Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development

Kathleen DeBoer, Su Melser, Jana Sperschneider, Lars G. Kamphuis, Gagan Garg, Ling-Ling Gao, Karen Frick, Karam B. Singh

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown.

By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. We observed up-regulation of members of the miRNA families miR167, miR399, miR156, miR319 and miR164 in narrow-leafed lupin seeds, and confirmed expression of miR156, miR166, miR164, miR1507 and miR396 using quantitative RT-PCR during five narrow-leafed lupin seed development stages. We identified potential targets for the conserved and novel miRNAs and were able to validate targets of miR399 and miR159 using 5' RLM-RACE. The conserved miRNAs are predicted to predominately target transcription factors and 93% of the conserved miRNAs originate from intergenic regions. In contrast, only 43% of the novel miRNAs originate from intergenic regions and their predicted targets were more functionally diverse.

This study provides important insights into the miRNA gene regulatory networks during narrow-leafed lupin seed development.

Original languageEnglish
Article number135
Number of pages16
JournalBMC Genomics
Volume20
Issue number1
DOIs
Publication statusPublished - 14 Feb 2019

Cite this

DeBoer, Kathleen ; Melser, Su ; Sperschneider, Jana ; Kamphuis, Lars G. ; Garg, Gagan ; Gao, Ling-Ling ; Frick, Karen ; Singh, Karam B. / Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development. In: BMC Genomics. 2019 ; Vol. 20, No. 1.
@article{e6b3d13ccd1045739acfdb0e28b1fa5c,
title = "Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development",
abstract = "Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown.By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. We observed up-regulation of members of the miRNA families miR167, miR399, miR156, miR319 and miR164 in narrow-leafed lupin seeds, and confirmed expression of miR156, miR166, miR164, miR1507 and miR396 using quantitative RT-PCR during five narrow-leafed lupin seed development stages. We identified potential targets for the conserved and novel miRNAs and were able to validate targets of miR399 and miR159 using 5' RLM-RACE. The conserved miRNAs are predicted to predominately target transcription factors and 93{\%} of the conserved miRNAs originate from intergenic regions. In contrast, only 43{\%} of the novel miRNAs originate from intergenic regions and their predicted targets were more functionally diverse.This study provides important insights into the miRNA gene regulatory networks during narrow-leafed lupin seed development.",
keywords = "Gene silencing, Legume, Lupin, microRNAs, Seed development, Small RNAs, CLASS IIIHD-ZIP, SMALL RNAS, DNA METHYLATION, GENE-EXPRESSION, PLANT, ARABIDOPSIS, MIRNA, EVOLUTION, PROTEIN, TRANSCRIPTOME",
author = "Kathleen DeBoer and Su Melser and Jana Sperschneider and Kamphuis, {Lars G.} and Gagan Garg and Ling-Ling Gao and Karen Frick and Singh, {Karam B.}",
year = "2019",
month = "2",
day = "14",
doi = "10.1186/s12864-019-5521-8",
language = "English",
volume = "20",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development. / DeBoer, Kathleen; Melser, Su; Sperschneider, Jana; Kamphuis, Lars G.; Garg, Gagan; Gao, Ling-Ling; Frick, Karen; Singh, Karam B.

In: BMC Genomics, Vol. 20, No. 1, 135, 14.02.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development

AU - DeBoer, Kathleen

AU - Melser, Su

AU - Sperschneider, Jana

AU - Kamphuis, Lars G.

AU - Garg, Gagan

AU - Gao, Ling-Ling

AU - Frick, Karen

AU - Singh, Karam B.

PY - 2019/2/14

Y1 - 2019/2/14

N2 - Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown.By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. We observed up-regulation of members of the miRNA families miR167, miR399, miR156, miR319 and miR164 in narrow-leafed lupin seeds, and confirmed expression of miR156, miR166, miR164, miR1507 and miR396 using quantitative RT-PCR during five narrow-leafed lupin seed development stages. We identified potential targets for the conserved and novel miRNAs and were able to validate targets of miR399 and miR159 using 5' RLM-RACE. The conserved miRNAs are predicted to predominately target transcription factors and 93% of the conserved miRNAs originate from intergenic regions. In contrast, only 43% of the novel miRNAs originate from intergenic regions and their predicted targets were more functionally diverse.This study provides important insights into the miRNA gene regulatory networks during narrow-leafed lupin seed development.

AB - Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown.By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. We observed up-regulation of members of the miRNA families miR167, miR399, miR156, miR319 and miR164 in narrow-leafed lupin seeds, and confirmed expression of miR156, miR166, miR164, miR1507 and miR396 using quantitative RT-PCR during five narrow-leafed lupin seed development stages. We identified potential targets for the conserved and novel miRNAs and were able to validate targets of miR399 and miR159 using 5' RLM-RACE. The conserved miRNAs are predicted to predominately target transcription factors and 93% of the conserved miRNAs originate from intergenic regions. In contrast, only 43% of the novel miRNAs originate from intergenic regions and their predicted targets were more functionally diverse.This study provides important insights into the miRNA gene regulatory networks during narrow-leafed lupin seed development.

KW - Gene silencing

KW - Legume

KW - Lupin

KW - microRNAs

KW - Seed development

KW - Small RNAs

KW - CLASS IIIHD-ZIP

KW - SMALL RNAS

KW - DNA METHYLATION

KW - GENE-EXPRESSION

KW - PLANT

KW - ARABIDOPSIS

KW - MIRNA

KW - EVOLUTION

KW - PROTEIN

KW - TRANSCRIPTOME

U2 - 10.1186/s12864-019-5521-8

DO - 10.1186/s12864-019-5521-8

M3 - Article

VL - 20

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 135

ER -