scholarly journals Gene Expression and Isoform Identification of PacBio Full-Length cDNA Sequences for Berberine Biosynthesis in Berberis koreana

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1314
Author(s):  
Neha Samir Roy ◽  
Ik-Young Choi ◽  
Taeyoung Um ◽  
Mi Jin Jeon ◽  
Bo-Yun Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bioactive Compound ◽  
Full Length ◽  
Sequencing Analysis ◽  
Biosynthesis Pathway ◽  
Full Length Cdna ◽  
Cdna Sequences ◽  
Pathway Gene ◽  
Benzylisoquinoline Alkaloid ◽  
Genes Encoding

Berberis koreana is a medicinal plant containing berberine, which is a bioactive compound of the benzylisoquinoline alkaloid (BIA) class. BIA is widely used in the food and drug industry for its health benefits. To investigate the berberine biosynthesis pathway, gene expression analysis was performed in leaves, flowers, and fruits at different stages of growth. This was followed by full-length cDNA sequencing analysis using the PacBio sequencer platform to determine the number of isoforms of those expressed genes. We identified 23,246 full-length unigenes, among which 8,479 had more than one isoform. The number of isoforms ranged between two to thirty-one among all genes. Complete isoform analysis was carried out on the unigenes encoding BIA synthesis. Thirteen of the sixteen genes encoding enzymes for berberine synthesis were present in more than one copy. This demonstrates that gene duplication and translation into isoforms may contribute to the functional specificity of the duplicated genes and isoforms in plant alkaloid synthesis. Our study also demonstrated the streamlining of berberine biosynthesis via the absence of genes for enzymes of other BIAs, but the presence of all the genes for berberine biosynthesize in B. koreana. In addition to genes encoding enzymes for the berberine biosynthesis pathway, the genes encoding enzymes for other BIAs were not present in our dataset except for those encoding corytuberine synthase (CTS) and berbamunine synthase (BS). Therefore, this explains how B. koreana produces berberine by blocking the pathways leading to other BIAs, effectively only allowing the pathway to lead to berberine synthesis.

scholarly journals Cloning and Sequencing Analysis of a Full-Length cDNA Encoding a G Protein [alpha] Subunit, SGA1, from Soybean

1995 ◽  
Vol 108 (3) ◽  
pp. 1315-1316 ◽  
Author(s):  
W. Y. Kim ◽  
N. E. Cheong ◽  
D. C. Lee ◽  
D. Y. Je ◽  
J. D. Bahk ◽  
...  
Keyword(s):  
G Protein ◽  
Full Length ◽  
Alpha Subunit ◽  
Sequencing Analysis ◽  
Cloning And Sequencing ◽  
Full Length Cdna ◽  
G Protein Alpha Subunit ◽  
Protein Alpha Subunit

Cloning, characterisation and expression profile of kisspeptin1 and the kisspeptin1 receptor in the hypothalamic–pituitary–ovarian axis of Chinese alligator Alligator sinensis during the reproductive cycle

2020 ◽  
Vol 32 (8) ◽  
pp. 792 ◽  
Author(s):  
Ruidong Zhang ◽  
Haitao Nie ◽  
Shulong Duan ◽  
Peng Yan ◽  
Ali Izaz ◽  
...  
Keyword(s):  
Amino Acid ◽  
Quantitative Polymerase Chain Reaction ◽  
Reproductive Period ◽  
Full Length ◽  
Reading Frame ◽  
Full Length Cdna ◽  
Cdna Sequences ◽  
Acid Protein ◽  
Amino Acid Precursor ◽  
Alligator Sinensis

