Phylogenomics,molecular evolution,and estimated ages of lineages from the deep phylogeny of Poaceae

The deeply diverging subfamilies of grasses: Anomochlooideae, Pharoideae, and Puelioideae, today inhabit tropical forest floors as sparsely distributed depauperate lineages. The BEP/PACMAD grasses, which make up the majority of the family, are the result of a more recent radiation. Species in the deeply diverging subfamilies were here investigated to better understand molecular evolutionary processes and ages of divergence. Complete chloroplast genomes (plastomes) of Pharus latifolius L., P. lappulaceus Aubl., and Puelia olyriformis (Franch.) Clayton were determined. Four plastome loci from seven species of the deep subfamilies were also sequenced. Phylogenetic and mutation analyses and divergence estimations were conducted on all sequences together with homologous sequences from other Poaceae. Mutation analyses surveyed insertion/deletion mutations across the plastomes, clarified a trend in the molecular evolution of the rpoC2 locus, and indicated unique pseudogenizations in the plastomes of Pharus and Puelia. Phylogenetic analyses largely confirmed earlier multi-gene phylogenies. Phylogenomic and divergence analyses produced estimated origins of the crown nodes of Anomochlooideae at 65–104 Ma, Pharoideae at 44–71 Ma, and Puelioideae at 62–96 Ma. The upper ends of our estimated ranges are in general agreement with previous estimates. However, the lower ends of our ranges are considerably older than previous estimates, reflecting the influence of the less commonly used oldest fossil calibration point. The deeply diverging subfamilies exhibited the accumulation of numerous substitution and indel mutations consistent with a long evolutionary history that predated the radiation of the BEP/PACMAD grasses. We hypothesize that relatively rapid warming and drying in Africa at 55–56.5 Ma may have acted as selective forces stimulating adaptive radiations of grasses from the African tropical forests into diverse habitats.     

Reproductive morphology of the early-divergent grass Streptochaeta and its bearing on the homologies of the grass spikelet

Reproductive morphology and development are described in the Brazilian grass Streptochaeta spicata, in order to assess the homologies of the characteristic grass inflorescence, termed a spikelet, and other reproductive organs. Streptochaeta possesses some features that are commonly found in Poaceae, including a well-differentiated embryo. It also possesses some relatively unusual, presumably derived features, such as non-plumose stigmas, which indicate that it could be insect-pollinated. It shares some features with other early-divergent grasses, such as Pharus, which could represent plesiomorphic conditions for grasses. The inflorescence unit in Streptochaeta has been interpreted as a compound branching system or pseudospikelet. The present data suggest that it is a highly modified spikelet, with a modified flower borne either on a different axis to the basal bracts (glumes) or on the same axis as the basal bracts. The three bracts below the stamens are interpreted as homologous to the lodicules. The Streptochaeta spikelet could be considered as morphologically intermediate between the true spikelet of grasses and reproductive units of close grass relatives.     

Microsporogenesis is simultaneous in the early‐divergent grass Streptochaeta,but successive in the closest grass relative,Ecdeiocolea

Simultaneous microsporogenesis is described for the first time in a grass, Streptochaeta spicata Schrad., a tropical Brazilian species that belongs in the early‐divergent subfamily Anomochlooideae. Microsporogenesis is successive in all other Poaceae examined so far, and most other members of the order Poales, to which grasses belong. The only other reports of simultaneous microsporogenesis in Poales are in Rapateaceae and some members of the cyperid clade (Juncaceae, Cyperaceae, Prionium and Thurnia). Among the graminids, Ecdeiocolea (the putative closest relative to Poaceae) is successive, as are Joinvillea, Flagellaria and all other Poaceae, indicating that the simultaneous condition is autapomorphic in Streptochaeta, though Anomochloa has yet to be examined. Anther wall development in Streptochaeta is of the reduced type, as also in another early‐divergent grass Pharus, though most other Poales, including most grasses, have the monocot type. In Streptochaeta, as in Pharus, the endothecium lacks thickenings, unlike other grasses that have a persistent endothecium with thickenings. The centrifixed anthers and nonplumose stigmas of Streptochaeta suggest entomophily.     

Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses

Background

Compared to their counterparts in animals, the mitochondrial (mt) genomes of angiosperms exhibit a number of unique features. However, unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. While next-generation sequencing technologies have revolutionized chloroplast genome sequencing, they are just beginning to be applied to angiosperm mt genomes. Chloroplast genomes of grasses (Poaceae) have undergone episodic evolution and the evolutionary rate was suggested to be correlated between chloroplast and mt genomes in Poaceae. It is interesting to investigate whether correlated rate change also occurred in grass mt genomes as expected under lineage effects. A time-calibrated phylogenetic tree is needed to examine rate change.

Methodology/Principal Findings

We determined a largely completed mt genome from a bamboo, Ferrocalamus rimosivaginus (Poaceae), through Illumina sequencing of total DNA. With combination of de novo and reference-guided assembly, 39.5-fold coverage Illumina reads were finally assembled into scaffolds totalling 432,839 bp. The assembled genome contains nearly the same genes as the completed mt genomes in Poaceae. For examining evolutionary rate in grass mt genomes, we reconstructed a phylogenetic tree including 22 taxa based on 31 mt genes. The topology of the well-resolved tree was almost identical to that inferred from chloroplast genome with only minor difference. The inconsistency possibly derived from long branch attraction in mtDNA tree. By calculating absolute substitution rates, we found significant rate change (∼4-fold) in mt genome before and after the diversification of Poaceae both in synonymous and nonsynonymous terms. Furthermore, the rate change was correlated with that of chloroplast genomes in grasses.

Conclusions/Significance

Our result demonstrates that it is a rapid and efficient approach to obtain angiosperm mt genome sequences using Illumina sequencing technology. The parallel episodic evolution of mt and chloroplast genomes in grasses is consistent with lineage effects.     

Phylogenetic relationships in the grass family (Poaceae) based on the nuclear single copy locus topoisomerase 6 compared with chloroplast DNA

Phylogenetic relationships within the grass family were studied using a newly obtained locus of the nuclear single copy gene topoisomerase 6 (Topo6) spanning the four exons 8–11 and the chloroplast matK gene. Data were evaluated using maximum parsimony, maximum likelihood and Bayesian methods. All analyses showed genera Streptochaeta and Anomochloa as early diverging, followed by Pharus as sister to the rest of the Poaceae, and monophyly of the subfamily Anomochlooideae was supported by the nuclear dataset. The remaining grasses formed a strongly supported and monophyletic group, which split into the major clades BEP and PACMAD in the Topo6 analyses. Monophyly of the BEP clade was strongly supported by the Topo6 data. The results showed clearly incongruity between the two sets of data, such as the different subfamilial relationships of Bambusoideae, Ehrhartoideae and Pooideae. Most of the analysed species are representatives of subfamily Pooideae, which was analysed in more detail by PCR fragment length differences of another Topo6 region spanning the exons 17–19. Monophyly of Pooideae was strongly supported by the matK data, whereas the nuclear data placed Brachyelytrum outside of the remaining Pooideae. Relationships within the early evolutionary lineages remained largely unresolved in the phylogenetic trees, but the ‘core’ Pooideae (Aveneae/Poeae tribe complex and Hordeeae) were highly supported in all analyses. The differences in amplification lengths illustrate the tribe and subtribe classification of Pooideae. The comparatively conserved structure of the newly studied Topo6 region makes it a promising marker from the nuclear genome that could be successfully PCR-amplified to study higher-level phylogenetic relationships within grasses and perhaps between families within the order Poales.     

Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences

Background

With the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants. While the genomic resources have accumulated rapidly for almost all major lineages of grasses, bamboo remains the only large subfamily of Poaceae with little genomic information available in databases, which seriously hampers our ability to take a full advantage of the wealth of grass genomic data for effective comparative studies.

