Selective Acquisition and Retention of Genomic Sequences by Pack-<i>Mutator</i>-Like Elements Based on Guanine-Cytosine Content and the Breadth of Expression

Ferguson, Ann A.; Zhao, Dongyan; Jiang, Ning

doi:10.1104/pp.113.223271

Cited by 26 publications

(58 citation statements)

References 65 publications

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“…While this is a small minority, it is clearly much higher than for all genes (chi-squared test, P < 1 × 10 of microsynteny (68-92%), indicative of conserved genomic position over periods of up to 2.4 million years. MDLs showed different characteristics from non-gene-containing MULEs, having for example higher GC content 70 ( Supplementary Fig. 18).…”

Section: −6mentioning

confidence: 99%

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

et al. 2018

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Section: −6mentioning

confidence: 99%

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

et al. 2018

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“…As a result, they may contribute to the high GC content of rice-specific genes. It is worthy of mention that, due to their ability to duplicate genes, Pack-MULEs have distinct GC content compared to other transposable elements (Ferguson et al 2013). …”

Section: Resultsmentioning

confidence: 99%

Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation

Zhao

Hamilton

Hardigan

et al. 2016

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Gene expression is controlled at transcriptional and post-transcriptional levels including decoding of messenger RNA (mRNA) into polypeptides via ribosome-mediated translation. Translational regulation has been intensively studied in the model dicot plant Arabidopsis thaliana, and in this study, we assessed the translational status [proportion of steady-state mRNA associated with ribosomes] of mRNAs by Translating Ribosome Affinity Purification followed by mRNA-sequencing (TRAP-seq) in rice (Oryza sativa), a model monocot plant and the most important food crop. A survey of three tissues found that most transcribed rice genes are translated whereas few transposable elements are associated with ribosomes. Genes with short and GC-rich coding regions are overrepresented in ribosome-associated mRNAs, suggesting that the GC-richness characteristic of coding sequences in grasses may be an adaptation that favors efficient translation. Transcripts with retained introns and extended 5′ untranslated regions are underrepresented on ribosomes, and rice genes belonging to different evolutionary lineages exhibited differential enrichment on the ribosomes that was associated with GC content. Genes involved in photosynthesis and stress responses are preferentially associated with ribosomes, whereas genes in epigenetic regulation pathways are the least enriched on ribosomes. Such variation is more dramatic in rice than that in Arabidopsis and is correlated with the wide variation of GC content of transcripts in rice. Taken together, variation in the translation status of individual transcripts reflects important mechanisms of gene regulation, which may have a role in evolution and diversification.

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“…This difference potentially reflects the historical difference in TE activity. Interestingly, Pack-MULEs preferentially obtain genic sequences (Ferguson et al, 2013), and a subset of Pack-MULE-carried genes are expressed and appear to be under selection (Hanada et al, 2009c). However, the mechanisms underlying this preferential acquisition and the functions of the acquired genes remain unclear.…”

Section: Mechanisms Of Gene Duplicationmentioning

confidence: 99%

Evolution of Gene Duplication in Plants

2016

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Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These duplicates have contributed to the evolution of novel functions, such as the production of floral structures, induction of disease resistance, and adaptation to stress. Additionally, recent whole-genome duplications that have occurred in the lineages of several domesticated crop species, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), and soybean (Glycine max), have contributed to important agronomic traits, such as grain quality, fruit shape, and flowering time. Therefore, understanding the mechanisms and impacts of gene duplication will be important to future studies of plants in general and of agronomically important crops in particular. In this review, we survey the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication.

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Selective Acquisition and Retention of Genomic Sequences by Pack-Mutator-Like Elements Based on Guanine-Cytosine Content and the Breadth of Expression

Cited by 26 publications

References 65 publications

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation

Evolution of Gene Duplication in Plants

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