Comprehensive annotation of the transcriptome of the human fungal pathogen <i>Candida albicans</i> using RNA-seq

Bruno, Vincent M.; Wang, Zhong; Marjani, Sadie L.; Euskirchen, Ghia; Martin, Jeffrey A.; Sherlock, Gavin; Snyder, M

doi:10.1101/gr.109553.110

Cited by 195 publications

(226 citation statements)

References 35 publications

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“…Previous studies have shown that NTRs have fewer and shorter exons, less protein-coding potential, and less tissue-specific expression than annotated protein-coding genes (Bruno et al, 2010;Lu et al, 2010;Wetterbom et al, 2010;Zhang et al, 2010;Aanes et al, 2011;Graveley et al, 2011). To determine whether endospermic and embryonic NTRs have similar features, we analyzed the structure, coding potentials, and expression levels of the NTRs.…”

Section: Discovery Of Ntrsmentioning

confidence: 99%

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Chen

Shu

et al. 2013

Plant Physiology

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Transcriptome analysis of early-developing maize (Zea mays) seed was conducted using Illumina sequencing. We mapped 11,074,508 and 11,495,788 paired-end reads from endosperm and embryo, respectively, at 9 d after pollination to define gene structure and alternative splicing events as well as transcriptional regulators of gene expression to quantify transcript abundance in both embryo and endosperm. We identified a large number of novel transcribed regions that did not fall within maize annotated regions, and many of the novel transcribed regions were tissue-specifically expressed. We found that 50.7% (8,556 of 16,878) of multiexonic genes were alternatively spliced, and some transcript isoforms were specifically expressed either in endosperm or in embryo. In addition, a total of 46 trans-splicing events, with nine intrachromosomal events and 37 interchromosomal events, were found in our data set. Many metabolic activities were specifically assigned to endosperm and embryo, such as starch biosynthesis in endosperm and lipid biosynthesis in embryo. Finally, a number of transcription factors and imprinting genes were found to be specifically expressed in embryo or endosperm. This data set will aid in understanding how embryo/endosperm development in maize is differentially regulated.Maize (Zea mays) seeds are one of the most important crop materials that provide resources for food, feed, biofuel, and raw material for processing. Maize seed development initiates from double fertilization, in which two of the pollen sperms fuse with an egg cell and a central cell to produce embryo and endosperm, respectively (Randolph, 1936;Chaudhury et al., 2001). The main function of endosperm is to provide nutrient for the developing embryo and germinating embryo.After fertilization, the zygote undergoes an asymmetric division into a small apical cell and a large basal cell, giving rise to the embryo proper and the suspensor, respectively. The radial symmetry of the proembryo is shifted to a bilateral symmetry at the transition stage, which is characterized by protoderm formation. The shoot apical meristem and the root apical meristem can be distinguished at the onset of the coleoptile stage, and then the position of the future coleoptile is marked by a small protuberance. The mature embryo is composed of the embryo axis, which is formed by the plumule with five or six short internodes, and leaf primordia and primary root surrounded by the coleoptile and the coleorhiza, respectively, and the scutellum (Randolph, 1936;Abbe and Stein, 1954;Diboll, 1968;Lammeren, 1986;Vernoud et al., 2005).Maize endosperm follows the nucleus-type endosperm development, where the fertilized central cell undergoes several rounds of synchronous division in the absence of cell wall formation and cytokinesis to produce a syncytium (Lopes and Larkins, 1993;Olsen, 2004). Cellularization allows the formation of the internuclear radial microtubule systems and open-ended alveolation from the periphery of the endosperm toward the central vacuole (Olsen et al., ...

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Section: Discovery Of Ntrsmentioning

confidence: 99%

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Chen

Shu

et al. 2013

Plant Physiology

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“…RNA interference (RNAi) in this organism has been recently discovered (Drinnenberg et al 2009). First reports on the transcriptome have been published, revealing an extensive antisense transcriptome (Bruno et al 2010;Sellam et al 2010;Tuch et al 2010).…”

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confidence: 99%

Transcriptional Regulatory Circuitries in the Human Pathogen Candida albicans Involving Sense–Antisense Interactions

Aḥmad¹,

Kravets

Rustchenko

2012

Genetics

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Candida albicans, a major human fungal pathogen, usually contains a diploid genome, but controls adaptation to a toxic alternative carbon source L-sorbose, by the reversible loss of one chromosome 5 (Ch5). We have previously identified multiple unique regions on Ch5 that repress the growth on sorbose. In one of the regions, the CSU51 gene determining the repressive property of the region was identified. We report here the identification of the CSU53 gene from a different region on Ch5. Most importantly, we find that CSU51 and CSU53 are associated with novel regulatory elements, ASUs, which are embedded within CSUs in an antisense configuration. ASUs act opposite to CSUs by enhancing the growth on sorbose. In respect to the CSU transcripts, the ASU long antisense transcripts are in lesser amounts, are completely overlapped, and are inversely related. ASUs interact with CSUs in natural CSU/ASU cis configurations, as well as when extra copies of ASUs are placed in trans to the CSU/ASU configurations. We suggest that ASU long embedded antisense transcripts modulate CSU sense transcripts.

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“…For example, experiments have revealed the widespread presence of antisense transcripts and untranslated regions of varying lengths, dependent both on cell state and environmental conditions [97,98,105]. In the case of the white-opaque switch, RNA-Seq analysis of sense-antisense transcript pairs showed a significant anti-correlation, suggesting that many antisense transcripts act to repress their sense counterparts [98].…”

Section: Investigation Of Chromatin Structure and Transcriptional Regmentioning

confidence: 99%

“…Most recent studies of gene expression have used RNA sequencing (RNA-Seq) to obtain greater sensitivity and to reduce bias in assayed gene targets. RNA-Seq studies have identified 600 novel coding and over 1000 noncoding transcripts in C. albicans, many of which are regulated by environment and cell state [97,98]. Transcriptional profiles have now been defined under a wide variety of conditions both in vitro and in vivo [99][100][101][102][103].…”

Section: Investigation Of Chromatin Structure and Transcriptional Regmentioning

confidence: 99%

Budding off: bringing functional genomics toCandida albicans

Anderson¹,

Bennett²

2015

Briefings in Functional Genomics

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Candida species are the most prevalent human fungal pathogens, with Candida albicans being the most clinically relevant species. Candida albicans resides as a commensal of the human gastrointestinal tract but is a frequent cause of opportunistic mucosal and systemic infections. Investigation of C. albicans virulence has traditionally relied on candidate gene approaches, but recent advances in functional genomics have now facilitated global, unbiased studies of gene function. Such studies include comparative genomics (both between and within Candida species), analysis of total RNA expression, and regulation and delineation of protein-DNA interactions. Additionally, large collections of mutant strains have begun to aid systematic screening of clinically relevant phenotypes. Here, we will highlight the development of functional genomics in C. albicans and discuss the use of these approaches to addressing both commensalism and pathogenesis in this species.

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Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

Cited by 195 publications

References 35 publications

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Transcriptional Regulatory Circuitries in the Human Pathogen Candida albicans Involving Sense–Antisense Interactions

Budding off: bringing functional genomics toCandida albicans

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