Results

Here we report the cloning and sequencing of 10,608 putative full length cDNAs (FL-cDNAs) primarily from Moso bamboo, Phyllostachys heterocycla cv. pubescens, a large woody bamboo with the highest ecological and economic values of all bamboos. This represents the third largest FL-cDNA collection to date of all plant species, and provides the first insight into the gene and genome structures of bamboos. We developed a Moso bamboo genomic resource database that so far contained the sequences of 10,608 putative FL-cDNAs and nearly 38,000 expressed sequence tags (ESTs) generated in this study.

Conclusion

Analysis of FL-cDNA sequences show that bamboo diverged from its close relatives such as rice, wheat, and barley through an adaptive radiation. A comparative analysis of the lignin biosynthesis pathway between bamboo and rice suggested that genes encoding caffeoyl-CoA O-methyltransferase may serve as targets for genetic manipulation of lignin content to reduce pollutants generated from bamboo pulping.     

Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice

Background  

Well preserved genomic colinearity among agronomically important grass species such as rice, maize, Sorghum, wheat and barley provides access to whole-genome structure information even in species lacking a reference genome sequence. We investigated footprints of whole-genome duplication (WGD) in barley that shaped the cereal ancestor genome by analyzing shared synteny with rice using a ~2000 gene-based barley genetic map and the rice genome reference sequence.     

Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae

Cornaceae is a core representative family in Cornales, the earliest branching lineage in the Asterids on the life tree of angiosperms. This family includes the only genus Cornus, a group of ~55 species. These species occur widely in Northern Hemisphere and have been used as resources for horticultural ornaments, medicinal and industrial manufacturing. However, no any genome sequences are available for this family. Here, we reported a chromosome­level genome for Cornus controversa. This was generated using high-fidelity plus Hi–C sequencing, and totally ~771.80 Mb assembled sequences and 39,886 protein-coding genes were obtained. We provided evidence for a whole-genome duplication event (WGD) unique to C. controversa. The evolutionary features of this genome indicated that the expanded and unique genes might have contributed to response to stress, stimulus and defense. By using chromosome-level syntenic blocks shared between eight living genomes, we found high degrees of genomic diversification from the ancestral core-eudicot genome to the present-day genomes, suggesting an important role of WGD in genomic plasticity that leads to speciation and diversification. These results provide foundational insights on the evolutionary history of Cornaceae, as well as on the Asterids diversification.     

