerate Primers ◽  
Band Shift ◽  
Beta Actin ◽  
Actin Mrna

Localization of beta-actin mRNA to the leading edge of fibroblasts requires the presence of conserved elements in the 3' untranslated region of the mRNA, including a 54-nucleotide element which has been termed the "zipcode" (E. Kislauskis, X. Zhu, and R. H. Singer, J. Cell Biol. 127:441-451, 1994). In order to identify proteins which bind to the zipcode and possibly play a role in localization, we performed band-shift mobility assays, UV cross-linking, and affinity purification experiments. A protein of 68 kDa was identified which binds to the proximal (to the coding region) half of the zipcode with high specificity (ZBP-1). Microsequencing provided unique peptide sequences of approximately 15 residues each. Degenerate primers corresponding to the codons derived from the peptides were synthesized and used for PCR amplification. Screening of a chicken cDNA library resulted in isolation of several clones providing a DNA sequence encoding a 67.7-kDa protein with regions homologous to several RNA-binding proteins, such as hnRNP E1 and E2, and with consensus mRNA recognition motif with RNP1 and 2 motifs and a putative REV-like nuclear export signal. Antipeptide antibodies were raised in rabbits which bound to ZBP-1 and coimmunoprecipitated proteins of 120 and 25 kDa. The 120-kDa protein was also obtained by affinity purification with the RNA zipcode sequence, along with a 53-kDa protein, but the 25-kDa protein appeared only in immunoprecipitations. Mutation of one of the conserved sequences within the zipcode, an ACACCC element in its proximal half, greatly reduced its protein binding and localization properties. These data suggest that the 68-kDa ZBP-1 we have isolated and cloned is an RNA-binding protein that functions within a complex to localize beta-actin mRNA.

scholarly journals SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis

2013 ◽  
Vol 14 (S1) ◽  
Author(s):  
Luis Carlos Belarmino ◽  
Roberta Lane de Oliveira Silva ◽  
Nina da Mota Soares Cavalcanti ◽  
Nicolas Krezdorn ◽  
Ederson Akio Kido ◽  
...  
Keyword(s):  
Arbuscular Mycorrhiza ◽  
Root Nodule ◽  
Orthologous Genes ◽  
Root Nodule Symbiosis ◽  
Nodule Symbiosis

scholarly journals Assessment of orthologous splicing isoforms in human and mouse orthologous genes

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
Author(s):  
Federico Zambelli ◽  
Giulio Pavesi ◽  
Carmela Gissi ◽  
David S Horner ◽  
Graziano Pesole
Keyword(s):  
Orthologous Genes ◽  
Splicing Isoforms ◽  
Human And Mouse
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