De novo assembly and annotation of the retinal transcriptome for the Nile grass rat (Arvicanthis ansorgei).
PLoS One
; 12(7): e0179061, 2017.
Article
en En
| MEDLINE
| ID: mdl-28759564
ABSTRACT
Cone photoreceptors are required for color vision and high acuity vision, and they die in a variety of retinal degenerations, leading to irreversible vision loss and reduced quality of life. To date, there are no approved therapies that promote the health and survival of cones. The development of novel treatments targeting cones has been challenging and impeded, in part, by the limitations inherent in using common rodent model organisms, which are nocturnal and rod-dominant, to study cone biology. The African Nile grass rat (Arvicanthis ansorgei), a diurnal animal whose photoreceptor population is more than 30% cones, offers significant potential as a model organism for the study of cone development, biology, and degeneration. However, a significant limitation in using the A. ansorgei retina for molecular studies is that A. ansorgei does not have a sequenced genome or transcriptome. Here we present the first de novo assembled and functionally annotated transcriptome for A. ansorgei. We performed RNA sequencing for A. ansorgei whole retina to a depth of 321 million pairs of reads and assembled 400,584 Trinity transcripts. Transcriptome-wide analyses and annotations suggest that our data set confers nearly full length coverage for the majority of retinal transcripts. Our high quality annotated transcriptome is publicly available, and we hope it will facilitate wider usage of A. ansorgei as a model organism for molecular studies of cone biology and retinal degeneration.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Retina
/
Células Fotorreceptoras Retinianas Conos
/
Murinae
/
Transcriptoma
Aspecto:
Patient_preference
Límite:
Animals
Idioma:
En
Revista:
PLoS One
Asunto de la revista:
CIENCIA
/
MEDICINA
Año:
2017
Tipo del documento:
Article
País de afiliación:
Estados Unidos