de novo transcriptome assembly  (Novogene)

Journal: mBio

Article Title: Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera

doi: 10.1128/mbio.03916-24

Figure Lengend Snippet: Images of foraminifera isolated in the Katz lab. Cells are organized roughly taxonomically and with all but three (labeled “exemplar”) pictures of individuals isolated for transcriptomes. Tubothalamids: (a) Miliammina- like sp. 1; (b, c) Miliammina sp. 1; (d) Miliammina sp. 2; (e, f) Triloculina sp.; (g, h) Quinqueloculina sp.; (i) Ammodiscus sp. Globothalamids: (j) Reophax -like; (k) a Trochammina test that we infer contained a Vellaria -like monothalamid squatter (see text); (l, m) Trochammina -like sp. 1; (n) Trochammina -like sp. 2; (o) Haynesina -like; (p) exemplar image of Haynesina orbiculare ; (q–s) Ammonia sp. 1; (t, u) Ammonia sp. 2; (v) Ammonia sp. 3. Monothalamids: (w) exemplar image of Allogromia arnoldi ; (x) freshwater foram; (y) Notodendrodes hyalinosphaira ; (z-aa) Psammophaga sp. Note that these images were taken efficiently ahead of RNA isolation for transcriptomics, and they are intended only to provide an overview of test morphology; all cells showed active pseudopods at the time of isolation.

Article Snippet: We performed a second round of data curation to address known issues with short-read Illumina data and de novo transcriptome assembly (e.g., cross-contamination by other samples, misassembly of transcripts, presence of partial transcripts).

Techniques: Isolation, Labeling

Journal: Scientific Reports

Article Title: Continuous cell lines derived from the Asian citrus psyllid, Diaphorina citri, harbor viruses and Wolbachia

doi: 10.1038/s41598-024-83671-2

Figure Lengend Snippet: Overview of continuous Diaphorina citri cell lines.

Article Snippet: Cell pellets of Dici1 (P18) and Dici3 (P24) containing approximately 4 × 10 6 cells each were shipped to Azenta/GENEWIZ for RNA extraction, transcriptomic sequencing, and de novo transcriptome assembly.

Techniques: Passaging

Journal: bioRxiv

Article Title: UnigeneFinder: An automated pipeline for gene calling from transcriptome assemblies without a reference genome

doi: 10.1101/2024.08.19.608648

Figure Lengend Snippet: A summary of the approximate numbers of species (A) and general availability of transcriptome data versus reference genome assemblies (B) for four major clades of organisms. The gap between the number of species with RNA-seq data available and those with high-quality reference genomes remains large for major groups of organisms. In the species-rich Arthropoda, Embryophyta, Fungi, and Vertebrata clades, containing around 1.2 million, 400 thousand, 150 thousand, and 75 thousand species, respectively, there are between 4 and 11-fold more species with transcriptome data than with reference genomes. Numbers of species with RNA-seq and genomic data were obtained from NCBI, and numbers of described species were obtained from the IUCN Red List Summary Statistics (iucnredlist.org/resources/summary-statistics).

Article Snippet: Sequence inflation of this nature is typical of raw de novo transcriptome assemblies, both provided by sequencing companies such as NovoGene and generated in house.

Techniques: RNA Sequencing