Molecular characterization of a flatworm Girardia isolate from Guanajuato, Mexico

Duncan, Elizabeth M.; Nowotarski, Stephanie H.; Guerrero‐Hernández, Carlos; Ross, E. J.; D'Orazio, Julia A.; Govea-Martínez, Leslie Yareli; Hernández-Fonseca, Cristell; Pérez-Sánchez, Benjamín; Torres-Alba, Israel; Ramirez-Morales, Maria; Navarro-Delgado, Erick; García-Rodríguez, Nohemí Carolina; Plascencia, Arizbeth; Rodríguez-Ortiz, José Luis; Moreno-Ciénega, L. Gerardo; Maciel-Avalos, Adrian; Gallegos-Casillas, Porfirio; Guerrero, Mónica Vázquez; Cruz, Eduardo Zamudio de la; Romero-Partida, Marcos; Martinez-Espinosa, Rodrigo Jonathan; Zuñiga-Arenas, Abigail; Yebra, Sofía Quiroz; Ambriz-Piña, Sara Elena; Segoviano, José; Fernández, Karla; Vázquez, Fernando Longoria; Curtis, Heather Leigh; Angeles-Abores, David; McKinney, Sean A.; McHargue, Mark C.; Guo, Longhua; McClain, Melainia; Alvarado, Alejandro Sánchez

doi:10.1016/j.ydbio.2022.06.003

Cited by 2 publications

(1 citation statement)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Although scientists have been studying these animals for hundreds of years (ELLIOTT AND SANCHEZ ALVARADO 2013) and using forward genetic tools to identify important planarian genes for decades (SANCHEZ ALVARADO AND NEWMARK 1999; NEWMARK AND SANCHEZ ALVARADO 2002;REDDIEN et al 2005), the field is now in a new phase of tool building and transformation. In the last few years, new chromosome level genomes have been assembled (GUO et al 2022;, dozens of transcriptomes for many different species have been constructed (ALMAZAN et al 2018;DUNCAN et al 2022;VILA-FARRE et al 2023), and methods for assaying the chromatin state and dynamics have been optimized (DUNCAN et al 2015;PASCUAL-CARRERAS et al 2023;POULET et al 2023;VERMA et al 2024) to better understand the context in which these genetic blueprints exist in planarian cells.…”

Section: Discussionmentioning

confidence: 99%

RNaseH-based ribodepletion of total planarian RNA improves detection of longer and non-polyadenylated transcripts

Barai,

Biswas,

Verma

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

The overwhelming majority of RNA species isolated from cells or tissues using organic extraction are ribosomal RNAs (rRNA), whereas a relatively small percentage are messenger RNAs (mRNA). For studies that seek to detect mRNA transcripts and measure changes in their expression, this lopsided ratio of desired transcripts to undesired transcripts creates a significant challenge to obtaining sensitive and reproducible results. One method for improving mRNA detection is to selectively amplify polyadenylated (polyA) mRNA molecules when generating RNA-seq libraries, a strategy that is generally very successful in many species. However, this strategy is less effective when starting with total RNA from some species e.g., the planarian species Schmidtea mediterranea (S.med), as it generates libraries that still contain significant and variable amounts of rRNA reads. Further, commercially available ribodepletion kits do not efficiently deplete rRNAs from these samples because their sequences are divergent from mammalian rRNAs. Here we report a customized, optimized, and economical ribodepletion strategy than allows the generation of comprehensive RNA-seq libraries with less than one percent rRNA contamination. We show that this method improves transcript detection, particularly for those without polyA tails (e.g., core histones) and those that are relatively long (e.g., microtubule motor proteins). Using this custom ribodepletion approach, we also detected many transcripts that are not represented in the most recent set of S.med gene annotations, including a subset that are likely expressed transposable elements (TEs). To facilitate future differential expression analyses of these newly identified loci, we created both an annotation file of the new loci we identified and a bioinformatic pipeline for generating additional annotations from future libraries. As significant recent research shows that TE activation is regulated and functionally important, the resources provided here will provide a starting point for investigating such mechanisms in planarians and other species with less conserved rRNA sequences.

show abstract