Sequenced Plant Genomes Research Articles

Genome-wide analysis of eukaryote thaumatin-like proteins (TLPs) with an emphasis on poplar.

BackgroundPlant inducible immunity includes the accumulation of a set of defense proteins during infection called pathogenesis-related (PR) proteins, which are grouped into families termed PR-1 to PR-17. The PR-5 family is composed of thaumatin-like proteins (TLPs), which are responsive to biotic and abiotic stress and are widely studied in plants. TLPs were also recently discovered in fungi and animals. In the poplar genome, TLPs are over-represented compared with annual species and their transcripts strongly accumulate during stress conditions.ResultsOur analysis of the poplar TLP family suggests that the expansion of this gene family was followed by diversification, as differences in expression patterns and predicted properties correlate with phylogeny. In particular, we identified a clade of poplar TLPs that cluster to a single 350 kb locus of chromosome I and that are up-regulated by poplar leaf rust infection. A wider phylogenetic analysis of eukaryote TLPs - including plant, animal and fungi sequences - shows that TLP gene content and diversity increased markedly during land plant evolution. Mapping the reported functions of characterized TLPs to the eukaryote phylogenetic tree showed that antifungal or glycan-lytic properties are widespread across eukaryote phylogeny, suggesting that these properties are shared by most TLPs and are likely associated with the presence of a conserved acidic cleft in their 3D structure. Also, we established an exhaustive catalog of TLPs with atypical architectures such as small-TLPs, TLP-kinases and small-TLP-kinases, which have potentially developed alternative functions (such as putative receptor kinases for pathogen sensing and signaling).ConclusionOur study, based on the most recent plant genome sequences, provides evidence for TLP gene family diversification during land plant evolution. We have shown that the diverse functions described for TLPs are not restricted to specific clades but seem to be universal among eukaryotes, with some exceptions likely attributable to atypical protein structures. In the perennial plant model Populus, we unravelled the TLPs likely involved in leaf rust resistance, which will provide the foundation for further functional investigations.

De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification

Chickpea ranks third among the food legume crops production in the world. However, the genomic resources available for chickpea are still very limited. In the present study, the transcriptome of chickpea was sequenced with short reads on Illumina Genome Analyzer platform. We have assessed the effect of sequence quality, various assembly parameters and assembly programs on the final assembly output. We assembled ∼107million high-quality trimmed reads using Velvet followed by Oases with optimal parameters into a non-redundant set of 53 409 transcripts (≥100 bp), representing about 28 Mb of unique transcriptome sequence. The average length of transcripts was 523 bp and N50 length of 900 bp with coverage of 25.7 rpkm (reads per kilobase per million). At the protein level, a total of 45 636 (85.5%) chickpea transcripts showed significant similarity with unigenes/predicted proteins from other legumes or sequenced plant genomes. Functional categorization revealed the conservation of genes involved in various biological processes in chickpea. In addition, we identified simple sequence repeat motifs in transcripts. The chickpea transcripts set generated here provides a resource for gene discovery and development of functional molecular markers. In addition, the strategy for de novo assembly of transcriptome data presented here will be helpful in other similar transcriptome studies.

Plant expressed sequence tags databases: practical uses and the improvement of their searches using network module analysis

Sequencing technology has been rapidly advancing. Giga-sequencers, which produce several gigabases of fragmented sequences per run, are attractive for decoding genomes and expressed sequence tags (ESTs). A variety of plant genomes and ESTs have been sequenced since the decoding of the genome of Arabidopsis thaliana, the model plant. ESTs are useful for functional analyses of genes and proteins and as biomarkers, which are used to identify particular tissues and conditions due to the specificity of their expression. Sequenced plant genomes and ESTs have been entered into public databases, where they are freely downloadable. Sequences representative of particular functions or structures have been collected from public databases to curate smaller databases useful for studying protein function. Here, we discuss the uses of the currently available plant EST datasets. We also demonstrate the use of network module analysis to perform more stable (or irrespective of the difference of performance in each analyzing PC) homology searches and to provide more information on molecular functions of plant ESTs and proteins.

