Exploring the plant transcriptome through phylogenetic profiling

Progresses of CRISPR/Cas9 genome editing in forage crops

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated-genome editing has evolved into a powerful tool that is widely used in plant species to induce editing in the genome for analyzing gene function and crop improvement. CRISPR/Cas9 is an RNA-guided genome editing tool consisting of a Cas9 nuclease and a single-guide RNA (sgRNA). The CRISPR/Cas9 system enables more accurate and efficient genome editing in crops. In this review, we summarized the advances of the CRISPR/Cas9 technology in plant genome editing and its applications in forage crops. We described briefly about the development of CRISPR/Cas9 technology in plant genome editing. We assessed the progress of CRISPR/Cas9-mediated targeted-mutagenesis in various forage crops, including alfalfa, Medicago truncatula, Hordeum vulgare, Sorghum bicolor, Setaria italica and Panicum virgatum. The potentials and challenges of CRISPR/Cas9 in forage breeding were discussed.

Multi-omics network-based functional annotation of unknown Arabidopsis genes

Unraveling gene function is pivotal to understanding the signaling cascades that control plant development and stress responses. As experimental profiling is costly and labor intensive, there is a clear need for high-confidence computational annotation. In contrast to detailed gene-specific functional information, transcriptomics data are widely available for both model and crop species. Here, we describe a novel automated function prediction method, which leverages complementary information from multiple expression datasets by analyzing study-specific gene co-expression networks. First, we benchmarked the prediction performance on recently characterized Arabidopsis thaliana genes, and showed that our method outperforms state-of-the-art expression-based approaches. Next, we predicted biological process annotations for known (n = 15 790) and unknown (n = 11 865) genes in A. thaliana and validated our predictions using experimental protein-DNA and protein-protein interaction data (covering >220 000 interactions in total), obtaining a set of high-confidence functional annotations. Our method assigned at least one validated annotation to 5054 (42.6%) unknown genes, and at least one novel validated function to 3408 (53.0%) genes with computational annotations only. These omics-supported functional annotations shed light on a variety of developmental processes and molecular responses, such as flower and root development, defense responses to fungi and bacteria, and phytohormone signaling, and help fill the information gap on biological process annotations in Arabidopsis. An in-depth analysis of two context-specific networks, modeling seed development and response to water deprivation, shows how previously uncharacterized genes function within the respective networks. Moreover, our automated function prediction approach can be applied in future studies to facilitate gene discovery for crop improvement.

Characterization of floral morphoanatomy and identification of marker genes preferentially expressed during specific stages of cotton flower development

Characterization of anther and ovule developmental programs and expression analyses of stage-specific floral marker genes in Gossypium hirsutum allowed to build a comprehensive portrait of cotton flower development before fiber initiation. Gossypium hirsutum is the most important cotton species that is cultivated worldwide. Although cotton reproductive development is important for fiber production, since fiber is formed on the epidermis of mature ovules, cotton floral development remains poorly understood. Therefore, this work aims to characterize the cotton floral morphoanatomy by performing a detailed description of anther and ovule developmental programs and identifying stage-specific floral marker genes in G. hirsutum. Using light microscopy and scanning electron microscopy, we analyzed anther and ovule development during 11 stages of flower development. To better characterize the ovule development in cotton, we performed histochemical analyses to evaluate the accumulation of phenolic compounds, pectin, and sugar in ovule tissues. After identification of major hallmarks of floral development, three key stages were established in G. hirsutum floral development: in stage 1 (early-EF), sepal, petal, and stamen primordia were observed; in stage 2 (intermediate-IF), primordial ovules and anthers are present, and the differentiating archesporial cells were observed, marking the beginning of microsporogenesis; and in stage 6 (late-LF), flower buds presented initial anther tapetum degeneration and microspore were released from the tetrad, and nucellus and both inner and outer integuments are developing. We used transcriptome data of cotton EF, IF and LF stages to identify floral marker genes and evaluated their expression by real-time quantitative PCR (qPCR). Twelve marker genes were preferentially expressed in a stage-specific manner, including the putative homologs for AtLEAFY, AtAPETALA 3, AtAGAMOUS-LIKE 19 and AtMALE STERILITY 1, which are crucial for several aspects of reproductive development, such as flower organogenesis and anther and petal development. We also evaluated the expression profile of B-class MADS-box genes in G. hirsutum floral transcriptome (EF, IF, and LF). In addition, we performed a comparative analysis of developmental programs between Arabidopsis thaliana and G. hirsutum that considered major morphoanatomical and molecular processes of flower, anther, and ovule development. Our findings provide the first detailed analysis of cotton flower development.