Kisspeptin1 (Kiss1), a product of the Kiss1 gene, plays an important role in the regulation of reproduction in vertebrates by activating the Kiss1 receptor (Kiss1R) and its coexpression with gonadotrophin-releasing hormone (GnRH) in GnRH neurons. The purpose of this study was to clone the Kiss1 and Kiss1R genes found in the brain of Alligator sinensis and to explore their relationship with reproduction. The full-length cDNA of Kiss1 is 816bp, the open reading frame (ORF) is 417bp and the gene encodes a 138-amino acid precursor protein. The full-length cDNA of Kiss1R is 2348bp, the ORF is 1086bp and the gene encodes a 361-amino acid protein. Quantitative polymerase chain reaction showed that, except for Kiss1R expression in the hypothalamus, the expression of Kiss1 and Kiss1Rduring the reproductive period of A. sinensis was higher than that in the hypothalamus, pituitary gland and ovary during the hibernation period. The changes in GnRH2 mRNA in the hypothalamus were similar to those of GnRH1 and peaked during the reproductive period. This study confirms the existence of Kiss1 and Kiss1R in A. sinensis and the findings strongly suggest that Kiss1 and Kiss1R may participate in the regulation of GnRH secretion in the hypothalamus of alligators during the reproductive period. Furthermore, this is the first report of the full-length cDNA sequences of Kiss1 and Kiss1R in reptiles.

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 Gene Organization in Rice Revealed by Full-Length cDNA Mapping and Gene Expression Analysis through Microarray

PLoS ONE ◽  
2007 ◽  
Vol 2 (11) ◽  
pp. e1235 ◽  
Author(s):  
Kouji Satoh ◽  
Koji Doi ◽  
Toshifumi Nagata ◽  
Naoki Kishimoto ◽  
Kohji Suzuki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Gene Organization ◽  
Full Length ◽  
Full Length Cdna

scholarly journals Full-length cDNA sequences from Rhesus monkey placenta tissue: analysis and utility for comparative mapping

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 427 ◽  
Author(s):  
Dae-Soo Kim ◽  
Jae-Won Huh ◽  
Young-Hyun Kim ◽  
Sang-Je Park ◽  
Sang-Rae Lee ◽  
...  
Keyword(s):  
Rhesus Monkey ◽  
Comparative Mapping ◽  
Full Length ◽  
Tissue Analysis ◽  
Full Length Cdna ◽  
Cdna Sequences

scholarly journals Generation and comparative analysis of full-length transcriptomes in sweetpotato and its putative wild ancestor I. trifida

2017 ◽  
Author(s):  
Yonghai Luo ◽  
Na Ding ◽  
Xuan Shi ◽  
Yunxiang Wu ◽  
Ruyuan Wang ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Ipomoea Batatas ◽  
Large Scale ◽  
Full Length ◽  
Open Reading Frames ◽  
High Quality ◽  
Evolutionary Pattern ◽  
Full Length Cdna ◽  
Cdna Sequences ◽  
Public Datasets

AbstractSweetpotato [Ipomoea batatas (L.) Lam.] is one of the most important crops in many developing countries and provides a candidate source of bioenergy. However, neither high-quality reference genome nor large-scale full-length cDNA sequences for this outcrossing hexaploid are still lacking, which in turn impedes progress in research studies in sweetpotato functional genomics and molecular breeding. In this study, we apply a combination of second- and third-generation sequencing technologies to sequence full-length transcriptomes in sweetpotato and its putative ancestor I. trifida. In total, we obtained 53,861/51,184 high-quality transcripts, which includes 34,963/33,637 putative full-length cDNA sequences, from sweetpotato/I. trifida. Amongst, we identified 104,540/94,174 open reading frames, 1476/1475 transcription factors, 25,315/27,090 simple sequence repeats, 417/531 long non-coding RNAs out of the sweetpotato/I. trifida dataset. By utilizing public available genomic contigs, we analyzed the gene features (including exon number, exon size, intron number, intron size, exon-intron structure) of 33,119 and 32,793 full-length transcripts in sweetpotato and I. trifida, respectively. Furthermore, comparative analysis between our transcript datasets and other large-scale cDNA datasets from different plant species enables us assessing the quality of public datasets, estimating the genetic similarity across relative species, and surveyed the evolutionary pattern of genes. Overall, our study provided fundamental resources of large-scale full-length transcripts in sweetpotato and its putative ancestor, for the first time, and would facilitate structural, functional and comparative genomics studies in this important crop.

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