scholarly journals Reference-Aided Full-length Transcript Assembly, cDNA Cloning, and Molecular Characterization of Coronatine-insensitive 1b (COI1b) Gene in Coconut (Cocos nucifera L.)

2020 ◽  
Author(s):  
Frenzee Kroeizha L. Pammit ◽  
Anand Noel C. Manohar ◽  
Darlon V. Lantican ◽  
Roanne R. Gardoce ◽  
Hayde F. Galvez
Keyword(s):  
Amino Acids ◽  
Defense Response ◽  
Homology Modelling ◽  
Cocos Nucifera ◽  
The Philippines ◽  
Full Length ◽  
Full Length Cdna ◽  
Insect Defense ◽  
Transcript Assembly

AbstractIn the Philippines, 26% of the total agricultural land is devoted to coconut production making coconut one of the most valuable industrial crop in the country. However, the country’s multimillion-dollar coconut industry is threatened by the outbreak of coconut-scale insect (CSI) and other re-emerging insect pests promoting national research institutes to work jointly on developing new tolerant coconut varieties. Here, we report the cloning and characterization of coronatine-insensitive 1 (COI1) gene, one of the candidate insect defense genes, using ‘Catigan Green Dwarf’ (CATD) genome sequence assembly as reference. Two (2) splicing variants were identified and annotated – CnCOI1b-1 and CnCOI1b-2. The full-length cDNA of CnCOI1b-1 was 7,919 bp with an ORF of 1,176 bp encoding for a deduced protein of 391 amino acids while CnCOI1b-2 has 2,360 bp full-length cDNA with an ORF of 1,743 bp encoding a deduced protein of 580 amino acids. The 3D structural model for the two (2) isoforms were generated through homology modelling. Functional analysis revealed that both isoforms are involved in various physiological and developmental plant processes including defense response of plants to insects and pathogens. Phylogenetic analysis confirms high degree of COI1 protein conservation during evolution, especially among monocot species.Key MessageThis paper reports the molecular cloning and characterization of corononatine-insensitive I (COI1) gene in coconut using reference-guided transcript assembly approach. As a well-known insect defense-response gene in other crops, the results of this study are expected to assist in the development of new resistant coconut varieties as one of the strategies to address threats in coconut production.

Cloning and characterization of full-length cDNA clones encoding chalcone synthase from the orchid Bromheadia finlaysoniana

1998 ◽  
Vol 36 (9) ◽  
pp. 647-656 ◽  
Author(s):  
Chye-Fong Liew ◽  
Chong-Jin Goh ◽  
Chiang-Shiong Loh ◽  
Saw-Hoon Lim
Keyword(s):  
Chalcone Synthase ◽  
Full Length ◽  
Cdna Clones ◽  
Full Length Cdna

scholarly journals Characterization of a pathogenic full-length cDNA clone of a virulent porcine epidemic diarrhea virus strain AH2012/12 in China

Virology ◽  
2017 ◽  
Vol 500 ◽  
pp. 50-61 ◽  
Author(s):  
Baochao Fan ◽  
Zhengyu Yu ◽  
Fengjiao Pang ◽  
Xiangwei Xu ◽  
Baimeng Zhang ◽  
...  
Keyword(s):  
Virus Strain ◽  
Cdna Clone ◽  
Porcine Epidemic Diarrhea Virus ◽  
Full Length ◽  
Diarrhea Virus ◽  
Full Length Cdna ◽  
Porcine Epidemic Diarrhea

Characterization of 2159 Unmapped Full-length cDNA Sequences of Oryza sativa L. ssp. japonica ‘Nipponbare’

2009 ◽  
Vol 28 (2) ◽  
pp. 357-362
Author(s):  
Hiroshi Mizuno ◽  
Tsuyoshi Tanaka ◽  
Hiroaki Sakai ◽  
Hiroyuki Kawahigashi ◽  
Takeshi Itoh ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Full Length ◽  
Full Length Cdna ◽  
Cdna Sequences

scholarly journals Rat P45017αfrom Testis: Characterization of a Full-Length cDNA Encoding a Unique Steroid Hydroxylase Capable of Catalyzing Both Δ4- and Δ5-Steroid-17,20-Lyase Reactions

1989 ◽  
Vol 3 (6) ◽  
pp. 968-975 ◽  
Author(s):  
H. Richard Fevold ◽  
Matthew C. Lorence ◽  
John L. McCarthy ◽  
John M. Trant ◽  
Masaaki Kagimoto ◽  
...  
Keyword(s):  
Full Length ◽  
Full Length Cdna ◽  
Steroid Hydroxylase

scholarly journals Genetic characterization of dengue virus type 1 isolated in Brunei in 2005–2006

2009 ◽  
Vol 90 (3) ◽  
pp. 678-686 ◽  
Author(s):  
Osmali Osman ◽  
Mun Yik Fong ◽  
Shamala Devi Sekaran
Keyword(s):  
Dengue Virus ◽  
Genetic Characterization ◽  
The Philippines ◽  
Full Length ◽  
Envelope Gene ◽  
Commercial Laboratory ◽  
Pcr Products ◽  
Primer Sets ◽  
Genotype V