Adaptive evolution of chloroplast genomes in ancestral grasses

The grass family, Poaceae, is one of the most successful families among angiosperms. Although it has long been suggested that the chloroplast genomes of the Poaceae have undergone an elevated evolutionary rate compared to other angiosperms, little was known about the details of this phenomenon. By using chloroplast genome data from 31 seed plants species, we recently showed that episodic rate acceleration occurred in the common ancestral branch of the core Poaceae (a clade formed by rice Oryza sativa, wheat Triticum aestivum, maize Zea mays and their allies) accompanied by elevated non-synonymous/synonymous rate ratio, while the rate and the non-synonymous/synonymous rate ratio reverted to the low level typical of most monocot species in the terminal branches. It was further shown that positive selection or adaptive evolution operated in several chloroplast proteins during the evolution of ancestral grasses, and the amino acid sites which putatively experienced positive selection have been identified. These findings illustrate the importance of future works of structural biological research of chloroplasts to understand the background of the evolution of the successful group, Poaceae.Key words: rate acceleration, positive selection, non-synonymous/synonymous rate ratio, Poaceae, structural biologyThe grass family, Poaceae, is one of the largest plant families, comprising about 10,000 species including the most important agricultural plants, rice, wheat and maize, as well as grass-dominated ecosystems which comprise about one-third of Earth''s vegetative cover and support a vast number of animals.¹ The chloroplast genes of the grass family Poaceae are known to have undergone accelerations in their evolutionary rates,^2,3 yet little was known about the details of this acceleration. It has become increasingly feasible to estimate the phylogenetic tree of angiosperms and to clarify the tempo and model of molecular evolution by using chloroplast genome sequences.^4–6 By using chloroplast genome data from 13 monocot species and 18 species from dicots and gymnosperms (31 species in total), we recently examined the details of this phenomenon from several aspects.Figure 1 shows the Poales + Musa part of the chloroplast ML tree of the 31 species, and the elongated branches of Poaceae show the rate acceleration in that particular group. Moreover, longer distances of the Poaceae species from Musa than the Typha/Musa distance by more than two times both in terms of non-synonymous and synonymous substitutions (Fig. 1) indicate that both types of substitutions have undergone rate acceleration along the line leading to Poaceae. To explore the pattern of rate change during the course of grass evolution more in detail, we estimated the time-scale of Angiosperm phylogeny with a relaxed clock based on the Bayesian method implemented in MCMCTREE program of PAML.⁷ As is apparent from Figure 1, the molecular evolutionary rate (substitution rate) differs among different lineages, and therefore we used the relaxed clock method which takes account of the evolution of the evolutionary rate in estimating the divergence times and the pattern of rate change. Based on fossil evidence, we assumed the followings in calibrating the relaxed clock; (1) the Gymnosperm/Angiosperm divergence occurred at 280–310 Ma (million years ago),^5,6 (2) the divergence of Poales from other monocots occurred before 115 Ma,^8,9 and (3) the most basal divergence in eudicots occurred before 125 Ma.⁵Open in a separate windowFigure 1Poales + Musa part of the chloroplast genome tree from 31 seed plant species. The branch lengths are proportional to the estimated lengths by the ML with the codon-substitution model (CODEML in PAML⁷). Non-synonymous (d_N) and synonymous (d_S) distances of Poales from Musa and ω = d_N/d_S (along branches) were estimated by the same program.We further gave a constraint of >65 Ma for the Zea/Oryza divergence based on the recent finding of 65 Ma grass phytoliths in dinosaur coprolites which places the diversification of the grasses to the Cretaceous period.^10,11 As a result, it was found that the rate acceleration was limited to the common ancestral branch of Poaceae after they diverged from Musa and that the rate reverted to the slow rate typical of most monocot species in the terminal branches. Even when the constraint was removed, almost the same pattern of rate change was obtained, suggesting that our conclusion regarding accelerated rate in the ancestral grasses followed by the reverted slow rate in contemporary Poaceae is robust.Non-synonymous/synonymous rate ratio (ω = d_N/d_S) is widely used as an indicator of positive selection or adaptive evolution.¹² Figure 1 also indicates a pronounced increase of ω ratio in the common ancestral branch of Poaceae after their divergence from Typha, followed by reversion in the terminal branches to the lower level typical of basal lineages. The elevation of the ω ratio can be due either by adaptive evolution or by relaxation of selective constraints. An ω value higher than 1 is usually regarded as an evidence of adaptive evolution, but since the ω values shown in the figure averages over the entire protein-encoding genes, we would not obtain such a high value even if positive selection operated in some regions of some proteins. To identify positively selected sites, among 75 protein-encoding genes, we at first selected 14 genes, for which the model with higher ω in the ancestral grass branch than others is significantly better than the model with homogeneous ω, and by using the branch-site model,^13,14 we identified 5 genes (atpE, cemA, clpP, rpoB and rps11) which have p value of the branch-site likelihood ratio test less than 0.05 and contain positively selected sites. The amino acid sites and substitutions identified to have experienced positive selection are as follows; atpE (2T→K, 17S→C, 41A→N, 64M→W, 132V→W), cemA (55N→R, 76Y→K, 161W→F, 190I→F, 204I→C), clpP (26R→V, 48V→T, 86F→T, 112I→P, 134E→R, 182T→D), rpoB (90R→F, 338G→K, 1026G→N), rps11 (54V→P, 62A→S, 82A→R, 105L→S, 115R→A, 120L→R) where the numberings of amino acid sites are those of Zea mays.¹⁵ We anticipate that these amino acid substitutions might have relevance to the successful evolution of grasses. To clarify the implication of these findings, structural biological studies of chloroplast proteins on how the amino acid changes affect their functions are needed.Rates of molecular evolution can be potentially linked to life history of organisms. By comparing evolutionary rates of chloroplast, nuclear and mitochondrial genes across five groups of angiosperms, Smith and Donoghue¹⁶ found that the rates are generally low in trees/shrubs compared to related herbs. Our finding, however, suggests that the pattern of rate change during evolution is more complicated than has previously been anticipated, and highlights the need for distinguishing rates of internal branches and those of terminal branches rather than averaging along a lineage in addressing this complicated problem.As Theodosius Dobzhansky¹⁷ wrote, nothing in biology makes sense except in the light of evolution, and the functional background of the molecular machinery in chloroplasts should be interpreted in the light of evolution. We hope our molecular evolutionary analysis of the chloroplast genomes is the first step towards this goal, and hope collaboration of molecular evolutionists with structural biologists becomes fruitful in the future.     

Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae

Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other systems including bacterial and animal mitochondrial genomes.     

Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50%. As a representative of the paraphyletic basal group of the fungal kingdom called “zygomycetes,” R. oryzae is also used as a model to study fungal evolution. Here we report the genome sequence of R. oryzae strain 99–880, isolated from a fatal case of mucormycosis. The highly repetitive 45.3 Mb genome assembly contains abundant transposable elements (TEs), comprising approximately 20% of the genome. We predicted 13,895 protein-coding genes not overlapping TEs, many of which are paralogous gene pairs. The order and genomic arrangement of the duplicated gene pairs and their common phylogenetic origin provide evidence for an ancestral whole-genome duplication (WGD) event. The WGD resulted in the duplication of nearly all subunits of the protein complexes associated with respiratory electron transport chains, the V-ATPase, and the ubiquitin–proteasome systems. The WGD, together with recent gene duplications, resulted in the expansion of multiple gene families related to cell growth and signal transduction, as well as secreted aspartic protease and subtilase protein families, which are known fungal virulence factors. The duplication of the ergosterol biosynthetic pathway, especially the major azole target, lanosterol 14α-demethylase (ERG11), could contribute to the variable responses of R. oryzae to different azole drugs, including voriconazole and posaconazole. Expanded families of cell-wall synthesis enzymes, essential for fungal cell integrity but absent in mammalian hosts, reveal potential targets for novel and R. oryzae-specific diagnostic and therapeutic treatments.     

Phylogenetics and character evolution in the grass family (Poaceae): Simultaneous analysis of morphological and Chloroplast DNA restriction site character sets

