Repositorio Institucional
Repositorio Institucional
CONICET Digital
  • Inicio
  • EXPLORAR
    • AUTORES
    • DISCIPLINAS
    • COMUNIDADES
  • Estadísticas
  • Novedades
    • Noticias
    • Boletines
  • Ayuda
    • General
    • Datos de investigación
  • Acerca de
    • CONICET Digital
    • Equipo
    • Red Federal
  • Contacto
JavaScript is disabled for your browser. Some features of this site may not work without it.
  • INFORMACIÓN GENERAL
  • RESUMEN
  • ESTADISTICAS
 
Artículo

Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing

Guan, Dailu; Halstead, Michelle M.; Islas Trejo, Alma D.; Goszczynski, Daniel EstanislaoIcon ; Cheng, Hans H.; Ross, Pablo J.; Zhou, Huaijun
Fecha de publicación: 10/2022
Editorial: Frontiers Media
Revista: Frontiers in Genetics
ISSN: 1664-8021
Idioma: Inglés
Tipo de recurso: Artículo publicado
Clasificación temática:
Ciencias Veterinarias

Resumen

To identify and annotate transcript isoforms in the chicken genome, we generated Nanopore long-read sequencing data from 68 samples that encompassed 19 diverse tissues collected from experimental adult male and female White Leghorn chickens. More than 23.8 million reads with mean read length of 790 bases and average quality of 18.2 were generated. The annotation and subsequent filtering resulted in the identification of 55,382 transcripts at 40,547 loci with mean length of 1,700 bases. We predicted 30,967 coding transcripts at 19,461 loci, and 16,495 lncRNA transcripts at 15,512 loci. Compared to existing reference annotations, we found ∼52% of annotated transcripts could be partially or fully matched while ∼47% were novel. Seventy percent of novel transcripts were potentially transcribed from lncRNA loci. Based on our annotation, we quantified transcript expression across tissues and found two brain tissues (i.e., cerebellum and cortex) expressed the highest number of transcripts and loci. Furthermore, ∼22% of the transcripts displayed tissue specificity with the reproductive tissues (i.e., testis and ovary) exhibiting the most tissue-specific transcripts. Despite our wide sampling, ∼20% of Ensembl reference loci were not detected. This suggests that deeper sequencing and additional samples that include different breeds, cell types, developmental stages, and physiological conditions, are needed to fully annotate the chicken genome. The application of Nanopore sequencing in this study demonstrates the usefulness of long-read data in discovering additional novel loci (e.g., lncRNA loci) and resolving complex transcripts (e.g., the longest transcript for the TTN locus).
Palabras clave: ANNOTATION , CHICKEN , LONG-READ SEQUENCING , NANOPORE , TRANSCRIPT ISOFORM , TRANSCRIPTOME
Ver el registro completo
 
Archivos asociados
Thumbnail
 
Tamaño: 1.959Mb
Formato: PDF
.
Descargar
Licencia
info:eu-repo/semantics/openAccess Excepto donde se diga explícitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
Identificadores
URI: http://hdl.handle.net/11336/206976
DOI: http://dx.doi.org/10.3389/fgene.2022.997460
Colecciones
Articulos(IGEVET)
Articulos de INST.DE GENETICA VET ING FERNANDO NOEL DULOUT
Citación
Guan, Dailu; Halstead, Michelle M.; Islas Trejo, Alma D.; Goszczynski, Daniel Estanislao; Cheng, Hans H.; et al.; Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing; Frontiers Media; Frontiers in Genetics; 13; 10-2022; 1-13
Compartir
Altmétricas
 

Enviar por e-mail
Separar cada destinatario (hasta 5) con punto y coma.
  • Facebook
  • X Conicet Digital
  • Instagram
  • YouTube
  • Sound Cloud
  • LinkedIn

Los contenidos del CONICET están licenciados bajo Creative Commons Reconocimiento 2.5 Argentina License

https://www.conicet.gov.ar/ - CONICET

Inicio

Explorar

  • Autores
  • Disciplinas
  • Comunidades

Estadísticas

Novedades

  • Noticias
  • Boletines

Ayuda

Acerca de

  • CONICET Digital
  • Equipo
  • Red Federal

Contacto

Godoy Cruz 2290 (C1425FQB) CABA – República Argentina – Tel: +5411 4899-5400 repositorio@conicet.gov.ar
TÉRMINOS Y CONDICIONES