RNA-sequencing reveals previously unannotated protein- and microRNA-coding genes expressed in aleurone cells of rice seeds

Watanabe, Kenneth A.; Ringler, Patricia; Gu, Lingkun; Shen, Qi

doi:10.1016/j.ygeno.2013.10.007

Cited by 13 publications

(13 citation statements)

References 60 publications

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“…The superior carbon recovery that PPDK allows would be advantageous to both bacteria and plants when growth is dependent on substrates such as lactate and gluconeogenic amino acids that can give rise to pyruvate. PPDK genes appear to be present in all plant genomes that have so far been sequenced 16 and there is also evidence that PPDK is expressed in the storage reserve tissues of germinated seeds from a taxonomically diverse range of species including castor bean 26 , poplar 37 ( Populus balsamifera ), rice 38 ( Oryza sativa ), barley 39 ( Hordeum vulgare ) and maize 40 ( Zea mays ; Supplementary Table 3 ). Although it is possible that Arabidopsis independently and convergently recruited PPDK for gluconeogenesis, it is therefore more likely that both bacterial and plant lineages have maintained PPDK for this purpose since their divergence around 1.3 billion years ago.…”

Section: Discussionmentioning

confidence: 99%

Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment

et al. 2015

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Gluconeogenesis is a fundamental metabolic process that allows organisms to make sugars from non-carbohydrate stores such as lipids and protein. In eukaryotes only one gluconeogenic route has been described from organic acid intermediates and this relies on the enzyme phosphoenolpyruvate carboxykinase (PCK). Here we show that two routes exist in Arabidopsis, and that the second uses pyruvate, orthophosphate dikinase (PPDK). Gluconeogenesis is critical to fuel the transition from seed to seedling. Arabidopsis pck1 and ppdk mutants are compromised in seed-storage reserve mobilization and seedling establishment. Radiolabelling studies show that PCK predominantly allows sugars to be made from dicarboxylic acids, which are products of lipid breakdown. However, PPDK also allows sugars to be made from pyruvate, which is a major product of protein breakdown. We propose that both routes have been evolutionarily conserved in plants because, while PCK expends less energy, PPDK is twice as efficient at recovering carbon from pyruvate.

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Section: Discussionmentioning

confidence: 99%

Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment

et al. 2015

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“…The short-read data from our previous publication were used in this study since we obtained the data and can vouch for its quality. 9 In addition, using the same data allowed for comparison between our previously published results and the results in this study. The short reads were aligned to MSU R7 using the latest available version of Bowtie and Tophat.…”

Section: Resultsmentioning

confidence: 81%

“…Recently, we published a clustering algorithm to identify novel protein- and microRNA-coding genes by searching only the unannotated regions of the rice genome. 9 However, this method relied on the genome being partially annotated. Analysis of the RNA-seq data with other transcript assembly software revealed that they failed to identify genes, were CPU intensive, or lacked documentation or recent software updates.…”

Section: Introductionmentioning

confidence: 99%

Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing

Watanabe

Homayouni

Tufano

et al. 2015

DNA Res

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Annotation of the rice (Oryza sativa) genome has evolved significantly since release of its draft sequence, but it is far from complete. Several published transcript assembly programmes were tested on RNA-sequencing (RNA-seq) data to determine their effectiveness in identifying novel genes to improve the rice genome annotation. Cufflinks, a popular assembly software, did not identify all transcripts suggested by the RNA-seq data. Other assembly software was CPU intensive, lacked documentation, or lacked software updates. To overcome these shortcomings, a heuristic ab initio transcript assembly algorithm, Tiling Assembly, was developed to identify genes based on short read and junction alignment. Tiling Assembly was compared with Cufflinks to evaluate its gene-finding capabilities. Additionally, a pipeline was developed to eliminate false-positive gene identification due to noise or repetitive regions in the genome. By combining Tiling Assembly and Cufflinks, 767 unannotated genes were identified in the rice genome, demonstrating that combining both programmes proved highly efficient for novel gene identification. We also demonstrated that Tiling Assembly can accurately determine transcription start sites by comparing the Tiling Assembly genes with their corresponding full-length cDNA. We applied our pipeline to additional organisms and identified numerous unannotated genes, demonstrating that Tiling Assembly is an organism-independent tool for genome annotation.

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“…The DNA, cDNA, and protein sequences of rice Japonica Nipponbare were obtained from Ensembl Plants (IRGSP‐1.0, http://plants.ensembl.org/Oryza_sativa/Info/Index) (Kersey et al, 2015). Rice RNA‐seq data of shoot (SRR037740), root (SRR037741), leaf (SRR037742) (Zhang et al, 2010), ovules (SRR1917382), spikelet (SRR2043072) (Yang et al, 2015), anther (SRR352190), pistil (SRR352192), seed 5 DAP (SRR352194), seed 10 DAP (SRR352207), embryo 25 DAP (SRR352204), endosperm 25 DAP (SRR352206) (Davidson et al, 2012), aleurone (SRR946529) (Watanabe et al, 2014), and dry seed (SRR2544786) (He et al, 2015) were downloaded from the National Center for Biotechnology Information (NCBI) Sequence Read Archive database (http://www.ncbi.nlm.nih.gov/sra). To investigate seed‐specific TFs during different developmental stages, we classified seed tissue into seed 5DAP, seed 10 DAP, embryo 25 DAP, endosperm 25 DAP, aleurone, and dry seed.…”

Section: Methodsmentioning

confidence: 99%

RicetissueTFDB: A Genome‐Wide Identification of Tissue‐Specific Transcription Factors in Rice

Chen

Luo

et al. 2019

The Plant Genome

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Core Ideas Validated TFs expressed in rice tissue types to study gene expression profiles in rice tissues. Tissue‐specific TFs were analyzed in different rice tissues. RicetissueTFDB integrates tissue expression characters, genomic location, and GO terms for TFs. Transcription factors (TFs) regulate plant gene expression in different tissues. To investigate TF genes in rice (Oryza sativa L.), a genome‐wide TF identification was conducted with the japonica rice genome. This study identified 3078 putative TFs in 59 families. The TF number of the top 10 TF families accounted for 58% of the 3078 rice TFs. The three largest TF families were the myeloblastosis (MYB) superfamily, basic helix–loop–helix (bHLH), and far‐red‐impaired response (FAR1), which contained 413, 228, and 210 TF members, respectively. The expression profiles of the 3078 TF genes were surveyed with the RNA sequencing (RNA‐seq) data of 13 rice tissue types. Based on these expression profiles, we validated 1087 TFs expressed in 13 rice tissue types, which accounted for 35.32% of the 3078 putative TFs. We further analyzed the tissue‐specific TFs in rice. In total, 28, 14, 14, 10, 9, 5, 5, 4, 3, 3, 2, 11, and 1 tissue‐specific TF sequences were identified in the dry seed, pistil, spikelet, aleurone, anther, ovules, embryo 25 d after pollination (DAP), seed 5 DAP, root, leaf, seed 10 DAP, shoot, and endosperm 25 DAP, respectively. Moreover, we constructed RicetissueTFDB (http://221.237.158.212:50009/index), a comprehensive and public rice TF database that integrates tissue expression characters, genomic location, and Gene Ontology (GO) terms for each TF. The RicetissueTFDB database will facilitate the identification of target TFs and the functional studies about rice TFs.

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RNA-sequencing reveals previously unannotated protein- and microRNA-coding genes expressed in aleurone cells of rice seeds

Cited by 13 publications

References 60 publications

Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment

Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment

Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing

RicetissueTFDB: A Genome‐Wide Identification of Tissue‐Specific Transcription Factors in Rice

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