Transcriptome profiling of peanut gynophores revealed global reprogramming of gene expression during early pod development in darkness

Abstract

BackgroundAfter the zygote divides few times, the development of peanut pre-globular embryo and fruit is arrested under white or red light. Embryo development could be resumed in dark condition after gynophore is buried in soil. It is interesting to study the mechanisms of gynophore development and pod formation in peanut.ResultsIn this study, transcriptome analysis of peanut gynophore was performed using Illumina HiSeq™ 2000 to understand the mechanisms of geocarpy. More than 13 million short sequences were assembled into 72527 unigenes with average size of 394 bp. A large number of genes that were not identified previously in peanut EST projects were identified in this study, including most genes involved in plant circadian rhythm, intra-cellular transportation, plant spliceosome, eukaryotes basal transcription factors, genes encoding ribosomal proteins, brassinosteriod biosynthesis, light-harvesting chlorophyll protein complex, phenylpropanoid biosynthesis and TCA cycle. RNA-seq based gene expression profiling results showed that before and after gynophore soil penetration, the transcriptional level of a large number of genes changed significantly. Genes encoding key enzymes for hormone metabolism, signaling, photosynthesis, light signaling, cell division and growth, carbon and nitrogen metabolism as well as genes involved in stress responses were high lighted.ConclusionsTranscriptome analysis of peanut gynophore generated a large number of unigenes which provide useful information for gene cloning and expression study. Digital gene expression study suggested that gynophores experience global changes and reprogram from light to dark grown condition to resume embryo and fruit development.

Identification and expression dynamics of three WUSCHEL related homeobox 13 (WOX13) genes in peanut

“…Cloning and characterization of peanut WOX13 subfamily genes Three WOX13 subfamily gene cDNAs were identified from peanut transcriptome data (BioProject: PRJNA181974) (Xia et al 2013) and named as AhWOX13A, AhWOX13B1, and AhWOX13B2. WOX13A contains an ORF of 630 bp, encoding a 209 amino acid polypeptide.…”

“…Cultivated peanut is allotetraploid (AABB, 4n=4x=40) which originated from a single hybridization event between AA and BB wild species and subsequently underwent spontaneous genome duplication (Stalker and Simpson 1995;Moretzsohn et al 2013;Kochert et al 1996;Ferguson et al 2005;Freitas et al 2007;Gregory and Gregory 1979;Hammons 1982;Knauft and Gorbet 1995). Peanut gynophore is a specialized and unique organ that carries and eventually pushes the fertilized ovules into the soil in order for seed and fruit development to occur (Xia et al 2013;Moctezuma 2003). The peanut gynophore has a typical shoot anatomy and responds positively to gravity, similar to a typical primary root (Moctezuma and Feldman 1998;Moctezuma and Feldman 1999).…”

Cloning and characterization of SPL-family genes in the peanut (Arachis hypogaea L.)

“…Peanut pod swelling is a complicated process that is controlled by several plant hormones, such as auxin, GA, ethylene, and abscisic acid (Xia et al, 2013). Previous studies have shown that AtSPL3 and AtSPL8 affect endogenous GA levels and signaling in Arabidopsis.…”

“…Peanut is an important global oil crop and protein source. Peanut plant flowers and finishes pollination above ground as do other plants, while the ovule-carrying peg (gynophore) starts to form above ground and then grows downwards to bury the fertilized ovule in the soil for pod development (Thompson et al, 1985;Xia et al, 2013;Zhu et al, 2014). In this study, we identified 15 potential peanut SPLs that all contained a conserved SBP domain.…”

Gynophore miRNA analysis at different developmental stages in Arachis duranensis

“…Chen et al (2013) took advantage of available transcriptome data to detect two cell-aging transcripts that significantly increased in the late stage of unburied gynophores and may participate in the abortion of gynophores on the ground. Xia et al (2013) found that a series of transcripts, including endogenous hormones, respond to optical signals, and that morphogenesis and cell division pathway transcripts showed distinct changes before and after the burying of the gynophore. Zhu et al (2014) compared the transcriptome of the gynophore before and after burying, and described the relevance of changes in expression and hormone levels of GA, IAA, and other hormone-related transcripts.…”