Monocot Genomes Research Articles

Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research

Glycoside hydrolases (GH) catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/). This database integrates multiple data types including the structural features, orthologous relationships, mutant availability, and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.

MIPS PlantsDB: a database framework for comparative plant genome research

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB–plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834–D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.

Ribosomal DNA distribution and a genus‐wide phylogeny reveal patterns of chromosomal evolution in Alstroemeria (Alstroemeriaceae)

Understanding the flexibility of monocot genomes requires a phylogenetic framework, which so far is available for few of the ca. 2800 genera. Here we use a molecular tree for the South American genus Alstroemeria to place karyological information, including fluorescent in situ hybridization (FISH) signals, in an explicit evolutionary context. From a phylogeny based on plastid, nuclear, and mitochondrial sequences for most species of Alstroemeria, we selected early-branching (Chilean) and derived (Brazilian) species for which we obtained 18S-25S and 5S rDNA FISH signals; we also analyzed chromosome numbers, 1C-values, and telomere FISH signals (in two species). Chromosome counts for Alstroemeria cf. rupestris and A. pulchella confirm 2n = 16 as typical of the genus, which now has chromosomes counted for 29 of its 78 species. The rDNA sites are polymorphic both among and within species, and interstitial telomeric sites in Alstroemeria cf. rupestris suggest chromosome fusion. In spite of a constant chromosome number, closely related species of Alstroemeria differ drastically in their rDNA, indicating rapid increase, decrease, or translocations of these genes. Previously proposed Brazilian and Chilean karyotype groups are not natural, and the n = 8 chromosomes in Alstroemeria compared to n = 9 in its sister genus Bomarea may result from a Robertsonian fusion.

Grass MicroRNA Gene Paleohistory Unveils New Insights into Gene Dosage Balance in Subgenome Partitioning after Whole-Genome Duplication

The recent availability of plant genome sequences, combined with a robust evolutionary scenario of the modern monocot and eudicot karyotypes from their diploid ancestors, offers an opportunity to gain insights into microRNA (miRNA) gene paleohistory in plants. Characterization and comparison of miRNAs and associated protein-coding targets in plants allowed us to unravel (1) contrasted genome conservation patterns of miRNAs in monocots and eudicots after whole-genome duplication (WGD), (2) an ancestral miRNA founder pool in the monocot genomes dating back to 100 million years ago, (3) miRNA subgenome dominance during the post-WGD diploidization process with selective miRNA deletion complemented with possible transposable element-mediated return flows, and (4) the miRNA/target interaction-directed differential loss/retention of miRNAs following the gene dosage balance rule. Together, our data suggest that overretained miRNAs in grass genomes may be implicated in connected gene regulations for stress responses, which is essential for plant adaptation and useful for crop variety innovation.

Developmental evolution of flowering plant pollen tube cell walls: callose synthase (CalS) gene expression patterns

BackgroundA number of innovations underlie the origin of rapid reproductive cycles in angiosperms. A critical early step involved the modification of an ancestrally short and slow-growing pollen tube for faster and longer distance transport of sperm to egg. Associated with this shift are the predominantly callose (1,3-β-glucan) walls and septae (callose plugs) of angiosperm pollen tubes. Callose synthesis is mediated by callose synthase (CalS). Of 12 CalS gene family members in Arabidopsis, only one (CalS5) has been directly linked to pollen tube callose. CalS5 orthologues are present in several monocot and eudicot genomes, but little is known about the evolutionary origin of CalS5 or what its ancestral function may have been.ResultsWe investigated expression of CalS in pollen and pollen tubes of selected non-flowering seed plants (gymnosperms) and angiosperms within lineages that diverged below the monocot/eudicot node. First, we determined the nearly full length coding sequence of a CalS5 orthologue from Cabomba caroliniana (CcCalS5) (Nymphaeales). Semi-quantitative RT-PCR demonstrated low CcCalS5 expression within several vegetative tissues, but strong expression in mature pollen. CalS transcripts were detected in pollen tubes of several species within Nymphaeales and Austrobaileyales, and comparative analyses with a phylogenetically diverse group of sequenced genomes indicated homology to CalS5. We also report in silico evidence of a putative CalS5 orthologue from Amborella. Among gymnosperms, CalS5 transcripts were recovered from germinating pollen of Gnetum and Ginkgo, but a novel CalS paralog was instead amplified from germinating pollen of Pinus taeda.ConclusionThe finding that CalS5 is the predominant callose synthase in pollen tubes of both early-diverging and model system angiosperms is an indicator of the homology of their novel callosic pollen tube walls and callose plugs. The data suggest that CalS5 had transient expression and pollen-specific functions in early seed plants and was then recruited to novel expression patterns and functions within pollen tube walls in an ancestor of extant angiosperms.