Comparative and evolutionary analyses of the divergence of plant oligosaccharyltransferase STT3 isoforms

STT3 is a catalytic subunit of hetero-oligomeric oligosaccharyltransferase (OST), which is important for asparagine-linked glycosylation. In mammals and plants, OSTs with different STT3 isoforms exhibit distinct levels of enzymatic efficiency or different responses to stressors. Although two different STT3 isoforms have been identified in both plants and animals, it remains unclear whether these isoforms result from gene duplication in an ancestral eukaryote. Furthermore, the molecular mechanisms underlying the functional divergences between the two STT3 isoforms in plant have not been well elucidated. Here, we conducted phylogenetic analysis of the major evolutionary node species and suggested that gene duplications of STT3 may have occurred independently in animals and plants. Across land plants, the exon-intron structure differed between the two STT3 isoforms, but was highly conserved for each isoform. Most angiosperm STT3a genes had 23 exons with intron phase 0, while STT3b genes had 6 exons with intron phase 2. Characteristic motifs (motif 18 and 19) of STT3s were mapped to different structure domains in the plant STT3 proteins. These two motifs overlap with regions of high nonsynonymous-to-synonymous substitution rates, suggesting the regions may be related to functional difference between STT3a and STT3b. In addition, promoter elements and gene expression profiles were different between the two isoforms, indicating expression pattern divergence of the two genes. Collectively, the identified differences may result in the functional divergence of plant STT3s.

Nodule-specific PLAT domain proteins are expanded in the Medicago lineage and required for nodulation

Symbiotic nitrogen fixation in legumes is mediated by an interplay of signaling processes between plant hosts and rhizobial symbionts. In legumes, several secreted protein families have undergone expansions and play key roles in nodulation. Thus, identifying lineage-specific expansions (LSEs) of nodulation-associated genes can be a strategy to discover candidate gene families. Using bioinformatic tools, we identified 13 LSEs of nodulation-related secreted protein families, each unique to either Glycine, Arachis or Medicago lineages. In the Medicago lineage, nodule-specific Polycystin-1, Lipoxygenase, Alpha Toxin (PLAT) domain proteins (NPDs) expanded to five members. We examined NPD function using CRISPR/Cas9 multiplex genome editing to create Medicago truncatula NPD knockout lines, targeting one to five NPD genes. Mutant lines with differing combinations of NPD gene inactivations had progressively smaller nodules, earlier onset of nodule senescence, or ineffective nodules compared to the wild-type control. Double- and triple-knockout lines showed dissimilar nodulation phenotypes but coincided in upregulation of a DHHC-type zinc finger and an aspartyl protease gene, possible candidates for the observed disturbance of proper nodule function. By postulating that gene family expansions can be used to detect candidate genes, we identified a family of nodule-specific PLAT domain proteins and confirmed that they play a role in successful nodule formation.

A Guide to the PLAZA 3.0 Plant Comparative Genomic Database

PLAZA 3.0 is an online resource for comparative genomics and offers a versatile platform to study gene functions and gene families or to analyze genome organization and evolution in the green plant lineage. Starting from genome sequence information for over 35 plant species, precomputed comparative genomic data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, and genomic colinearity information within and between species. Complementary functional data sets, a Workbench, and interactive visualization tools are available through a user-friendly web interface, making PLAZA an excellent starting point to translate sequence or omics data sets into biological knowledge. PLAZA is available at http://bioinformatics.psb.ugent.be/plaza/ .

Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules

Molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. These traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. Here, we established a method that combines large-scale genomic and phylogenetic data with gene co-expression networks to extensively study the evolutionary make-up of modules in the moss Physcomitrella patens, and in the angiosperms Arabidopsis thaliana and Oryza sativa (rice). We first show that younger genes are less annotated than older genes. By mapping genomic data onto the co-expression networks, we found that genes from the same evolutionary period tend to be connected, whereas old and young genes tend to be disconnected. Consequently, the analysis revealed modules that emerged at a specific time in plant evolution. To uncover the evolutionary relationships of the modules that are conserved across the plant kingdom, we added phylogenetic information that revealed duplication and speciation events on the module level. This combined analysis revealed an independent duplication of cell wall modules in bryophytes and angiosperms, suggesting a parallel evolution of cell wall pathways in land plants. We provide an online tool allowing plant researchers to perform these analyses at http://www.gene2function.de.