Systems Biology in a Commercial Quality Study of the JapaneseAngelicaRadix: Toward an Understanding of Traditional Medicinal Plants

The commercial quality of Japanese Angelica radices -- Angelica acutiloba Kitagawa (Yamato-toki) and A. acutiloba Kitagawa var. sugiyama Hikino (Hokkai-toki) -- used in Kampo traditional herbal medicines, was studied by use of omics technologies. Complementary and alternative medical providers have observed in their clinical experience that differences in radix commercial quality reflect the differences in pharmacological responses; however, there has been little scientific examination of this phenomenon. The approach of omics, including metabolomics, transcriptomics, genomics, and informatics revealed a distinction between the radix-quality grades based on their metabolites, gene expression in human subjects, and plant genome sequences. Systems biology, constructing a network of omics data used to analyze this complex system, is expected to be a powerful tool for enhancing the study of radix quality and furthering a comprehensive understanding of all medicinal plants.

Genomic tools development for Aquilegia: construction of a BAC-based physical map

BackgroundThe genus Aquilegia, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relatively unstudied clade in the angiosperm phylogenetic tree that bridges the gap between these two major plant groups. Aquilegia species are closely related and their distribution covers highly diverse habitats. These provide rich resources to better understand the genetic basis of adaptation to different pollinators and habitats that in turn leads to rapid speciation. To gain insights into the genome structure and facilitate gene identification, comparative genomics and whole-genome shotgun sequencing assembly, BAC-based genomics resources are of crucial importance.ResultsBAC-based genomic resources, including two BAC libraries, a physical map with anchored markers and BAC end sequences, were established from A. formosa. The physical map was composed of a total of 50,155 BAC clones in 832 contigs and 3939 singletons, covering 21X genome equivalents. These contigs spanned a physical length of 689.8 Mb (~2.3X of the genome) suggesting the complex heterozygosity of the genome. A set of 197 markers was developed from ESTs induced by drought-stress, or involved in anthocyanin biosynthesis or floral development, and was integrated into the physical map. Among these were 87 genetically mapped markers that anchored 54 contigs, spanning 76.4 Mb (25.5%) across the genome. Analysis of a selection of 12,086 BAC end sequences (BESs) from the minimal tiling path (MTP) allowed a preview of the Aquilegia genome organization, including identification of transposable elements, simple sequence repeats and gene content. Common repetitive elements previously reported in both monocots and core eudicots were identified in Aquilegia suggesting the value of this genome in connecting the two major plant clades. Comparison with sequenced plant genomes indicated a higher similarity to grapevine (Vitis vinifera) than to rice and Arabidopsis in the transcriptomes.ConclusionsThe A. formosa BAC-based genomic resources provide valuable tools to study Aquilegia genome. Further integration of other existing genomics resources, such as ESTs, into the physical map should enable better understanding of the molecular mechanisms underlying adaptive radiation and elaboration of floral morphology.

Scaffolding a Caenorhabditis nematode genome with RNA-seq.

Efficient sequencing of animal and plant genomes by next-generation technology should allow many neglected organisms of biological and medical importance to be better understood. As a test case, we have assembled a draft genome of Caenorhabditis sp. 3 PS1010 through a combination of direct sequencing and scaffolding with RNA-seq. We first sequenced genomic DNA and mixed-stage cDNA using paired 75-nt reads from an Illumina GAII. A set of 230 million genomic reads yielded an 80-Mb assembly, with a supercontig N50 of 5.0 kb, covering 90% of 429 kb from previously published genomic contigs. Mixed-stage poly(A)(+) cDNA gave 47.3 million mappable 75-mers (including 5.1 million spliced reads), which separately assembled into 17.8 Mb of cDNA, with an N50 of 1.06 kb. By further scaffolding our genomic supercontigs with cDNA, we increased their N50 to 9.4 kb, nearly double the average gene size in C. elegans. We predicted 22,851 protein-coding genes, and detected expression in 78% of them. Multigenome alignment and data filtering identified 2672 DNA elements conserved between PS1010 and C. elegans that are likely to encode regulatory sequences or previously unknown ncRNAs. Genomic and cDNA sequencing followed by joint assembly is a rapid and useful strategy for biological analysis.