The Green Proteome: Challenges in Plant Proteomics

An organism is an expression of its underlying molecular composition that reacts and responds to a variety of stimuli. Central to this response are proteins, which undertake a multitude of functional and structural roles throughout an organism. The ability to readily identify and analyze protein populations (proteomics) represents a recent technological advance in the field of biological sciences. Although the term proteomics was coined in the mid 1990’s (Wilkins, 2009), the technique was significantly hampered by a lack of cohesive genomics data and advanced instrumentation. The field of proteomics has expanded rapidly in recent years due to the completion of genomes, access and improvements to mass spectrometers and the development of new techniques all of which have increased its role in biological research (Han et al., 2008).

Efficient Plant Gene Identification Based on Interspecies Mapping of Full-Length cDNAs

We present an annotation pipeline that accurately predicts exon–intron structures and protein-coding sequences (CDSs) on the basis of full-length cDNAs (FLcDNAs). This annotation pipeline was used to identify genes in 10 plant genomes. In particular, we show that interspecies mapping of FLcDNAs to genomes is of great value in fully utilizing FLcDNA resources whose availability is limited to several species. Because low sequence conservation at 5′- and 3′-ends of FLcDNAs between different species tends to result in truncated CDSs, we developed an improved algorithm to identify complete CDSs by the extension of both ends of truncated CDSs. Interspecies mapping of 71 801 monocot FLcDNAs to the Oryza sativa genome led to the detection of 22 142 protein-coding regions. Moreover, in comparing two mapping programs and three ab initio prediction programs, we found that our pipeline was more capable of identifying complete CDSs. As demonstrated by monocot interspecies mapping, in which nucleotide identity between FLcDNAs and the genome was ∼80%, the resultant inferred CDSs were sufficiently accurate. Finally, we applied both inter- and intraspecies mapping to 10 monocot and dicot genomes and identified genes in 210 551 loci. Interspecies mapping of FLcDNAs is expected to effectively predict genes and CDSs in newly sequenced genomes.

Genome Size Dynamics and Evolution in Monocots

Monocot genomic diversity includes striking variation at many levels. This paper compares various genomic characters (e.g., range of chromosome numbers and ploidy levels, occurrence of endopolyploidy, GC content, chromosome packaging and organization, genome size) between monocots and the remaining angiosperms to discern just how distinctive monocot genomes are. One of the most notable features of monocots is their wide range and diversity of genome sizes, including the species with the largest genome so far reported in plants. This genomic character is analysed in greater detail, within a phylogenetic context. By surveying available genome size and chromosome data it is apparent that different monocot orders follow distinctive modes of genome size and chromosome evolution. Further insights into genome size-evolution and dynamics were obtained using statistical modelling approaches to reconstruct the ancestral genome size at key nodes across the monocot phylogenetic tree. Such approaches reveal that while the ancestral genome size of all monocots was small ( pg), there have been several major increases and decreases during monocot evolution. In addition, notable increases in the rates of genome size-evolution were found in Asparagales and Poales compared with other monocot lineages.

Insights into the Musa genome: Syntenic relationships to rice and between Musa species

BackgroundMusa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome.ResultsWe produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya.ConclusionThese results point to the utility of comparative analyses between distantly-related monocot species such as rice and Musa for improving our understanding of monocot genome evolution. Sequencing the genome of M. acuminata would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated Musa polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes.

Computational Analysis of RNA Editing Sites in Plant Mitochondrial Genomes Reveals Similar Information Content and a Sporadic Distribution of Editing Sites

A computational analysis of RNA editing sites was performed on protein-coding sequences of plant mitochondrial genomes from Arabidopsis thaliana, Beta vulgaris, Brassica napus, and Oryza sativa. The distribution of nucleotides around edited and unedited cytidines was compared in 41 nucleotide segments and included 1481 edited cytidines and 21,390 unedited cytidines in the 4 genomes. The distribution of nucleotides was examined in 1, 2, and 3 nucleotide windows by comparison of nucleotide frequency ratios and relative entropy. The relative entropy analyses indicate that information is encoded in the nucleotide sequences in the 5 prime flank (-18 to -14, -13 to -10, -6 to -4, -2/-1) and the immediate 3 prime flanking nucleotide (+1), and these regions may be important in editing site recognition. The relative entropy was large when 2 or 3 nucleotide windows were analyzed, suggesting that several contiguous nucleotides may be involved in editing site recognition. RNA editing sites were frequently preceded by 2 pyrimidines or AU and followed by a guanidine (HYCG) in the monocot and dicot mitochondrial genomes, and rarely preceded by 2 purines. Analysis of chloroplast editing sites from a dicot, Nicotiana tabacum, and a monocot, Zea mays, revealed a similar distribution of nucleotides around editing sites (HYCA). The similarity of this motif around editing sites in monocots and dicots in both mitochondria and chloroplasts suggests that a mechanistic basis for this motif exists that is common in these different organelle and phylogenetic systems. The preferred sequence distribution around RNA editing sites may have an important impact on the acquisition of editing sites in evolution because the immediate sequence context of a cytidine residue may render a cytidine editable or uneditable, and consequently determine whether a T to C mutation at a specific position may be corrected by RNA editing. The distribution of editing sites in many protein-coding sequences is shown to be non-random with editing sites clustered in groups separated by regions with no editing sites. The sporadic distribution of editing sites could result from a mechanism of editing site loss by gene conversion utilizing edited sequence information, possibly through an edited cDNA intermediate.