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

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.

C3 photosynthesis in the desert plant Rhazya stricta is fully functional at high temperatures and light intensities

The C3 plant Rhazya stricta is native to arid desert environment zones, where it experiences daily extremes of heat, light intensity (PAR) and high vapour pressure deficit (VPD). We measured the photosynthetic parameters in R. stricta in its native environment to assess the mechanisms that permit it to survive in these extreme conditions. Infrared gas exchange analysis examined diel changes in assimilation (A), stomatal conductance (gs ) and transpiration (E) on mature leaves of R. stricta. A/ci analysis was used to determine the effect of temperature on carboxylation capacity (Vc,max ) and the light- and CO2 -saturated rate of photosynthesis (Amax ). Combined chlorophyll fluorescence and gas exchange light response curve analysis at ambient and low oxygen showed that both carboxylation and oxygenation of Rubisco acted as the major sinks for the end products of electron transport. Physiological analysis in conjunction with gene expression analysis suggested that there are two isoforms of Rubisco activase which may provide an explanation for the ability of R. stricta to maintain Rubisco function at high temperatures. The potential to exploit this ability to cope with extreme temperatures is discussed in the context of future crop improvement.

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast and efficient processing of assembled RNA-Seq transcriptome data, developed to mitigate these challenges. TRAPID offers high-throughput open reading frame detection, frameshift correction and includes a functional, comparative and phylogenetic toolbox, making use of 175 reference proteomes. Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system. TRAPID is freely available at http://bioinformatics.psb.ugent.be/webtools/trapid/.

Comparative co-expression analysis in plant biology

The analysis of gene expression data generated by high-throughput microarray transcript profiling experiments has shown that transcriptionally coordinated genes are often functionally related. Based on large-scale expression compendia grouping multiple experiments, this guilt-by-association principle has been applied to study modular gene programmes, identify cis-regulatory elements or predict functions for unknown genes in different model plants. Recently, several studies have demonstrated how, through the integration of gene homology and expression information, correlated gene expression patterns can be compared between species. The incorporation of detailed functional annotations as well as experimental data describing protein-protein interactions, phenotypes or tissue specific expression, provides an invaluable source of information to identify conserved gene modules and translate biological knowledge from model organisms to crops. In this review, we describe the different steps required to systematically compare expression data across species. Apart from the technical challenges to compute and display expression networks from multiple species, some future applications of plant comparative transcriptomics are highlighted.

Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice

Microarray experiments have yielded massive amounts of expression information measured under various conditions for the model species Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Expression compendia grouping multiple experiments make it possible to define correlated gene expression patterns within one species and to study how expression has evolved between species. We developed a robust framework to measure expression context conservation (ECC) and found, by analyzing 4,630 pairs of orthologous Arabidopsis and rice genes, that 77% showed conserved coexpression. Examples of nonconserved ECC categories suggested a link between regulatory evolution and environmental adaptations and included genes involved in signal transduction, response to different abiotic stresses, and hormone stimuli. To identify genomic features that influence expression evolution, we analyzed the relationship between ECC, tissue specificity, and protein evolution. Tissue-specific genes showed higher expression conservation compared with broadly expressed genes but were fast evolving at the protein level. No significant correlation was found between protein and expression evolution, implying that both modes of gene evolution are not strongly coupled in plants. By integration of cis-regulatory elements, many ECC conserved genes were significantly enriched for shared DNA motifs, hinting at the conservation of ancestral regulatory interactions in both model species. Surprisingly, for several tissue-specific genes, patterns of concerted network evolution were observed, unveiling conserved coexpression in the absence of conservation of tissue specificity. These findings demonstrate that orthologs inferred through sequence similarity in many cases do not share similar biological functions and highlight the importance of incorporating expression information when comparing genes across species.

