De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

BJ Haas, A Papanicolaou, M Yassour, M Grabherr… - Nature protocols, 2013 - nature.com
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the
need for a genome sequence; this approach can be usefully applied, for instance, in …

Transcriptomic responses to environmental change in fishes: insights from RNA sequencing

RA Oomen, JA Hutchings - Facets, 2017 - facetsjournal.com
The need to better understand how plasticity and evolution affect organismal responses to
environmental variability is paramount in the face of global climate change. The potential for …

Assessing De Novo transcriptome assembly metrics for consistency and utility

ST O'Neil, SJ Emrich - BMC genomics, 2013 - Springer
Background Transcriptome sequencing and assembly represent a great resource for the
study of non-model species, and many metrics have been used to evaluate and compare …

SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

H Lopez-Maestre, L Brinza, C Marchet… - Nucleic Acids …, 2016 - academic.oup.com
Abstract SNPs (Single Nucleotide Polymorphisms) are genetic markers whose precise
identification is a prerequisite for association studies. Methods to identify them are currently …

Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

Y Hara, K Tatsumi, M Yoshida, E Kajikawa, H Kiyonari… - BMC genomics, 2015 - Springer
Background RNA-seq enables gene expression profiling in selected spatiotemporal
windows and yields massive sequence information with relatively low cost and time …

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery

M Moazzzam Jazi, SM Seyedi, E Ebrahimie… - BMC genomics, 2017 - Springer
Abstract Background Pistachio (Pistacia vera L.) is one of the most important commercial nut
crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in …

A de novo transcriptome of the Malpighian tubules in non-blood-fed and blood-fed Asian tiger mosquitoes Aedes albopictus: insights into diuresis, detoxification, and …

CJ Esquivel, BJ Cassone, PM Piermarini - PeerJ, 2016 - peerj.com
Background. In adult female mosquitoes, the renal (Malpighian) tubules play an important
role in the post-prandial diuresis, which removes excess ions and water from the …

Coleoptera genome and transcriptome sequences reveal numerous differences in neuropeptide signaling between species

JA Veenstra - PeerJ, 2019 - peerj.com
Background Insect neuropeptides are interesting for the potential their receptors hold as
plausible targets for a novel generation of pesticides. Neuropeptide genes have been …

Transcriptome Sequencing and Analysis of Wild Amur Ide (Leuciscus waleckii) Inhabiting an Extreme Alkaline-Saline Lake Reveals Insights into Stress Adaptation

J Xu, P Ji, B Wang, L Zhao, J Wang, Z Zhao, Y Zhang… - PloS one, 2013 - journals.plos.org
Background Amur ide (Leuciscus waleckii) is an economically and ecologically important
species in Northern Asia. The Dali Nor population inhabiting Dali Nor Lake, a typical saline …

Molecular Evolution of Glycoside Hydrolase Genes in the Western Corn Rootworm (Diabrotica virgifera virgifera)

S Eyun, H Wang, Y Pauchet, RH Ffrench-Constant… - PloS one, 2014 - journals.plos.org
Cellulose is an important nutritional resource for a number of insect herbivores. Digestion of
cellulose and other polysaccharides in plant-based diets requires several types of enzymes …