scholarly journals Elucidating genes involved in sesquiterpenoid and flavonoid biosynthetic pathways in Saussurea lappa by de novo leaf transcriptome analysis

Genomics ◽  
2019 ◽  
Vol 111 (6) ◽  
pp. 1474-1482 ◽  
Author(s):  
Savita Bains ◽  
Vasundhara Thakur ◽  
Jagdeep Kaur ◽  
Kashmir Singh ◽  
Ravneet Kaur
Gene ◽  
2018 ◽  
Vol 645 ◽  
pp. 146-156 ◽  
Author(s):  
Soumyadev Sarkar ◽  
Somnath Chakravorty ◽  
Avishek Mukherjee ◽  
Debanjana Bhattacharya ◽  
Semantee Bhattacharya ◽  
...  

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0150273 ◽  
Author(s):  
Shivanjali Kotwal ◽  
Sanjana Kaul ◽  
Pooja Sharma ◽  
Mehak Gupta ◽  
Rama Shankar ◽  
...  

Author(s):  
V. C. de Souza ◽  
M. M. Aragão ◽  
L. S. Tavares ◽  
P. V. S. Z. Capriles ◽  
L. F. Viccini ◽  
...  

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Inés González-Castellano ◽  
Chiara Manfrin ◽  
Alberto Pallavicini ◽  
Andrés Martínez-Lage

Abstract Background The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. Results A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. Conclusions This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.


2021 ◽  
Vol 12 ◽  
Author(s):  
Tao Liu ◽  
Xiaoting Liu ◽  
Rangrang Zhou ◽  
Hong Chen ◽  
Huaigang Zhang ◽  
...  

Selenium is an essential microelement for humans and animals. The specific processing technique of oats can maximize the preservation of its nutrients. In this study, to understand the genetic response of oats in a high-selenium environment, oats were treated with sodium selenate for 24 h, and transcriptome analysis was performed. A total of 211,485,930 clean reads composing 31.30 Gb of clean data were retained for four samples. After assembly, 186,035 unigenes with an average length of 727 bp were generated, and the N50 length was 1,149 bp. Compared with that in the control group, the expression of 7,226 unigenes in the treatment group was upregulated, and 2,618 unigenes were downregulated. Based on the sulfur assimilation pathway and selenocompound metabolic pathway, a total of 27 unigenes related to selenate metabolism were identified. Among them, the expression of both key genes APS (ATP sulfurylase) and APR (adenosine 5′-phosphosulfate reductase) was upregulated more than 1,000-fold under selenate treatment, while that of CBL (cystathionine-β-synthase) was upregulated 3.12-fold. Based on the transcriptome analysis, we suspect that the high-affinity sulfur transporter Sultr1;2 plays a key role in selenate uptake in oats. A preliminary regulatory mechanism explains the oat response to selenate treatment was ultimately proposed based on the transcriptome analysis and previous research.


2012 ◽  
Vol 109 ◽  
pp. 282-286 ◽  
Author(s):  
Masato Baba ◽  
Motohide Ioki ◽  
Nobuyoshi Nakajima ◽  
Yoshihiro Shiraiwa ◽  
Makoto M. Watanabe

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