A guideline to family-wide comparative state-of-the-art quantitative RT-PCR analysis exemplified with a Brassicaceae cross-species seed germination case study

Comparative biology includes the comparison of transcriptome and quantitative real-time RT-PCR (qRT-PCR) data sets in a range of species to detect evolutionarily conserved and divergent processes. Transcript abundance analysis of target genes by qRT-PCR requires a highly accurate and robust workflow. This includes reference genes with high expression stability (i.e., low intersample transcript abundance variation) for correct target gene normalization. Cross-species qRT-PCR for proper comparative transcript quantification requires reference genes suitable for different species. We addressed this issue using tissue-specific transcriptome data sets of germinating Lepidium sativum seeds to identify new candidate reference genes. We investigated their expression stability in germinating seeds of L. sativum and Arabidopsis thaliana by qRT-PCR, combined with in silico analysis of Arabidopsis and Brassica napus microarray data sets. This revealed that reference gene expression stability is higher for a given developmental process between distinct species than for distinct developmental processes within a given single species. The identified superior cross-species reference genes may be used for family-wide comparative qRT-PCR analysis of Brassicaceae seed germination. Furthermore, using germinating seeds, we exemplify optimization of the qRT-PCR workflow for challenging tissues regarding RNA quality, transcript stability, and tissue abundance. Our work therefore can serve as a guideline for moving beyond Arabidopsis by establishing high-quality cross-species qRT-PCR.

Evolutionary transients in the rice transcriptome

In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may—in principle—be attributable to what we will refer to as “evolutionary transients”, referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots.

Journey through the past: 150 million years of plant genome evolution

The genome sequence of the plant model organism Arabidopsis thaliana was presented in December of the year 2000. Since then, the 125 Mb sequence has revealed many of its evolutionary secrets. Through comparative analyses with other plant genomes, we know that the genome of A. thaliana, or better that of its ancestors, has undergone at least three whole genome duplications during the last 120 or so million years. The first duplication seems to have occurred at the dawn of dicot evolution, while the later duplications probably occurred <70 million years ago (Ma). One of those younger genome-wide duplications might be linked to the K-T extinction. Following these duplication events, the ancestral A. thaliana genome was hugely rearranged and gene copies have been massively lost. During the last 10 million years of its evolution, almost half of its genome was lost due to hundreds of thousands of small deletions. Here, we reconstruct plant genome evolution from the early angiosperm ancestor to the current A. thaliana genome, covering about 150 million years of evolution characterized by gene and genome duplications, genome rearrangements and genome reduction.

A chromatin perspective of plant cell cycle progression

The finely regulated series of events that span from the birth of a cell to the production of two new born cells encompass the cell cycle. Cell cycle progression occurs in a unidirectional manner and requires passing through a number of stages in response to cellular, developmental and environmental cues. In addition to these signaling cascades, transcriptional regulation plays a major role and acts coordinately with genome duplication during S-phase and chromosome segregation during mitosis. In this context, chromatin is revealing as a highly dynamic and major player in cell cycle regulation not only owing to the changes that occur as a consequence of cell cycle progression but also because some specific chromatin modifications are crucial to move across the cell cycle. These are particularly relevant for controlling transcriptional activation and repression as well as initiation of DNA replication and chromosome compaction. As a consequence the epigenetic landscape of a proliferating cell is very complex throughout the cell cycle. These aspects of chromatin dynamics together with the impact of epigenetic modifications on cell proliferation will be discussed in this article. This article is part of a Special Issue entitled: Epigenetic Control of cellular and developmental processes in plants.

Peroxidase profiling reveals genetic linkage between peroxidase gene clusters and basal host and non-host resistance to rusts and mildew in barley

BACKGROUND

Higher plants possess a large multigene family encoding secreted class III peroxidase (Prx) proteins. Peroxidases appear to be associated with plant disease resistance based on observations of induction during disease challenge and the presence or absence of isozymes in resistant vs susceptible varieties. Despite these associations, there is no evidence that allelic variation of peroxidases directly determines levels of disease resistance.

METHODOLOGY/PRINCIPAL FINDINGS

The current study introduces a new strategy called Prx-Profiling. We showed that with this strategy a large number of peroxidase genes can be mapped on the barley genome. In order to obtain an estimate of the total number of Prx clusters we followed a re-sampling procedure, which indicated that the barley genome contains about 40 peroxidase gene clusters. We examined the association between the Prxs mapped and the QTLs for resistance of barley to homologous and heterologous rusts, and to the barley powdery mildew fungus. We report that 61% of the QTLs for partial resistance to P. hordei, 61% of the QTLs for resistance to B. graminis and 47% of the QTLs for non-host resistance to other Puccinia species co-localize with Prx based markers.