Organization and variation of angiosperm mitochondrial genome

The mitochondrial genomes of angiosperms are the largest mitochondrial genomes so far reported and are highly variable in size among plant species. The comparative analysis of the angiosperm mitochondrial genomes at the nucleotide level has now become feasible for addressing long‐standing questions, owing to the publication of five dicot and three monocot genomes. Whereas the identified genes and introns are rather well conserved, intergenic regions are highly variable in sequence, even between two close relatives. Promiscuous DNA and horizontally transferred sequence constitute part of the intergenic regions, but the origin of the majority of these regions is unknown. On the other hand, duplication and extensive rearrangement of preexisting sequences may be one of the explanations for the occurrence of unknown sequences. Functional aspects of the mitochondrial genome, such as RNA editing and expression of unique open reading frames (ORFs), can be changed under certain nuclear genotypes.

Comparative analysis of expressed sequences reveals a conserved pattern of optimal codon usage in plants

Codon usage bias is a ubiquitous phenomenon, which may be caused by mutational bias, selection, or both. The patterns of codon usage in plants are not well understood. Datasets of expressed sequence tags (ESTs) available for many plant species provide the resources for large-scale comparative analysis of codon usage patterns. We developed a computational approach to translate EST or assembled contig sequences, and then used the coding information for comparative analysis of codon usage in 12 plant species, including 6 eudicots, 5 monocots and the green alga Chlamydomonas reinhardtii. While codon nucleotide composition is highly conserved within eudicots or monocots, there is a significant difference between these two major taxonomic groups of higher plants. The third nucleotide position of codons is AU-rich in the eudicot genomes (35-42% of G+C content), but GC-rich in the monocot genomes (59-61% of G+C content). To identify optimal codons in these species, we used EST counts to estimate gene transcript levels. It was demonstrated that codon usage bias is correlated positively with gene transcript levels. Interestingly, the use of optimal codons appears to be well conserved between eudicots and monocots, and to a lesser degree between the higher plants and C. reinhardtii. Most of the optimal codons end with a C or G base, regardless of the different nucleotide composition in these genomes. The results suggest that plant codon usage is affected by translational selection, and the selective pressure appears to be conserved in the plant kingdom.

A bacterial artificial chromosome library for sugarcane

Modern cultivated sugarcane is a complex aneuploid polyploid with an estimated genome size of 3000 Mb. Although most traits in sugarcane show complex inheritance, a rust locus showing monogenic inheritance has been documented. In order to facilitate cloning of the rust locus, we have constructed a bacterial artificial chromosome (BAC) library for the cultivar R570. The library contains 103,296 clones providing 4.5 sugarcane genome equivalents. A random sampling of 240 clones indicated an average insert size of 130 kb allowing a 98% probability of recovering any specific sequence of interest. High-density filters were gridded robotically using a Genetix Q-BOT in a 4 × 4 double-spotted array on 22.5-cm(2) filters. Each set of five filters provides a genome coverage of 4x with 18,432 clones represented per filter. Screening of the library with three different barley chloroplast gene probes indicated an exceptionally low chloroplast DNA content of less than 1%. To demonstrate the library's potential for map-based cloning, single-copy RFLP sugarcane mapping probes anchored to nine different linkage groups and three different gene probes were used to screen the library. The number of positive hybridization signals resulting from each probe ranged from 8 to 60. After determining addresses of the signals, clones were evaluated for insert size and HindIII-fingerprinted. The fingerprints were then used to determine clone relationships and assemble contigs. For comparison with other monocot genomes, sugarcane RFLP probes were also used to screen a Sorghum bicolor BAC library and two rice BAC libraries. The rice and sorghum BAC clones were characterized for insert size and fingerprinted, and the results compared to sugarcane. The library was screened with a rust resistance RFLP marker and candidate BAC clones were subjected to RFLP fragment matching to identify those corresponding to the same genomic region as the rust gene.

Rapid reorganization of resistance gene homologues in cereal genomes.

We used conserved domains in the major class (nucleotide binding site plus leucine-rich repeat) of dicot resistance (R) genes to isolate related gene fragments via PCR from the monocot species rice and barley. Peptide sequence comparison of dicot R genes and monocot R-like genes revealed shared motifs but provided no evidence for a monocot-specific signature. Mapping of these genes in rice and barley showed linkage to genetically characterized R genes and revealed the existence of mixed clusters, each harboring at least two highly dissimilar R-like genes. Diversity was detected intraspecifically with wide variation in copy number between varieties of a particular species. Interspecific analyses of R-like genes frequently revealed nonsyntenic map locations between the cereal species rice, barley, and foxtail millet although tight collinear gene order is a hallmark of monocot genomes. Our data suggest a dramatic rearrangement of R gene loci between related species and implies a different mechanism for nucleotide binding site plus leucine-rich repeat gene evolution compared with the rest of the monocot genome.