Small RNA and Degradome Deep Sequencing Reveals the roles of microRNAs in Seed Expansion in Peanut (Arachis hypogaea L.)
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ABSTRACT:
PROVIDER: PRJNA433116 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6676290.fastq.gz | Fastqsanger.gz | |||
| SRR6676300.fastq.gz | Fastqsanger.gz | |||
| SRR6676291.fastq.gz | Fastqsanger.gz | |||
| SRR6676301.fastq.gz | Fastqsanger.gz | |||
| SRR6676292.fastq.gz | Fastqsanger.gz |
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Project description:Seed expansion in peanut is a complex biological process involving many gene regulatory pathways. MicroRNAs (miRNAs) play important regulatory roles in plant growth and development, but little is known about their functions during seed expansion, or how they contribute to seed expansion in different peanut lines. We examined seed miRNA expression patterns at 15 and 35 days after flowering ( DAF ) in two peanut 8th generation recombinant inbred lines (RIL8); 8106, a medium-pod variety, and 8107, a super-pod variety. Using high-throughput sequencing, we identified 1082 miRNAs in developing peanut seeds including 434 novel miRNAs. We identified 316 differentially expressed miRNAs by comparing expression levels between the two peanut lines. Interestingly, 24 miRNAs showed contrasting patterns of expression in the two RILs, and 149 miRNAs were expressed predominantly in only one RIL at 35 DAF. Also, potential target genes for some conserved and novel miRNAs were identified by degradome sequencing; target genes were predicted to be involved in auxin mediated signaling pathways and cell division. We validated the expression patterns of some representative miRNAs and 12 target genes by qPCR, and found negative correlations between the expression level of miRNAs and their targets. miR156e, miR159b, miR160a, miR164a, miR166b, miR168a, miR171n, miR172c-5p, and miR319d and their corresponding target genes may play key roles in seed expansion in peanut. The results of our study also provide novel insights into the dynamic changes in miRNAs that occur during peanut seed development, and increase our understanding of miRNA function in seed expansion.
2021-01-31 | GSE110195 | GEO
Project description:The Goal of this study is to develop NGS derived Arachis hypogaea root-nodule symbiotic Transcriptome Profile (RNAseq).
2018-08-29 | GSE98997 | GEO
Project description:Peanut is one of the most important cash crops with high quality oil, high protein content, and many other nutritional elements, and grown globally. Cultivated peanut (Arachis hypogaea L.) is allotetraploid with a narrow genetic base, and its genetics and molecular mechanisms controlling the agronomic traits are poorly understood. The array SNP data was used for revaling of key candidate loci and genes associated with important agronomic traits in peanut
2022-02-22 | GSE197103 | GEO
Project description:Peanut (Arachis hypogaea) has a large (~2.7 Gbp) allotetraploid genome with closely related component genomes making its genome very challenging to assemble. Here we report genome sequences of its diploid ancestors (A. duranensis and A. ipaënsis). We show they are similar to the peanutâs A- and B-genomes and use them use them to identify candidate disease resistance genes, create improved tetraploid transcript assemblies, and show genetic exchange between peanutâs component genomes. Based on remarkably high DNA identity and biogeography, we conclude that A. ipaënsis may be a descendant of the very same population that contributed the B-genome to cultivated peanut. Whole Genome Bisulphite Sequencing of the peanut species Arachis duranensis and Arachis ipaensis.
2016-07-03 | E-GEOD-71357 | biostudies-arrayexpress
Project description:Plant Protease Inhibitors (PIs) plays an important role in defense and combat against insect pests and pathogens. In the present study, Bowman-Birk Inhibitor (BBI) was purified(���������8 kDa) from mature seeds of an interspecific advanced hybrid peanut variety (4368-1) using trypsin affinity and size exclusion chromatographic techniques. The one and two-dimensional (2-D) gel electrophoresis revealed the existence of purified protein as several isoinhibitors in higher ordered oligomers. However, all the resolved isoforms exhibited inhibitory activity against bovine trypsin and chymotrypsin which is observed under one and 2-D in-gel activity staining. One of the high intensity isoinhibitor spot (pI 5.9) from 2-D gel was subjected to MALDI TOF-TOF analysis. The MS-MS ionization of PMF peak 3313.817 m/z revealed the amino acid sequence ���������APPYFECVCVDTFDHCPASCNSCVCTR��������� showed identity with BBIs of Arachis hypogaea along with significant similarity with other legume BBIs, hence the purified protein from peanut is named as PnBBI. Also, other biochemical and biophysical characteristics of PnBBI such as low molecular mass, presence of several isoinhibitors and their oligomerization, predominance of antiparallel ������-sheets and random coils in secondary structure, reactive sites against trypsin and chymotrypsin, broad spectrum of stability towards extreme pH and temperature similar to the typical characteristics of BBIs. Surface plasmon resonance competitive binding analysis revealed the bifuncitonal PnBBI is a trypsin specific inhibitor with 1:2 stoiciometry compared to chymotrypsin. A concentration dependent self-assocition tendency of PnBBI was further confirmed by red shift in far-UV CD spectra. Furthermore, the insecticidal potential of PnBBI against Helicoverpa armigera was assessed by in vitro assays and in vivo feeding experiments. A significant reduction in larval body weight was observed with concomitant attenuation in activity of midgut trypsin-like proteases of H. armigera (HaTPs) fed on PnBBI supplemented diet. The one and two-dimensional zymography studies revealed disappearence of several isoforms of HaTP upon feeding with PnBBI. qRT-PCR analysis further suggest the role of PnBBI in not only inhibiting the activity of midgut trypsin and chymotrypsin-like proteases but also in modulating their expression. Taken together, the results provide a biochemical and molecular basis for introgressed resistance in peanut interspecific advanced hybrid variety against H. armigera.
2020-02-18 | PXD016933 | Pride
Project description:Seed expansion in peanut is a complex biological process involving many gene regulatory pathways. MicroRNAs (miRNAs) play important regulatory roles in plant growth and development, but little is known about their functions during seed expansion, or how they contribute to seed expansion in different peanut lines. We examined seed miRNA expression patterns at 15 and 35 days after flowering (DAF) in two peanut eighth-generation recombinant inbred lines (RIL8); 8106, a medium-pod variety, and 8107, a super-pod variety. Using high-throughput sequencing, we identified 1,082 miRNAs in developing peanut seeds including 434 novel miRNAs. We identified 316 differentially expressed miRNAs by comparing expression levels between the two peanut lines. Interestingly, 24 miRNAs showed contrasting patterns of expression in the two RILs, and 149 miRNAs were expressed predominantly in only one RIL at 35 DAF. Also, potential target genes for some conserved and novel miRNAs were identified by degradome sequencing; target genes were predicted to be involved in auxin mediated signaling pathways and cell division. We validated the expression patterns of some representative miRNAs and 12 target genes by qPCR, and found negative correlations between the expression level of miRNAs and their targets. miR156e, miR159b, miR160a, miR164a, miR166b, miR168a, miR171n, miR172c-5p, and miR319d and their corresponding target genes may play key roles in seed expansion in peanut. The results of our study also provide novel insights into the dynamic changes in miRNAs that occur during peanut seed development, and increase our understanding of miRNA function in seed expansion.
| S-EPMC5890158 | biostudies-literature