CONCLUSIONS/SIGNIFICANCE

We conclude that Prx-Profiling was effective in finding the genetic location of Prx genes on the barley genome. The finding that QTLs for basal resistance to rusts and powdery mildew fungi tend to co-locate with Prx clusters provides a base for exploring the functional role of Prx-related genes in determining natural differences in levels of basal resistance.

PLAZA: a comparative genomics resource to study gene and genome evolution in plants

The number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis has significantly altered our view on the complexity of genome organization, gene function, and regulatory pathways. To explore all this genome information, a centralized infrastructure is required where all data generated by different sequencing initiatives is integrated and combined with advanced methods for data mining. Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/). This resource integrates structural and functional annotation of published plant genomes together with a large set of interactive tools to study gene function and gene and genome evolution. Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intraspecies whole-genome dot plots, and genomic colinearity between species. Through the integration of high confidence Gene Ontology annotations and tree-based orthology between related species, thousands of genes lacking any functional description are functionally annotated. Advanced query systems, as well as multiple interactive visualization tools, are available through a user-friendly and intuitive Web interface. In addition, detailed documentation and tutorials introduce the different tools, while the workbench provides an efficient means to analyze user-defined gene sets through PLAZA's interface. In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage.

The flowering world: a tale of duplications

Flowering plants contain many genes, most of which were created during the past 200 or so million years through small- and large-scale duplications. Paleo-polyploidy events, in particular, have been the subject of much recent research. There is a growing consensus that one or more genome doubling or merging events occurred early during the evolution of the flowering plants, and that many lineages have since undergone additional, independent and more recent duplication events. Here, we review the difficulties in determining the number of genome duplications and discuss how the completion of some additional genome sequences of species occupying key phylogenetic positions has led to a better understanding of the timing of certain duplication events. This is important if we want to demonstrate the significance of genome duplications for the evolution and radiation of (different groups of) flowering plants.

Unique genes in plants: specificities and conserved features throughout evolution

Background

Plant genomes contain a high proportion of duplicated genes as a result of numerous whole, segmental and local duplications. These duplications lead up to the formation of gene families, which are the usual material for many evolutionary studies. However, all characterized genomes include single-copy (unique) genes that have not received much attention. Unlike gene duplication, gene loss is not an unspecific mechanism but is rather influenced by a functional selection. In this context, we have established and used stringent criteria in order to identify suitable sets of unique genes present in plant proteomes. Comparisons of unique genes in the green phylum were used to characterize the gene and protein features exhibited by both conserved and species-specific unique genes.

Results

We identified the unique genes within both A. thaliana and O. sativa genomes and classified them according to the number of homologs in the alternative species: none (U{1:0}), one (U{1:1}) or several (U{1:m}). Regardless of the species, all the genes in these groups present some conserved characteristics, such as small average protein size and abnormal intron number. In order to understand the origin and function of unique genes, we further characterized the U{1:1} gene pairs. The possible involvement of sequence convergence in the creation of U{1:1} pairs was discarded due to the frequent conservation of intron positions. Furthermore, an orthology relationship between the two members of each U{1:1} pair was strongly supported by a high conservation in the protein sizes and transcription levels. Within the promoter of the unique conserved genes, we found a number of TATA and TELO boxes that specifically differed from their mean number in the whole genome. Many unique genes have been conserved as unique through evolution from the green alga Ostreococcus lucimarinus to higher plants. Plant unique genes may also have homologs in bacteria and we showed a link between the targeting towards plastids of proteins encoded by plant nuclear unique genes and their homology with a bacterial protein.

Conclusion

Many of the A. thaliana and O. sativa unique genes are conserved in plants for which the ancestor diverged at least 725 million years ago (MYA). Half of these genes are also present in other eukaryotic and/or prokaryotic species. Thus, our results indicate that (i) a strong negative selection pressure has conserved a number of genes as unique in genomes throughout evolution, (ii) most unique genes are subjected to a low divergence rate, (iii) they have some features observed in housekeeping genes but for most of them there is no functional annotation and (iv) they may have an ancient origin involving a possible gene transfer from ancestral chloroplasts or bacteria to the plant nucleus.