Harvesting the apple genome

The genome sequence of the domesticated apple has been assembled and compared to previously sequenced plant genomes. The genetic sequence of the 17 apple chromosomes shows evidence of a recent genome duplication that may have spawned the additional gene family members needed for the evolution and development of the unique fruit structure of the apple termed the pome.

Implementing a Rational and Consistent Nomenclature for Serine/Arginine-Rich Protein Splicing Factors (SR Proteins) in Plants

Growing interest in alternative splicing in plants and the extensive sequencing of new plant genomes necessitate more precise definition and classification of genes coding for splicing factors. SR proteins are a family of RNA binding proteins, which function as essential factors for constitutive and alternative splicing. We propose a unified nomenclature for plant SR proteins, taking into account the newly revised nomenclature of the mammalian SR proteins and a number of plant-specific properties of the plant proteins. We identify six subfamilies of SR proteins in Arabidopsis thaliana and rice (Oryza sativa), three of which are plant specific. The proposed subdivision of plant SR proteins into different subfamilies will allow grouping of paralogous proteins and simple assignment of newly discovered SR orthologs from other plant species and will promote functional comparisons in diverse plant species.

MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences

We present MASiVE, an expertly built tool for the large-scale, yet sensitive and highly accurate, discovery, preliminary analysis and insertion age estimation of intact Sirevirus LTR-retrotransposons in plant genomic sequences. Validation was based on the recently available and annotated large maize chromosome one. Results show a considerable improvement in the annotation of Sireviruses, and support our approach as an important addition to the bioinformatics toolbox of plant biologists. PERL source code and essential files are available online at http://bat.ina.certh.gr/tools/masive/. The freely available Vmatch, LTRharvest, Wise2, and MAFFT algorithms are required.

Insights from the Comparison of Plant Genome Sequences

The next decade will see essentially completed sequences for multiple branches of virtually all angiosperm clades that include major crops and/or botanical models. These sequences will provide a powerful framework for relating genome-level events to aspects of morphological and physiological variation that have contributed to the colonization of much of the planet by angiosperms. Clarification of the fundamental angiosperm gene set, its arrangement, lineage-specific variations in gene repertoire and arrangement, and the fates of duplicated gene pairs will advance knowledge of functional and regulatory diversity and perhaps shed light on adaptation by lineages to whole-genome duplication, which is a distinguishing feature of angiosperm evolution. Better understanding of the relationships among angiosperm genomes promises to provide a firm foundation upon which to base translational genomics: the leveraging of hard-won structural and functional genomic information from crown botanical models to dissect novel and, in some cases, economically important features in many additional organisms.

Genomic organization of plant aminopropyl transferases

Aminopropyl transferases like spermidine synthase (SPDS; EC 2.5.1.16), spermine synthase and thermospermine synthase (SPMS, tSPMS; EC 2.5.1.22) belong to a class of widely distributed enzymes that use decarboxylated S-adenosylmethionine as an aminopropyl donor and putrescine or spermidine as an amino acceptor to form in that order spermidine, spermine or thermospermine. We describe the analysis of plant genomic sequences encoding SPDS, SPMS, tSPMS and PMT (putrescine N-methyltransferase; EC 2.1.1.53). Genome organization (including exon size, gain and loss, as well as intron number, size, loss, retention, placement and phase, and the presence of transposons) of plant aminopropyl transferase genes were compared between the genomic sequences of SPDS, SPMS and tSPMS from Zea mays, Oryza sativa, Malus x domestica, Populus trichocarpa, Arabidopsis thaliana and Physcomitrella patens. In addition, the genomic organization of plant PMT genes, proposed to be derived from SPDS during the evolution of alkaloid metabolism, is illustrated. Herein, a particular conservation and arrangement of exon and intron sequences between plant SPDS, SPMS and PMT genes that clearly differs with that of ACL5 genes, is shown. The possible acquisition of the plant SPMS exon II and, in particular exon XI in the monocot SPMS genes, is a remarkable feature that allows their differentiation from SPDS genes. In accordance with our in silico analysis, functional complementation experiments of the maize ZmSPMS1 enzyme (previously considered to be SPDS) in yeast demonstrated its spermine synthase activity. Another significant aspect is the conservation of intron sequences among SPDS and PMT paralogs. In addition the existence of microsynteny among some SPDS paralogs, especially in P. trichocarpa and A. thaliana, supports duplication events of plant SPDS genes. Based in our analysis, we hypothesize that SPMS genes appeared with the divergence of vascular plants by a processes of gene duplication and the acquisition of unique exons of as-yet unknown origin.