A phylogenetic analysis of the grass family (Poaceae) was conducted using two character sets, one representing variation in 364 mapped and cladistically informative restriction sites from all regions of the chloroplast genome, the other representing variation in 42 informative “structural characters.” The structural character set includes morphological, anatomical, chromosomal, and biochemical features, plus structural features of the chloroplast genome. The taxon sample comprises 75 exemplar taxa, including 72 representatives of Poaceae and one representative of each of three related families (Flagellariaceae, Restionaceae, and Join-villeaceae);Flagellaria served as the outgroup for the purpose of cladogram rooting. Among the grasses, 24 tribes and all 16 subfamilies of grasses recognized by various modern authors were sampled. Transformations of structural characters are mapped onto the phylogenetic hypotheses generated by the analysis, and interpreted with respect to biogeography and the evolution of wind pollination in the grass family. A major goal of the study was to test the monophyly of several putatively natural groups, including Bambusoideae, Pooideae, Arundinoideae, and the “PACC clade” (the latter comprising subfamilies Panicoideae, Arundinoideae, Chloridoideae, and Centothecoideae), as well as to analyze the phylogenetic structure within these groups and others. Several genera of controversial placement (Amphipogon, Anisopogon, Anomochloa, Brachyelytrum, Diarrhena, Eremitis, Ehrharta, Lithachne, Lygeum, Nardus, Olyra, Pharus, andStreptochaeta) also were included, with the goal of determining their phylogenetic affinities. The two character sets were analyzed separately, and a simultaneous analysis of the combined matrices also was conducted. The combined data set also was analyzed using homoplasy-implied weights. Among major results of the combined unweighted analysis were resolution of a sister-group relationship betweenJoinvillea and Poaceae; resolution of a clade comprisingAnomochloa andStreptochaeta as the sister of all other grasses, withPharus the next group to diverge from the lineage that includes all remaining grasses; and resolution of other taxa often assigned to Bambusoideae s.l. (includingEhrharta and Oryzeae, and excluding a few other taxa as noted) as a paraphyletic assemblage, within which is nested a clade that consists ofBrachyelytrum, the PACC clade (includingAmphipogon), and Pooideae (including Brachypodieae, Stipeae,Anisopogon, Diarrhena, Lygeum, andNardus). Within the PACC clade,Aristida is identified as the sister of all other elements of the group; Chloridoideae, Centothecoideae, and Panicoideae are each resolved as monophyletic, the latter two being sister-groups; and the remaining Arundinoid elements constitute a paraphyletic group within which are nested these three subfamilies. Within the Pooideae, four “core tribes” (Bromeae, Hordeeae [i.e., Triticeae], Agrostideae [i.e., Aveneae], andPoeae, the latter includingSesleria) are resolved as a monophyletic group that is nested among the remaining elements of the subfamily (Brachypodieae, Meliceae, Stipeae,Anisopogon, Diarrhena, Lygeum, andNardus). A second principal goal of the analysis was to identify structural synapomorphies of clades. Among the synapomorphies identified for some of the major clades are the following: gain of a 6.4 kb inversion in the chloroplast genome inJoinvillea and the grasses; reduction to 1 ovule per pistil, gain of a lateral “grass-type” embryo, and gain of an inversion around the gene trnT in the chloroplast genome in the grasses; loss of arm cells in the clade that consists ofBrachyelytrum, Pooideae, and the PACC clade; loss of the epiblast and gain of an elongate mesocotyl internode in the PACC clade; gain of proximal female-sterile florets in female-fertile spikelets, gain of overlapping embryonic leaf margins, and gain ofPanicum- type endosperm starch grains in the clade that comprises Centothecoideae and Panicoideae; and loss of the scutellar tail of the embryo in Pooideae (in one of two alternative placements of Pooideae among other groups). These findings are consistent with an origin and early diversification of grasses as forest understory herbs, followed by one or more radiations into open habitats, concomitant with multiple origins of C₄ photosynthesis and specialization for wind pollination.     

Setaria genome sequencing: an overview

The genus Setaria includes two important C₄ Panicoid grass species, namely S. italica (cultivated) and S. viridis (weed; wild ancestor), which together represent an appropriate model system for architectural, physiological, evolutionary, and genomic studies in related grasses. It is a diploid, inbreeder, self-fertile annual cereal grass having short life cycle and minimal growth requirements. There close relatedness to biofuel crops like switch grass and napier grass further signifies their importance. Further, foxtail millet is an important food and fodder grain crop grown in arid and semi-arid regions in many parts of the world. Therefore, an increasing interest in these species has led to a gradual accumulation and development of genomic data and genetic resources. Setaria genome sequencing is an outcome of such endeavors. These sequencing efforts uncovered several distinctive attributes of Setaria genome that may help in understanding its physiology, evolution and adaptation. This will not only aid in comparative genomics studies of Setaria and related crops including bioenergy grasses but also help in rapid advancements of genomics information for developing varieties with superior traits either through marker-assisted selection (MAS) or using transgenic approaches in these crops.     

水稻和其他禾本科植物基因组多倍体起源的证据

基因加倍(Gene duplication)被认为是进化的加速器。古老的基因组加倍事件已经在多个物种中被确定,包括酵母、脊椎动物以及拟南芥等。本研究发现水稻基因组同样存在全基因组加倍事件,大概发生在禾谷类作物分化之前,距今约7000万年。在水稻基因组中,共找到117个加倍区段(Duplicated block),分布在水稻的全部12条染色体,覆盖约60％的水稻基因组。在加倍区段,大约有20％的基因保留了加倍后的姊妹基因对(Duplicated pairs)。与此形成鲜明对照的是加倍区段的转录因子保留了60％的姊妹基因。禾本科植物全基因组加倍事件的确定对研究禾本科植物基因组的进化具有重要影响,暗示了多倍体化及随后的基因丢失、染色体重排等在禾谷类物种分化中扮演了重要角色。     

