Dataset Information

Transcriptome analysis of alternative splicing in peanut (Arachis hypogaea L.).

ABSTRACT: BACKGROUND:Alternative splicing (AS) represents a mechanism widely used by eukaryotes for the post-transcriptional regulation of genes. The detailed exploration of AS in peanut has not been documented. RESULTS:The strand-specific RNA-Seq technique was exploited to characterize the distribution of AS in the four samples of peanut (FH1-seed1, FH1-seed2, FH1-root and FH1-leaf). AS was detected as affecting around 37.2% of the full set of multi-exon genes. Some of these genes experienced AS throughout the plant, while in the case of others, the effect was organ-specific. Overall, AS was more frequent in the seed than in either the root or leaf. The predominant form of AS was intron retention, and AS in transcription start site and transcription terminal site were commonly identified in all the four samples. It is interesting that in genes affected by AS, the majority experienced only a single type of event. Not all of the in silico predicted transcripts appeared to be translated, implying that these are either degraded or sequestered away from the translation machinery. With respect to genes involved in fatty acid metabolism, about 61.6% were shown to experience AS. CONCLUSION:Our report contributes significantly in AS analysis of peanut genes in general, and these results have not been mentioned before. The specific functions of different AS forms need further investigation.

SUBMITTER: Ruan J

PROVIDER: S-EPMC6032549 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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Transcriptome analysis of alternative splicing in peanut (Arachis hypogaea L.).

Ruan Jian J Guo Feng F Wang Yingying Y Li Xinguo X Wan Shubo S Shan Lei L Peng Zhenying Z

BMC plant biology 20180704 1

<h4>Background</h4>Alternative splicing (AS) represents a mechanism widely used by eukaryotes for the post-transcriptional regulation of genes. The detailed exploration of AS in peanut has not been documented.<h4>Results</h4>The strand-specific RNA-Seq technique was exploited to characterize the distribution of AS in the four samples of peanut (FH1-seed1, FH1-seed2, FH1-root and FH1-leaf). AS was detected as affecting around 37.2% of the full set of multi-exon genes. Some of these genes experien ...[more]

PMID: 29973157

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Project description:BACKGROUND:Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely distributed across the entire plant genome and can be used to develop SSR markers, which can then be used to conduct genetic analyses and molecular breeding. Cultivated peanut (A. hypogaea L.), an important oil crop worldwide, is an allotetraploid (AABB, 2n = 4× = 40) plant species. Because of its complex genome, genomic marker development has been very challenging. However, sequencing of cultivated peanut genome allowed us to develop genomic markers and construct a high-density physical map. RESULTS:A total of 8,329,496 SSRs were identified, including 3,772,653, 4,414,961, and 141,882 SSRs that were distributed in subgenome A, B, and nine scaffolds, respectively. Based on the flanking sequences of the identified SSRs, a total of 973,984 newly developed SSR markers were developed in subgenome A (462,267), B (489,394), and nine scaffolds (22,323), with an average density of 392.45 markers per Mb. In silico PCR evaluation showed that an average of 88.32% of the SSR markers generated only one in silico-specific product in two tetraploid A. hypogaea varieties, Tifrunner and Shitouqi. A total of 39,599 common SSR markers were identified among the two A. hypogaea varieties and two progenitors, A. duranensis and A. ipaensis. Additionally, an amplification effectiveness of 44.15% was observed by real PCR validation. Moreover, a total of 1276 public SSR loci were integrated with the newly developed SSR markers. Finally, a previously known leaf spot quantitative trait locus (QTL), qLLS_T13_A05_7, was determined to be in a 1.448-Mb region on chromosome A05. In this region, a total of 819 newly developed SSR markers were located and 108 candidate genes were detected. CONCLUSIONS:The availability of these newly developed and public SSR markers both provide a large number of molecular markers that could potentially be used to enhance the process of trait genetic analyses and improve molecular breeding strategies for cultivated peanut.

Dataset Information

Transcriptome analysis of alternative splicing in peanut (Arachis hypogaea L.).

Publications

Transcriptome analysis of alternative splicing in peanut (Arachis hypogaea L.).

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