RNase T2 genes from rice and the evolution of secretory ribonucleases in plants

The plant RNase T2 family is divided into two different subfamilies. S-RNases are involved in rejection of self-pollen during the establishment of self-incompatibility in three plant families. S-like RNases, on the other hand, are not involved in self-incompatibility, and although gene expression studies point to a role in plant defense and phosphate recycling, their biological roles are less well understood. Although S-RNases have been subjects of many phylogenetic studies, few have included an extensive analysis of S-like RNases, and genome-wide analyses to determine the number of S-like RNases in fully sequenced plant genomes are missing. We characterized the eight RNase T2 genes present in the Oryza sativa genome; and we also identified the full complement of RNase T2 genes present in other fully sequenced plant genomes. Phylogenetics and gene expression analyses identified two classes among the S-like RNase subfamily. Class I genes show tissue specificity and stress regulation. Inactivation of RNase activity has occurred repeatedly throughout evolution. On the other hand, Class II seems to have conserved more ancestral characteristics; and, unlike other S-like RNases, genes in this class are conserved in all plant species analyzed and most are constitutively expressed. Our results suggest that gene duplication resulted in high diversification of Class I genes. Many of these genes are differentially expressed in response to stress, and we propose that protein characteristics, such as the increase in basic residues can have a defense role independent of RNase activity. On the other hand, constitutive expression and phylogenetic conservation suggest that Class II S-like RNases may have a housekeeping role.

Analysis of histone acetyltransferase and deacetylase families of Vitis vinifera

Histone acetyltransferases (HATs) and deacetylases (HDACs) play critical roles in the regulation of chromatin structure and gene expression. In plants, these genes are emerging as crucial players in all aspects of development. As part of our study regarding the growth and development of grapevine (Vitis vinifera), we report the genome-wide analysis of HAT and HDAC genes. This analysis revealed the presence of 7 and 13 genes coding for putative HATs and HDACs, respectively. In this work, we present a complete analysis of these families with regards to their phylogenetic relationships with orthologous genes identified in other sequenced plant genomes, their genome location, gene structure and expression. The genes identified can be grouped into different families as has been previously described for other eukaryotic species. The organ-specific expression pattern of HAT and HDAC genes indicates that some genes have different expression profiles, and their potential involvement during grape development is discussed.

Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis

Isochorismate synthase (ICS) converts chorismate to isochorismate for the biosynthesis of phylloquinone, an essential cofactor for photosynthetic electron transport. ICS is also required for salicylic acid (SA) synthesis during Arabidopsis defense. In several other species, including Populus, SA is derived primarily from the phenylpropanoid pathway. We therefore sought to investigate ICS regulation in Populus to learn the extent of ICS involvement in SA synthesis and defense. Arabidopsis harbors duplicated AtICS genes that differ in their exon-intron structure, basal expression, and stress inducibility. In contrast, we found a single ICS gene in Populus and six other sequenced plant genomes, pointing to the AtICS duplication as a lineage-specific event. The Populus ICS encodes a functional plastidic enzyme, and was not responsive to stresses that stimulated phenylpropanoid accumulation. Populus ICS underwent extensive alternative splicing that was rare for the duplicated AtICSs. Sequencing of 184 RT-PCR Populus clones revealed 37 alternative splice variants, with normal transcripts representing approximately 50% of the population. When expressed in Arabidopsis, Populus ICS again underwent alternative splicing, but did not produce normal transcripts to complement AtICS1 function. The splice-site sequences of Populus ICS are unusual, suggesting a causal link between junction sequence, alternative splicing, and ICS function. We propose that gene duplication and alternative splicing of ICS evolved independently in Arabidopsis and Populus in accordance with their distinct defense strategies. AtICS1 represents a divergent isoform for inducible SA synthesis during defense. Populus ICS primarily functions in phylloquinone biosynthesis, a process that can be sustained at low ICS transcript levels.

