scholarly journals Transcriptome analysis of Euonymus europaeus fruits at different stages of development

2020 ◽  
Author(s):  
O. S. Pavlenko ◽  
N. S. Sadovskaya ◽  
O. N. Mustafayev ◽  
Yu. V. Akashkina ◽  
I. V. Goldenkova-Pavlova
Keyword(s):  
Comparative Analysis ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Globular Embryo ◽  
Mature Fruit ◽  
Stages Of Development ◽  
Euonymus Europaeus

The transcript Euonymus europaeus was collected de novo. A comparative analysis of transcriptomes from the stage of the globular embryo and the mature fruit made it possible to identify key DGAT genes at the contrasting stages of the development of E. europaeus fruits.

scholarly journals Transcriptome Analysis of the Emerald Ash Borer (EAB), Agrilus planipennis: De Novo Assembly, Functional Annotation and Comparative Analysis

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0134824 ◽  
Author(s):  
Jun Duan ◽  
Tim Ladd ◽  
Daniel Doucet ◽  
Michel Cusson ◽  
Kees vanFrankenhuyzen ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Transcriptome Analysis ◽  
De Novo Assembly ◽  
Functional Annotation ◽  
De Novo ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis

scholarly journals Extended snake venomics by top-down in-source decay: Investigating the newly discovered Anatolian Meadow viper subspecies, Vipera anatolica senliki

2019 ◽  
Author(s):  
Benjamin-Florian Hempel ◽  
Maik Damm ◽  
Mrinalini ◽  
Bayram Göçmen ◽  
Mert Karış ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Comparative Analysis ◽  
Disulfide Bond ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Venom Gland ◽  
Top Down ◽  
Venom Toxin ◽  
Snake Venomics ◽  
Insight Into

AbstractHerein we report on the venom proteome of Vipera anatolica senliki, a recently discovered and hitherto unexplored subspecies of the critically endangered Anatolian Meadow viper endemic to the Antalya Province of Turkey. Integrative venomics, including venom gland transcriptomics as well as complementary bottom-up and top-down proteomic analyses, were applied to fully characterize the venom of V. a. senliki. Furthermore, the classical top-down venomics approach was extended to elucidate the venom proteome by an alternative in-source decay (ISD) proteomics workflow using the reducing matrix 1,5-diaminonaphthalene (1,5-DAN). Top-down ISD proteomics allows for disulfide bond mapping as well as effective de novo identification of high molecular weight venom constituents, both of which are difficult to achieve by commonly established top-down approaches. Venom gland transcriptome analysis identified 42 venom transcript annotations from 13 venom toxin families. Relative quantitative snake venomics revealed snake venom metalloproteinases (svMP, 42.9%) as the most abundant protein family, followed by several less dominant toxin families. Online mass profiling and top-down venomics provide a detailed insight into the venom proteome of V. a. senliki and facilitates a comparative analysis of venom variability for the closely related subspecies, V. a. anatolica.TOC Figure

De novo transcriptome analysis of Ammopiptanthus nanus and its comparative analysis with A. mongolicus

Trees ◽  
2017 ◽  
Vol 32 (1) ◽  
pp. 287-300 ◽  
Author(s):  
Fei Gao ◽  
Huayun Li ◽  
Zihua Xiao ◽  
Chunxiang Wei ◽  
Jinchao Feng ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Transcriptome Analysis ◽  
De Novo ◽  
De Novo Transcriptome ◽  
Ammopiptanthus Nanus

De novo RNA-Seq based transcriptome analysis of Papiliotrema laurentii strain RY1 under nitrogen starvation

Gene ◽  
2018 ◽  
Vol 645 ◽  
pp. 146-156 ◽  
Author(s):  
Soumyadev Sarkar ◽  
Somnath Chakravorty ◽  
Avishek Mukherjee ◽  
Debanjana Bhattacharya ◽  
Semantee Bhattacharya ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Nitrogen Starvation ◽  
De Novo ◽  
Rna Seq

scholarly journals De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0150273 ◽  
Author(s):  
Shivanjali Kotwal ◽  
Sanjana Kaul ◽  
Pooja Sharma ◽  
Mehak Gupta ◽  
Rama Shankar ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Rna Seq ◽  
Plantago Ovata ◽  
De Novo Transcriptome

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
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Biosynthetic Pathways ◽  
Saussurea Lappa ◽  
Leaf Transcriptome

scholarly journals De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Inés González-Castellano ◽  
Chiara Manfrin ◽  
Alberto Pallavicini ◽  
Andrés Martínez-Lage
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Specific Expression ◽  
Development Processes ◽  
The Common

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.

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