Evolution Analysis of Simple Sequence Repeats in Plant Genome

Qin, Zhen; Wang, Yanping; Li, Aixian; Hou, Fuyun; Zhang, Liming

doi:10.1371/journal.pone.0144108

Cited by 48 publications

(42 citation statements)

References 61 publications

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“…Using the RNA-Seq data from these populations, we were able to both estimate gene expression levels and consistently genotype microsatellites in 2,640 transcripts containing 3325 microsatellites. Motif type and length searches across the 3325 microsatellites showed frequency estimates consistent with similar surveys conducted on eukaryotic genomes (Qin et al 2015; Tóth et al 2000) including those conducted on the Helianthus annuus transcriptome with the use of an EST database (Pramod et al 2014). These results demonstrate that the microsatellites used to test the predictions of the tuning knob hypothesis in this study substantially represent the composition of microsatellites in eukaryotic genomes (Supplemental Table S5; Supplemental Table S6).…”

Section: Discussionsupporting

confidence: 70%

Transcribed microsatellite allele lengths are often correlated with gene expression levels in natural sunflower populations

Ranathunge

Wheeler

Chimahusky

et al. 2018

Preprint

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ABSTRACTMicrosatellites are common in most species. While an adaptive role for these highly mutable regions has been considered, little is known concerning their contribution towards phenotypic variation. We used populations of the common sunflower (Helianthus annuus) at two latitudes to quantify the effect of microsatellite allele length on phenotype at the level of gene expression. We conducted a common garden experiment with seed collected from sunflower populations in Kansas and Oklahoma followed by an RNA-Seq experiment on 95 individuals. The effect of microsatellite allele length on gene expression was assessed across 3325 microsatellites that could be consistently scored. Our study revealed 479 microsatellites at which allele length significantly correlates with gene expression (eSTRs). When irregular allele sizes not conforming to the motif length were removed, the number of eSTRs rose to 2379. The percentage of variation in gene expression explained by eSTRs ranged from 1–86% when controlling for population and allele-by-population interaction effects at the 479 eSTRs. Of these, 70.4% are in untranslated regions (UTRs). A Gene Ontology (GO) analysis revealed that eSTRs are significantly enriched for GO terms associated with cis- and trans-regulatory processes. These findings suggest that a substantial number of transcribed microsatellites can influence gene expression.

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Section: Discussionsupporting

confidence: 70%

Transcribed microsatellite allele lengths are often correlated with gene expression levels in natural sunflower populations

Ranathunge

Wheeler

Chimahusky

et al. 2018

Preprint

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“…In case of tandem repeat, some of the conifers have been noted for the presence of large number of such repeats [64]. These repeats have been associated with gene duplication and chloroplast rearrangement [65].…”

Section: Resultsmentioning

confidence: 99%

The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman

et al. 2017

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Boswellia sacra (Burseraceae), a keystone endemic species, is famous for the production of fragrant oleo-gum resin. However, the genetic make-up especially the genomic information about chloroplast is still unknown. Here, we described for the first time the chloroplast (cp) genome of B. sacra. The complete cp sequence revealed a circular genome of 160,543 bp size with 37.61% GC content. The cp genome is a typical quadripartite chloroplast structure with inverted repeats (IRs 26,763 bp) separated by small single copy (SSC; 18,962 bp) and large single copy (LSC; 88,055 bp) regions. De novo assembly and annotation showed the presence of 114 unique genes with 83 protein-coding regions. The phylogenetic analysis revealed that the B. sacra cp genome is closely related to the cp genome of Azadirachta indica and Citrus sinensis, while most of the syntenic differences were found in the non-coding regions. The pairwise distance among 76 shared genes of B. sacra and A. indica was highest for atpA, rpl2, rps12 and ycf1. The cp genome of B. sacra reveals a novel genome, which could be used for further studied to understand its diversity, taxonomy and phylogeny.

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“…The dominant SSRs are different in various plant species. For instance, in monocots (except maize), most of the dominant SSRs are CCG/CGG/CGC/GCG/GCC/GGC, while most of the dominant SSRs in dicots (except Arabidopsis) are AAT/ATT/ATA/TAT/TAA/TTA [56]. Based on the results of Qin et al (2015), the type of dominant SSRs is taxon-dependent, and the abundance of AT in the dicots genome is higher than that of the monocots.…”

Section: Discussionmentioning

confidence: 99%

“…For instance, in monocots (except maize), most of the dominant SSRs are CCG/CGG/CGC/GCG/GCC/GGC, while most of the dominant SSRs in dicots (except Arabidopsis) are AAT/ATT/ATA/TAT/TAA/TTA [56]. Based on the results of Qin et al (2015), the type of dominant SSRs is taxon-dependent, and the abundance of AT in the dicots genome is higher than that of the monocots. In the future, SSR polymorphisms in TaFADs may be investigated in different cultivars and may be suitable for marker-assisted selection development in wheat breeding programs to select genotypes with a better quality of germ oil.…”

Section: Discussionmentioning

confidence: 99%

Identification, Evolution, Expression, and Docking Studies of Fatty Acid Desaturase Genes in Wheat (Triticum aestivum L.)

Hajiahmadi

Abedi

Wei

et al. 2020

Preprint

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Backgrounds: Fatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids that have essential roles in plant development and response to biotic and abiotic stresses. Wheat germ oil, one of the important by-products of wheat, can be a good alternative for edible oils with clinical advantages due to the high amount of unsaturated fatty acids. Therefore, we performed a genome-wide analysis of the wheat FAD gene family (TaFADs).Results: 68 FAD genes were identified from the wheat genome. Based on the phylogenetic analysis, wheat FADs clustered into five subfamilies, including FAB2, FAD2/FAD6, FAD4, DES/SLD, and FAD3/FAD7/FAD8. The TaFADs were distributed on chromosomes 2A-7B with 0 to 10 introns. The Ka/Ks ratio was less than one for most of the duplicated pair genes revealed that the function of the genes had been maintained during the evolution. Several cis-acting elements related to hormones and stresses in the TaFADs promoters indicated the role of these genes in plant development and responses to environmental stresses. Likewise, 72 SSRs and 91 miRNAs in 36 and 47 TaFADs have been identified. According to RNA-seq data analysis, the highest expression in all developmental stages and tissues was related to TaFAB2.5, TaFAB2.12, TaFAB2.15, TaFAB2.17, TaFAB2.20, TaFAD2.1, TaFAD2.6, and TaFAD2.8 genes while the highest expression in response to temperature stress was related to TaFAD2.6, TaFAD2.8, TaFAB2.15, TaFAB2.17, and TaFAB2.20. Furthermore, docking simulations revealed several residues in the active site of TaFAD2.6 and TaFAD2.8 in close contact with the docked oleic acid that could be useful in future site-directed mutagenesis studies to increase the catalytic efficiency of them and subsequently improve agronomic quality and tolerance of wheat against environmental stresses. Conclusions: This study provides comprehensive information that can lead to the detection of candidate genes for wheat genetic modification.

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Evolution Analysis of Simple Sequence Repeats in Plant Genome

Cited by 48 publications

References 61 publications

Transcribed microsatellite allele lengths are often correlated with gene expression levels in natural sunflower populations

Transcribed microsatellite allele lengths are often correlated with gene expression levels in natural sunflower populations

The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman

Identification, Evolution, Expression, and Docking Studies of Fatty Acid Desaturase Genes in Wheat (Triticum aestivum L.)

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