Rating Last Year's Areas to Watch

Science 's editors clearly foresaw this year's burgeoning of plant genome sequences, progress on emissions reductions in the run-up to the U.N. conference in Copenhagen, and the continued failure to spot dark matter. Last year's other predictions will take more time to come to fruition.

Plant genome sequencing: applications for crop improvement

DNA sequencing technology is undergoing a revolution with the commercialization of second generation technologies capable of sequencing thousands of millions of nucleotide bases in each run. The data explosion resulting from this technology is likely to continue to increase with the further development of second generation sequencing and the introduction of third generation single-molecule sequencing methods over the coming years. The question is no longer whether we can sequence crop genomes which are often large and complex, but how soon can we sequence them? Even cereal genomes such as wheat and barley which were once considered intractable are coming under the spotlight of the new sequencing technologies and an array of new projects and approaches are being established. The increasing availability of DNA sequence information enables the discovery of genes and molecular markers associated with diverse agronomic traits creating new opportunities for crop improvement. However, the challenge remains to convert this mass of data into knowledge that can be applied in crop breeding programs.

SolEST database: a "one-stop shop" approach to the study of Solanaceae transcriptomes

BackgroundSince no genome sequences of solanaceous plants have yet been completed, expressed sequence tag (EST) collections represent a reliable tool for broad sampling of Solanaceae transcriptomes, an attractive route for understanding Solanaceae genome functionality and a powerful reference for the structural annotation of emerging Solanaceae genome sequences.DescriptionWe describe the SolEST database http://biosrv.cab.unina.it/solestdb which integrates different EST datasets from both cultivated and wild Solanaceae species and from two species of the genus Coffea. Background as well as processed data contained in the database, extensively linked to external related resources, represent an invaluable source of information for these plant families. Two novel features differentiate SolEST from other resources: i) the option of accessing and then visualizing Solanaceae EST/TC alignments along the emerging tomato and potato genome sequences; ii) the opportunity to compare different Solanaceae assemblies generated by diverse research groups in the attempt to address a common complaint in the SOL community.ConclusionDifferent databases have been established worldwide for collecting Solanaceae ESTs and are related in concept, content and utility to the one presented herein. However, the SolEST database has several distinguishing features that make it appealing for the research community and facilitates a "one-stop shop" for the study of Solanaceae transcriptomes.

De novo sequencing of plant genomes using second-generation technologies

The ability to sequence the DNA of an organism has become one of the most important tools in modern biological research. Until recently, the sequencing of even small model genomes required substantial funds and international collaboration. The development of 'second-generation' sequencing technology has increased the throughput and reduced the cost of sequence generation by several orders of magnitude. These new methods produce vast numbers of relatively short reads, usually at the expense of read accuracy. Since the first commercial second-generation sequencing system was produced by 454 Technologies and commercialised by Roche, several other companies including Illumina, Applied Biosystems, Helicos Biosciences and Pacific Biosciences have joined the competition. Because of the relatively high error rate and lack of assembly tools, short-read sequence technology has mainly been applied to the re-sequencing of genomes. However, some recent applications have focused on the de novo assembly of these data. De novo assembly remains the greatest challenge for DNA sequencing and there are specific problems for second generation sequencing which produces short reads with a high error rate. However, a number of different approaches for short-read assembly have been proposed and some have been implemented in working software. In this review, we compare the current approaches for second-generation genome sequencing, explore the future direction of this technology and the implications for plant genome research.

