[PDF][PDF] A simple guide to de novo transcriptome assembly and annotation

V Raghavan, L Kraft, F Mesny… - Briefings in …, 2022 - academic.oup.com
A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily
attainable proxy catalog of protein-coding genes when genome assembly is unnecessary …

Diversification of mammalian deltaviruses by host shifting

LM Bergner, RJ Orton, A Broos… - Proceedings of the …, 2021 - National Acad Sciences
Hepatitis delta virus (HDV) is an unusual RNA agent that replicates using host machinery
but exploits hepatitis B virus (HBV) to mobilize its spread within and between hosts. In doing …

Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

KM Nip, S Hafezqorani, KK Gagalova, R Chiu… - Nature …, 2023 - nature.com
Long-read sequencing technologies have improved significantly since their emergence.
Their read lengths, potentially spanning entire transcripts, is advantageous for …

Advances in long-read single-cell transcriptomics

P Kumari, M Kaur, K Dindhoria, B Ashford… - Human Genetics, 2024 - Springer
Long-read single-cell transcriptomics (scRNA-Seq) is revolutionizing the way we profile
heterogeneity in disease. Traditional short-read scRNA-Seq methods are limited in their …

Identification and analysis of odorant receptors expressed in the two main olfactory organs, antennae and palps, of Schistocerca americana

A Boronat-Garcia, J Iben, E Dominguez-Martin… - Scientific Reports, 2022 - nature.com
Locusts depend upon their sense of smell and provide useful models for understanding
olfaction. Extending this understanding requires knowledge of the molecular and structural …

Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas

WE Gordon, S Baek, HP Nguyen, YM Kuo… - Nature …, 2024 - nature.com
Frugivory evolved multiple times in mammals, including bats. However, the cellular and
molecular components driving it remain largely unknown. Here, we use integrative single …

De novo transcriptome assemblies of C3 and C4 non-model grass species reveal key differences in leaf development

S Prochetto, AJ Studer, R Reinheimer - BMC genomics, 2023 - Springer
Background C4 photosynthesis is a mechanism that plants have evolved to reduce the rate
of photorespiration during the carbon fixation process. The C4 pathway allows plants to …

Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats

YT Gutierrez-Guerrero, E Ibarra-Laclette… - …, 2020 - academic.oup.com
Abstract Background The New World leaf-nosed bats (Phyllostomids) exhibit a diverse
spectrum of feeding habits and innovations in their nutrient acquisition and foraging …

Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis

J Cheng, X Cao, X Wang, J Wang, B Yue… - Journal of Animal …, 2023 - Springer
Background Sharply increased beef consumption is propelling the genetic improvement
projects of beef cattle in China. Three-dimensional genome structure is confirmed to be an …

Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing

AM Lizano, I Smolina, M Choquet, M Kopp… - Ecology and …, 2022 - Wiley Online Library
Copepods of the zooplankton genus Calanus play a key role in marine ecosystems in the
northern seas. Although being among the most studied organisms on Earth, due to their …