TY - JOUR
T1 - Identification of genuine and novel miRNAs in Amaranthus hypochondriacus from high-throughput sequencing data
AU - Martínez Núñez, Marcelino
AU - Ruíz Rivas, Magali
AU - Gregorio Jorge, Josefat
AU - Hernández, Pedro Fernando Vera
AU - Luna Suárez, Silvia
AU - de Folter, Stefan
AU - Chávez Montes, Ricardo A.
AU - Rosas Cárdenas, Flor de Fátima
N1 - Publisher Copyright:
© 2020
PY - 2021/1
Y1 - 2021/1
N2 - Amaranth has been proposed as an exceptional alternative for food security and climate change mitigation. Information about the distribution, abundance, or specificity of miRNAs in amaranth species is scare. Here, small RNAs from seedlings under control, drought, heat, and cold stress conditions of the Amaranthus hypocondriacus variety “Gabriela” were sequenced and miRNA loci identified in the amaranth genome using the ShortStack software. Fifty-three genuine miRNA clustersthirty-nine belonging to conserved families, and fourteen novel, were identified. Identification of their target genes suggests that conserved amaranth miRNAs are involved in growth and developmental processes, as well as stress responses. MiR0005, an amaranth-specific miRNA, exhibited an unusual high level of expression, akin to that of conserved miRNAs. Overall, our results broaden our knowledge regarding the distribution, abundance and expression of miRNAs in amaranth, providing the basis for future research on miRNAs and their functions in this important species.
AB - Amaranth has been proposed as an exceptional alternative for food security and climate change mitigation. Information about the distribution, abundance, or specificity of miRNAs in amaranth species is scare. Here, small RNAs from seedlings under control, drought, heat, and cold stress conditions of the Amaranthus hypocondriacus variety “Gabriela” were sequenced and miRNA loci identified in the amaranth genome using the ShortStack software. Fifty-three genuine miRNA clustersthirty-nine belonging to conserved families, and fourteen novel, were identified. Identification of their target genes suggests that conserved amaranth miRNAs are involved in growth and developmental processes, as well as stress responses. MiR0005, an amaranth-specific miRNA, exhibited an unusual high level of expression, akin to that of conserved miRNAs. Overall, our results broaden our knowledge regarding the distribution, abundance and expression of miRNAs in amaranth, providing the basis for future research on miRNAs and their functions in this important species.
KW - Abiotic stress
KW - Amaranth
KW - ShortStack
KW - Small RNA sequencing
KW - miRNA
KW - miRNA loci
UR - http://www.scopus.com/inward/record.url?scp=85097249395&partnerID=8YFLogxK
U2 - 10.1016/j.ygeno.2020.11.027
DO - 10.1016/j.ygeno.2020.11.027
M3 - Artículo
C2 - 33271330
AN - SCOPUS:85097249395
SN - 0888-7543
VL - 113
SP - 88
EP - 103
JO - Genomics
JF - Genomics
IS - 1
ER -