Poplar and Pathogen Interactions: Insights from Populus Genome-Wide Analyses of Resistance and Defense Gene Families and Gene Expression Profiling

Our understanding of the molecular basis of plant-pathogen interactions is derived mostly from studies of model annual plant species, and until recently, few addressed disease resistance and defense responses in long-lived species such as trees. The release of the Populus genome sequence has permitted extensive genome-wide surveys of gene families and comparative analyses of other sequenced plant genomes. These have revealed striking features for gene families that play key roles in the plant defense response. For example, the NBS-LRR resistance ( R )-gene family is expanded compared with other plant genomes, including R -gene subfamilies not previously reported in plants. Some of these genes are clustered on the subtelomeric part of a chromosome that shows segregation distortion in genetic studies. Similar expansion is observed for other genes playing key roles in plant defense such as pathogenesis-related proteins. Among the many pathogens that infect poplar trees, Melampsora spp. fungi, which cause rust diseases in plants, are responsible for considerable damage in poplar plantations. This biotrophic pathogen has attracted recent attention and here we describe molecular insights into the Populusdefense response against rust infection. Transcript profiles derived from compatible (susceptible) and incompatible (specific host -resistance) Populus-Melampsora interactions were leveraged to describe molecular changes occurring during defense responses against rust fungi. This highlighted responses that are similar to defense responses of annual plant species, such as up-regulation of transcripts encoding pathogenesis-related proteins. The molecular evidence gathered for the poplar-rust pathosystem indicates a temporal delay in the activation of defense responses between susceptibility and partial or full resistance that is consistent with the signal conversion model described for Arabidopsis. The genome of Melampsora larici-populina, which infects several species of Populus, was recently sequenced and provides a model pathosystem for forest pathology and offers unprecedented opportunities to understand how tree species cope with disease. Ultimately, understanding the molecular basis of Populus rust resistance will greatly improve our understanding of other major diseases of poplar.

A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences

BackgroundThe Brassica species include an important group of crops and provide opportunities for studying the evolutionary consequences of polyploidy. They are related to Arabidopsis thaliana, for which the first complete plant genome sequence was obtained and their genomes show extensive, although imperfect, conserved synteny with that of A. thaliana. A large number of EST sequences, derived from a range of different Brassica species, are available in the public database, but no public microarray resource has so far been developed for these species.ResultsWe assembled unigenes using ~800,000 EST sequences, mainly from three species: B. napus, B. rapa and B. oleracea. The assembly was conducted with the aim of co-assembling ESTs of orthologous genes (including homoeologous pairs of genes in B. napus from each of the A and C genomes), but resolving assemblies of paralogous, or paleo-homoeologous, genes (i.e. the genes related by the ancestral genome triplication observed in diploid Brassica species). 90,864 unique sequence assemblies were developed. These were incorporated into the BAC sequence annotation for the Brassica rapa Genome Sequencing Project, enabling the identification of cognate genomic sequences for a proportion of them. A 60-mer oligo microarray comprising 94,558 probes was developed using the unigene sequences. Gene expression was analysed in reciprocal resynthesised B. napus lines and the B. oleracea and B. rapa lines used to produce them. The analysis showed that significant expression could consistently be detected in leaf tissue for 35,386 unigenes. Expression was detected across all four genotypes for 27,355 unigenes, genome-specific expression patterns were observed for 7,851 unigenes and 180 unigenes displayed other classes of expression pattern. Principal component analysis (PCA) clearly resolved the individual microarray datasets for B. rapa, B. oleracea and resynthesised B. napus. Quantitative differences in expression were observed between the resynthesised B. napus lines for 98 unigenes, most of which could be classified into non-additive expression patterns, including 17 that showed cytoplasm-specific patterns. We further characterized the unigenes for which A genome-specific expression was observed and cognate genomic sequences could be identified. Ten of these unigenes were found to be Brassica-specific sequences, including two that originate from complex loci comprising gene clusters.ConclusionWe succeeded in developing a Brassica community microarray resource. Although expression can be measured for the majority of unigenes across species, there were numerous probes that reported in a genome-specific manner. We anticipate that some proportion of these will represent species-specific transcripts and the remainder will be the consequence of variation of sequences within the regions represented by the array probes. Our studies demonstrated that the datasets obtained from the arrays can be used for typical analyses, including PCA and the analysis of differential expression. We have also demonstrated that Brassica-specific transcripts identified in silico in the sequence assembly of public EST database accessions are indeed reported by the array. These would not be detectable using arrays designed using A. thaliana sequences.