Chromatin dynamics during the plant cell cycle

Cell cycle progression depends on a highly regulated series of events of which transcriptional control plays a major role. In addition, during the S-phase not only DNA but chromatin as a whole needs to be faithfully duplicated. Therefore, both nucleosome dynamics as well as local changes in chromatin organization, including introduction and/or removal of covalent DNA and histone modifications, at genes with a key role in cell proliferation, are of primary relevance. Chromatin duplication during the S-phase and the chromosome segregation during mitosis are cell cycle stages critical for maintenance of epigenetic marks or for allowing the daughter products to acquire a distinct epigenetic landscape and, consequently, a unique cell fate decision. These aspects of chromatin dynamics together with the strict coupling of cell proliferation, cell differentiation and post-embryonic organogenesis have a profound impact on plant growth, development and response to external signals.

Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

The chromalveolates form a highly diverse and fascinating assemblage of organisms, ranging from obligatory parasites such as Plasmodium to free-living ciliates and algae such as kelps, diatoms, and dinoflagellates. Many of the species in this monophyletic grouping are of major medical, ecological, and economical importance. Nevertheless, their genome evolution is much less well studied than that of higher plants, animals, or fungi. In the current study, we have analyzed and compared 12 chromalveolate species for which whole-sequence information is available and provide a detailed picture on gene loss and gene gain in the different lineages. As expected, many gene loss and gain events can be directly correlated with the lifestyle and specific adaptations of the organisms studied. For instance, in the obligate intracellular Apicomplexa we observed massive loss of genes that play a role in general basic processes such as amino acid, carbohydrate, and lipid metabolism, reflecting the transition of a free-living to an obligate intracellular lifestyle. In contrast, many gene families show species-specific expansions, such as those in the plant pathogen oomycete Phytophthora that are involved in degrading the plant cell wall polysaccharides to facilitate the pathogen invasion process. In general, chromalveolates show a tremendous difference in genome structure and evolution and in the number of genes they have lost or gained either through duplication or horizontal gene transfer.

Identification and characterization of lineage-specific genes within the Poaceae

Using the rice (Oryza sativa) sp. japonica genome annotation, along with genomic sequence and clustered transcript assemblies from 184 species in the plant kingdom, we have identified a set of 861 rice genes that are evolutionarily conserved among six diverse species within the Poaceae yet lack significant sequence similarity with plant species outside the Poaceae. This set of evolutionarily conserved and lineage-specific rice genes is termed conserved Poaceae-specific genes (CPSGs) to reflect the presence of significant sequence similarity across three separate Poaceae subfamilies. The vast majority of rice CPSGs (86.6%) encode proteins with no putative function or functionally characterized protein domain. For the remaining CPSGs, 8.8% encode an F-box domain-containing protein and 4.5% encode a protein with a putative function. On average, the CPSGs have fewer exons, shorter total gene length, and elevated GC content when compared with genes annotated as either transposable elements (TEs) or those genes having significant sequence similarity in a species outside the Poaceae. Multiple sequence alignments of the CPSGs with sequences from other Poaceae species show conservation across a putative domain, a novel domain, or the entire coding length of the protein. At the genome level, syntenic alignments between sorghum (Sorghum bicolor) and 103 of the 861 rice CPSGs (12.0%) could be made, demonstrating an additional level of conservation for this set of genes within the Poaceae. The extensive sequence similarity in evolutionarily distinct species within the Poaceae family and an additional screen for TE-related structural characteristics and sequence discounts these CPSGs as being misannotated TEs. Collectively, these data confirm that we have identified a specific set of genes that are highly conserved within, as well as specific to, the Poaceae.

