MicroRNA profiles and their control of male gametophyte development in rice

Hua, Peng; Chun, Jun Sung; Ai, Ting; Tong, Yongao; Zhang, Rong; Zhao, Mingming; Chen, Fang; Wang, Shenghua

doi:10.1007/s11103-012-9898-x

Cited by 41 publications

(25 citation statements)

References 86 publications

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“…High levels of OsSUT5 transcripts were also detected in ovary and stigma during fertilization and embryogenesis (Figure 5A). Similar spatiotemporal expression patterns were observed in indica rice (Wang et al, 2010; Peng et al, 2012) (data not shown). The complementary expression patterns of clades P2 and P3 SUTs in reproductive tissues are consistent with subfunctionalization following their divergence from clade P1 by positive selection in monocots.…”

Section: Resultssupporting

confidence: 84%

Bayesian phylogeny of sucrose transporters: ancient origins, differential expansion and convergent evolution in monocots and dicots

Peng

Xue

et al. 2014

Front. Plant Sci.

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Sucrose transporters (SUTs) are essential for the export and efficient movement of sucrose from source leaves to sink organs in plants. The angiosperm SUT family was previously classified into three or four distinct groups, Types I, II (subgroup IIB), and III, with dicot-specific Type I and monocot-specific Type IIB functioning in phloem loading. To shed light on the underlying drivers of SUT evolution, Bayesian phylogenetic inference was undertaken using 41 sequenced plant genomes, including seven basal lineages at key evolutionary junctures. Our analysis supports four phylogenetically and structurally distinct SUT subfamilies, originating from two ancient groups (AG1 and AG2) that diverged early during terrestrial colonization. In both AG1 and AG2, multiple intron acquisition events in the progenitor vascular plant established the gene structures of modern SUTs. Tonoplastic Type III and plasmalemmal Type II represent evolutionarily conserved descendants of AG1 and AG2, respectively. Type I and Type IIB were previously thought to evolve after the dicot-monocot split. We show, however, that divergence of Type I from Type III SUT predated basal angiosperms, likely associated with evolution of vascular cambium and phloem transport. Type I SUT was subsequently lost in monocots along with vascular cambium, and independent evolution of Type IIB coincided with modified monocot vasculature. Both Type I and Type IIB underwent lineage-specific expansion. In multiple unrelated taxa, the newly-derived SUTs exhibit biased expression in reproductive tissues, suggesting a functional link between phloem loading and reproductive fitness. Convergent evolution of Type I and Type IIB for SUT function in phloem loading and reproductive organs supports the idea that differential vascular development in dicots and monocots is a strong driver for SUT family evolution in angiosperms.

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Section: Resultssupporting

confidence: 84%

Bayesian phylogeny of sucrose transporters: ancient origins, differential expansion and convergent evolution in monocots and dicots

Peng

Xue

et al. 2014

Front. Plant Sci.

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“…There was a major peak at 24 nt in the total small RNAs from our sRNA libraries (Fig. 2), consistent with previous results on rice (Peng et al 2012), soybean (Song et al 2011), cotton (Yin et al 2012), Medicago truncatula (Eyles et al 2013) and a recent research on tomato (Zuo et al 2012). One possible reason for the prevalence of 24 nt sRNA is that 24 nt sRNA is involved in heterochromatin modification, in particular for genomes with high repetitive sequence content (Schauer et al 2002;Jia et al 2009).…”

Section: Autoregulation Of Mirna Biogenesissupporting

confidence: 91%

Small RNA and degradome sequencing reveals microRNAs and their targets involved in tomato pedicel abscission

Wang

Liu

et al. 2015

Planta

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We constructed small RNA and degradome sequencing libraries to identify miRNAs and targets involved in tomato pedicel abscission, and confirmed their roles via quantitative real-time PCR. MicroRNAs (miRNAs) are endogenous small RNAs which play crucial negatively regulatory roles at both the transcriptional and post-transcriptional levels in plants; however, limited knowledge is available on the expression profiles of miRNAs and their target genes during tomato pedicel abscission. Taking advantage of small RNA (sRNA) and degradome sequencing technology, a total of 56 known and 11 novel candidate miRNAs targeting 223 mRNA genes were confirmed during pedicel abscission. Gene ontology annotation and KEGG pathway analysis showed that these target genes were significantly enriched in intracellular, membrane-bounded organelle-related biological processes as well as in metabolic, plant-pathogen interaction and hormone signaling pathways. We screened 17 miRNA/target pairs for further analysis and performed quantitative real-time PCR to identify the roles. Cluster analysis of selected miRNAs revealed that the expression profiles of miRNAs varied in different stages of abscission and could be impacted by ethylene treatment. In the present study, the correlations between miRNAs and targets suggested a complex regulatory network of miRNA-mediated target interaction during pedicel abscission. Additionally, the expression profiles of miRNAs and their targets changed by ethylene might be a considerable reason why ethylene promotes pedicel abscission. Our study provides new insights into the expression and regulatory profiles of miRNAs during tomato pedicel abscission.

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“…For rice, 137 microarray samples from four data series (GEO accession numbers: GSE14304 [Fujita et al, 2010], GSE17002 [Russell et al, 2012], GSE27988 [Wei et al, 2010], GSE29212 [Peng et al, 2012]) were obtained and classified into 18 groups of tissues. For Arabidopsis, 244 microarray samples from seven data series (GEO accession numbers: GSE5630, GSE5631, GSE5632, GSE5633, GSE5634 [Schmid et al, 2005]; GSE6162 [Honys and Twell, 2004]; GSE17343 [Qin et al, 2009]; ArrayExpress accession: E-ATMX-35 [Borges et al, 2008]) were obtained and classified into 22 tissue groups.…”

Section: Microarray Data Set Preparation and Data Analysismentioning

confidence: 99%

Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome

Chen

et al. 2015

Molecular Plant

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The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis (Betrán et al., 2002; Begun et al., 2007; Dubruille et al., 2012), and thus an "out of testis" hypothesis for the emergence of new genes has been proposed (Vinckenbosch et al., 2006; Kaessmann, 2010). However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a number of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and anti-microbial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an "innovation incubator" for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the "new genes out of the male" model revealed a common evolutionary force that drives reproductive barriers, species specification, and the upgrading of defensive mechanisms against pathogens.

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MicroRNA profiles and their control of male gametophyte development in rice

Cited by 41 publications

References 86 publications

Bayesian phylogeny of sucrose transporters: ancient origins, differential expansion and convergent evolution in monocots and dicots

Bayesian phylogeny of sucrose transporters: ancient origins, differential expansion and convergent evolution in monocots and dicots

Small RNA and degradome sequencing reveals microRNAs and their targets involved in tomato pedicel abscission

Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome

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