The full-length genomes of two DENV-1 viruses isolated during the 2005–2006 dengue incidents in Brunei were sequenced. Twenty five primer sets were designed to amplify contiguous overlapping fragments of approximately 500–600 base pairs spanning the entire sequence of the genome. The amplified PCR products were sent to a commercial laboratory for sequencing and the nucleotides and the deduced amino acids were determined. Sequence analysis of the envelope gene at the nucleotide and amino acid levels between the two isolates showed 92 and 96 % identity, respectively. Comparison of the envelope gene sequences with 68 other DENV-1 viruses of known genotypes placed the two isolates into two different genotypic groups. Isolate DS06/210505 belongs to genotype V together with some of the recent isolates from India (2003) and older isolates from Singapore (1990) and Burma (1976), while isolate DS212/110306 was clustered in genotype IV with the prototype Nauru strain (1974) and with some of the recent isolates from Indonesia (2004) and the Philippines (2002, 2001). In the full-length genome analysis at the nucleotide level, isolate DS06/210505 showed 94 % identity to the French Guyana strain (1989) in genotype V while isolate DS212/110306 had 96 % identity to the Nauru Island strain (1974) in genotype IV. This work constitutes the first complete genetic characterization of not only Brunei DENV-1 virus isolates, but also the first strain from Borneo Island. This study was the first to report the isolation of dengue virus in the country.

CHARACTERIZATION OF THE SPLICE SITES IN GT–AG AND GC–AG INTRONS IN HIGHER EUKARYOTES USING FULL-LENGTH cDNAs

2004 ◽  
Vol 02 (02) ◽  
pp. 309-331 ◽  
Author(s):  
SUMIE KITAMURA–ABE ◽  
HITOMI ITOH ◽  
TAKANORI WASHIO ◽  
AKIHIRO TSUTSUMI ◽  
MASARU TOMITA
Keyword(s):  
Alternative Splice ◽  
Splice Site ◽  
Consensus Sequence ◽  
Full Length ◽  
Splice Sites ◽  
Consensus Sequences ◽  
Full Length Cdna ◽  
Strong Consensus ◽  
Higher Eukaryotes

For the purpose of analyzing the relation between the splice sites and the order of introns, we conducted the following analysis for the GT–AG and GC–AG splice site groups. First, the pre-mRNAs of H. sapiens, M. musculus, D. melanogaster, A. thaliana and O. sativa were sampled by mapping the full-length cDNA to the genomes. Next, the consensus sequences at different regions of pre-mRNAs were analyzed in the five species. We also investigated the mononucleotide and dinucleotide frequencies in the extensive regions around the 5' splice sites (5'ss) and 3' splice sites (3'ss). As a result, differential frequencies of nucleotides at the first 5'ss in both the GT–AG and GC–AG splice site groups were observed in A. thaliana and O. sativa pre-mRNAs. The trend, which indicates that GC 5'ss possess strong consensus sequences, was observed not only in mammalian pre-mRNAs but also in the pre-mRNAs of D. melanogaster, A. thaliana and O. sativa. Furthermore, we examined the consensus sequences of the constitutive and alternative splice sites. It was suggested that in the case of the alternative GC–AG introns, the tendency to have a weak consensus sequence at 5'ss is different between H. sapiens and M. musculus pre-mRNAs.

A Novel Human Actin-Binding Protein Homologue That Binds to Platelet Glycoprotein Ib

Blood ◽  
1998 ◽  
Vol 92 (4) ◽  
pp. 1268-1276 ◽  
Author(s):  
Wen-feng Xu ◽  
Zhi-wei Xie ◽  
Dominic W. Chung ◽  
Earl W. Davie
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Binding Protein ◽  
Full Length ◽  
Actin Binding ◽  
Intracellular Domain ◽  
Platelet Surface ◽  
Full Length Cdna ◽  
Actin Binding Protein ◽  
Amino Terminal

Glycoprotein (GP)Ib-IX-V is one of the major transmembrane complexes present on the platelet surface. Its extracellular domain binds von Willebrand factor (vWF) and thrombin, while its intracellular domain associates tightly with the cytoskeleton through the actin-binding protein (ABP)-280, also known as filamin. In the present study, a full-length cDNA coding for a human ABP homologue has been cloned and sequenced. This protein was identified by the yeast two-hybrid screening procedure via its interaction with the intracellular domain of GPIb. Initially, a 1.3-kb partial cDNA was isolated from a megakaryocyte-like cell line (K562) cDNA library followed by a full-length cDNA of 9.4 kb that was identified in a human placenta library. The full-length cDNA encoded a protein of 2,578 amino acids with a calculated molecular weight of 276 kD (ABP-276). The amino terminal 248 amino acids contained an apparent actin binding domain followed by 24 tandem repeats each containing about 96 amino acids. The amino acid sequence of the protein shared a high degree of homology with human endothelial ABP-280 (70% identity) and chicken filamin (83% identity). However, the 32 amino acid Hinge I region in ABP-280 that contains a calpain cleavage site conferring flexibility on the molecule, was absent in the homologue. An isoform containing a 24 amino acid insertion with a unique sequence at the missing Hinge I region was also identified (ABP-278). This isoform resulted from alternative RNA splicing. ABP-276 and/or ABP-278 were present in all tissues examined, but the relative amount varied in that some tissue contained both forms, while other tissue contained predominately one or the other. © 1998 by The American Society of Hematology.

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