[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 …

De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms–a brief guide

DJ Jackson, N Cerveau, N Posnien - Frontiers in Zoology, 2024 - Springer
Many questions in biology benefit greatly from the use of a variety of model systems. High-
throughput sequencing methods have been a triumph in the democratization of diverse …

Modern venomics—Current insights, novel methods, and future perspectives in biological and applied animal venom research

BM von Reumont, G Anderluh, A Antunes… - …, 2022 - academic.oup.com
Venoms have evolved> 100 times in all major animal groups, and their components, known
as toxins, have been fine-tuned over millions of years into highly effective biochemical …

Proteome metabolome and transcriptome data for three Symbiodiniaceae under ambient and heat stress conditions

EF Camp, T Kahlke, B Signal, CA Oakley, A Lutz… - Scientific data, 2022 - nature.com
The Symbiodiniaceae are a taxonomically and functionally diverse family of marine
dinoflagellates. Their symbiotic relationship with invertebrates such as scleractinian corals …

[PDF][PDF] The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity

JR Pardos-Blas, I Irisarri, S Abalde, CML Afonso… - …, 2021 - academic.oup.com
Background Venoms are deadly weapons to subdue prey or deter predators that have
evolved independently in many animal lineages. The genomes of venomous animals are …

The genome of the reef-building glass sponge Aphrocallistes vastus provides insights into silica biomineralization

WR Francis, M Eitel, S Vargas… - Royal Society …, 2023 - royalsocietypublishing.org
Well-annotated and contiguous genomes are an indispensable resource for understanding
the evolution, development, and metabolic capacities of organisms. Sponges, an …

A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data

S Abalde, U Jondelius - Systematic Biology, 2025 - academic.oup.com
Xenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many
structures typical of other bilaterians. Xenacoelomorphs—which include three main groups …

Transcriptomic analysis across crayfish (Cherax quadricarinatus) claw regeneration reveals potential stem cell sources for cultivated crustacean meat

L Musgrove, A Bhojwani, C Hyde… - International …, 2024 - pmc.ncbi.nlm.nih.gov
In the face of rising global demand and unsustainable production methods, cultivated
crustacean meat (CCM) is proposed as an alternative means to produce delicious lobster …

A novel target‐enriched multilocus assay for sponges (Porifera): Red Sea Haplosclerida (Demospongiae) as a test case

J van der Sprong, NJ de Voogd… - Molecular Ecology …, 2024 - Wiley Online Library
With declining biodiversity worldwide, a better understanding of species diversity and their
relationships is imperative for conservation and management efforts. Marine sponges are …

Alphaflexivirus genomes in stony coral tissue loss disease-affected, disease-exposed, and disease-unexposed coral colonies in the US Virgin Islands

AJ Veglia, K Beavers, EW Van Buren… - Microbiology …, 2022 - journals.asm.org
Stony coral tissue loss disease (SCTLD) is decimating Caribbean corals. Here, through the
metatranscriptomic assembly and annotation of two alphaflexivirus-like strains, we provide …