A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies

Relatively few indica rice full-length cDNAs were available to aid in the annotation of rice genes. The data presented here described the sequencing and analysis of 10,096 full-length cDNAs from Oryza sativa subspecies indica Guangluai 4. Of them, 9,029 matched rice genomic sequences in publicly-available databases, and 1,200 were identified as new rice genes. Comparison with the knowledge-based Oryza Molecular Biological Encyclopedia japonica cDNA collection indicated that 3,316 (41.6%) of the 7,965 indica-japonica cDNA pairs showed no distinct variations at protein level (2,117 indica-japonica cDNA pairs showed fully identical and 1,199 indica-japonica cDNA pairs showed no frame shift). Moreover, 3,645 (45.8%) of the indica-japonica pairs showed substantial differences at the protein level due to single nucleotide polymorphisms (SNPs), insertions or deletions, and sequence-segment variations between indica and japonica subspecies. Further experimental verifications using PCR screening and quantitative reverse transcriptional PCR revealed unique transcripts for indica subspecies. Comparative analysis also showed that most of rice genes were evolved under purifying selection. These variations might distinguish the phenotypic changes of the two cultivated rice subspecies indica and japonica. Analysis of these cDNAs extends known rice genes and identifies new ones in rice.

Large-scale comparative genomic analyses of cytoplasmic membrane transport systems in prokaryotes

The recent advancements in genome sequencing make it possible for the comparative analyses of essential cellular processes like transport in organisms across the three domains of life. Membrane transporters play crucial roles in fundamental cellular processes and functions in prokaryotic systems. Between 3 and 16% of open reading frames in prokaryotic genomes were predicted to encode membrane transport proteins, emphasizing the importance of transporters in their lifestyles. Hierarchical clustering of phylogenetic profiles of transporter families, which are derived from the presence or absence of a certain transporter family, showed distinct clustering patterns for obligate intracellular organisms, plant/soil-associated microbes and autotrophs. Obligate intracellular organisms possess the fewest types and number of transporters presumably due to their relatively stable living environment, while plant/soil-associated organisms generally encode the largest variety and number of transporters. A group of autotrophs are clustered together largely due to their absence of transporters for carbohydrate and organic nutrients and the presence of transporters for inorganic nutrients. Inside of each group, organisms are further clustered by their phylogenetic properties. These findings strongly suggest the correlation of transporter profiles to both evolutionary history and the overall physiology and lifestyles of the organisms.

Dating the early evolution of plants: detection and molecular clock analyses of orthologs

Orthologs generally are under selective pressure against loss of function, while paralogs usually accumulate mutations and finally die or deviate in terms of function or regulation. Most ortholog detection methods contaminate the resulting datasets with a substantial amount of paralogs. Therefore we aimed to implement a straightforward method that allows the detection of ortholog clusters with a reduced amount of paralogs from completely sequenced genomes. The described cross-species expansion of the reciprocal best BLAST hit method is a time-effective method for ortholog detection, which results in 68% truly orthologous clusters and the procedure specifically enriches single-copy orthologs. The detection of true orthologs can provide a phylogenetic toolkit to better understand evolutionary processes. In a study across six photosynthetic eukaryotes, nuclear genes of putative mitochondrial origin were shown to be over-represented among single copy orthologs. These orthologs are involved in fundamental biological processes like amino acid metabolism or translation. Molecular clock analyses based on this dataset yielded divergence time estimates for the red/green algae (1,142 MYA), green algae/land plant (725 MYA), mosses/seed plant (496 MYA), gymno-/angiosperm (385 MYA) and monocotyledons/core eudicotyledons (301 MYA) divergence times.

Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics

A strategy combining classical motif overrepresentation in co-regulated genes with comparative footprinting is applied to identify 80 transcription factor binding sites and 139 regulatory modules in Arabidopsis thaliana.

Background

Transcriptional regulation plays an important role in the control of many biological processes. Transcription factor binding sites (TFBSs) are the functional elements that determine transcriptional activity and are organized into separable cis-regulatory modules, each defining the cooperation of several transcription factors required for a specific spatio-temporal expression pattern. Consequently, the discovery of novel TFBSs in promoter sequences is an important step to improve our understanding of gene regulation.

Results

Here, we applied a detection strategy that combines features of classic motif overrepresentation approaches in co-regulated genes with general comparative footprinting principles for the identification of biologically relevant regulatory elements and modules in Arabidopsis thaliana, a model system for plant biology. In total, we identified 80 TFBSs and 139 regulatory modules, most of which are novel, and primarily consist of two or three regulatory elements that could be linked to different important biological processes, such as protein biosynthesis, cell cycle control, photosynthesis and embryonic development. Moreover, studying the physical properties of some specific regulatory modules revealed that Arabidopsis promoters have a compact nature, with cooperative TFBSs located in close proximity of each other.

Conclusion

These results create a starting point to unravel regulatory networks in plants and to study the regulation of biological processes from a systems biology point of view.

Gene expression during the induction, maintenance, and release of dormancy in apical buds of poplar

The perennial lifestyle of trees is characterized by seasonal cycles of growth and dormancy. The recurrent transitions into and out of dormancy represent an adaptation mechanism that largely determines survival and, hence, the geographical distribution of tree species. To understand better the molecular basis of bud dormancy, cDNA-amplified fragment length polymorphism (AFLP) transcript profiling was used to map differential gene expression during dormancy induction, dormancy, dormancy release by chilling, and subsequent bud break in apical buds of poplar (Populus tremulaxP. alba). Unexpectedly, besides poplar transcript sequences, the cDNA-AFLP profiles revealed sequence signatures originating from a complex bacterial community, which was more pronounced during dormancy and displayed temporal dynamics in composition and complexity. Based on poplar gene expression dynamics, processes and potential regulators during different phases of dormancy are described. Novel genes were linked to a crucial transitory step in dormancy induction, and to dormancy release through chilling, a molecularly unresolved phenomenon. One WRKY- and two ERF-related transcription factors were similarly expressed during the transition to dormancy in apical and axillary buds. These regulatory genes could be involved in the differentiation of stipule-like leaf organs protecting the bud, or act during the growth-dormancy transition in the meristem, revealing commonalities between para- and endodormancy.

Comparative genomics as a tool for gene discovery

With the increasing availability of data from multiple eukaryotic genome sequencing projects, attention has focused on interspecific comparisons to discover novel genes and transcribed genomic sequences. Generally, these extrinsic strategies combine ab initio gene prediction with expression and/or homology data to identify conserved gene candidates between two or more genomes. Interspecific sequence analyses have proven invaluable for the improvement of existing annotations, automation of annotation, and identification of novel coding regions and splice variants. Further, comparative genomic approaches hold the promise of improved prediction of terminal or small exons, microRNA precursors, and small peptide-encoding open reading frames--sequence elements that are difficult to identify through purely intrinsic methodologies in the absence of experimental data.

Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes

Whole-genome transporter analyses have been conducted on 141 organisms whose complete genome sequences are available. For each organism, the complete set of membrane transport systems was identified with predicted functions, and classified into protein families based on the transporter classification system. Organisms with larger genome sizes generally possessed a relatively greater number of transport systems. In prokaryotes and unicellular eukaryotes, the significant factor in the increase in transporter content with genome size was a greater diversity of transporter types. In contrast, in multicellular eukaryotes, greater number of paralogs in specific transporter families was the more important factor in the increase in transporter content with genome size. Both eukaryotic and prokaryotic intracellular pathogens and endosymbionts exhibited markedly limited transport capabilities. Hierarchical clustering of phylogenetic profiles of transporter families, derived from the presence or absence of a certain transporter family, showed that clustering patterns of organisms were correlated to both their evolutionary history and their overall physiology and lifestyles.

Membrane transporters are the cell's equivalent of delivery vehicles, garbage disposals, and communication systems—proteins that negotiate through cell membranes to deliver essential nutrients, eject waste products, and help the cell sense environmental conditions around it. Membrane transport systems play crucial roles in fundamental cellular processes of all organisms. The suite of transporters in any one organism also sheds light on its lifestyle and physiology. Up to now, analysis of membrane transporters has been limited mainly to the examination of transporter genes of individual organisms. But advances in genome sequencing have now made it possible for scientists to compare transport and other essential cellular processes across a range of organisms in all three domains of life.

Ren and Paulsen present the first comprehensive bioinformatic analysis of the predicted membrane transporter content of 141 different prokaryotic and eukaryotic organisms. The scientists developed a new computational application of the phylogenetic profiling approach to cluster together organisms that appear to have similar suites of transporters. For example, a group of obligate intracellular pathogens and endosymbionts possess only limited transporter systems in spite of the massive metabolite fluxes one would expect between the symbionts and their host. This is likely due to the relatively static nature of their intracellular environment. In contrast, a cluster of plant/soil-associated microbes encode a robust array of transporters, reflecting the organisms' versatility as well as their exposure to a wide range of different substrates in their natural environment.