Alternative pathways in grass spikelet development

To the casual observer, one grass inflorescence looks very much like another and yet the family has diverged to nearly 800 genera and almost 10 000 species; is distributed worldwide and has become the centrepiece of agriculture. Such predominance can, in part, be explained by the subtlety with which spikelet operates since there is an elaborate interplay between the physiology of the spikelet and the immense reproductive versatility of the Poaceae.Physiological studies have centred on maize, wheat, rice and to a lesser extent, barley and sorghum. A grass taxonomist can readily demonstrate that maize, wheat and barley are relatively atypical grasses. Less familiar genera are able to provide the physiologist with problems that are unusual and stimulating.From such a viewpoint, the physiological problems presented by the spikelets of such genera as Cenchrus, Eragrostis, Phragmites, and Rottboellia will be examined.     

Teleost fish with specific genome duplication as unique models of vertebrate evolution

Whole-genome duplication (WGD) is believed to be one of the major evolutionary events that shaped the genome organization of vertebrates. Here, we review recent research on vertebrate genome evolution, specifically on WGD and its consequences for gene and genome evolution in teleost fishes. Recent genome analyses confirmed that all vertebrates experienced two rounds of WGD early in their evolution, and that teleosts experienced a subsequent additional third-round (3R)-WGD. The 3R-WGD was estimated to have occurred 320–400 million years ago in a teleost ancestor, but after its divergence from a common ancestor with living non-teleost actinopterygians (Bichir, Sturgeon, Bowfin, and Gar) based on the analyses of teleost-specific duplicate genes. This 3R-WGD was confirmed by synteny analysis and ancestral karyotype inference using the genome sequences of Tetraodon and medaka. Most of the tetrapods, on the other hand, have not experienced an additional WGD; however, they have experienced repeated chromosomal rearrangements throughout the whole genome. Therefore, different types of chromosomal events have characterized the genomes of teleosts and tetrapods, respectively. The 3R-WGD is useful to investigate the consequences of WGD because it is an evolutionarily recent WGD and thus teleost genomes retain many more WGD-derived duplicates and “traces” of their evolution. In addition, the remarkable morphological, physiological, and ecological diversity of teleosts may facilitate understanding of macrophenotypic evolution on the basis of genetic/genomic information. We highlight the teleosts with 3R-WGD as unique models for future studies on ecology and evolution taking advantage of emerging genomics technologies and systems biology environments.     

Epidermal Patterning and Silica Phytoliths in Grasses: An Evolutionary History

Due to the immense ecological and economic significance of grasses, their highly characteristic long–short epidermal patterning and associated silica phytoliths represent significant diagnostic markers in studies of ancient climate change and agriculture. We explore the link between epidermal cell patterning and phytolith development and review the evolutionary history of phytoliths in the context of recent well-resolved phylogenetic analyses of grasses and allied Poales, focusing on early-divergent grasses and the subfamilies that constitute the BEP group (the bamboos and their allies). Dimorphic epidermal patterning is a common feature of Poaceae and the related family Joinvilleaceae, where phytoliths are located primarily in the short cells. However, Joinvillea lacks the short-cell pairs that occur in many grasses. The costal rows of phytoliths that characterize some grasses could represent loss of long–short cell patterning over the veins. Unlobed phytoliths probably represent the ancestral condition in grasses, though bilobate phytoliths evolved at an early stage. Either transverse-unlobed or transverse-bilobate phytoliths predominate in the early-divergent lineages, whereas axial-bilobates (or polylobates) primarily characterize the PACMAD clade and the BEP subfamily Pooideae.     

Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots

Unraveling widespread polyploidy events throughout plant evolution is a necessity for inferring the impacts of whole-genome duplication (WGD) on speciation, functional innovations, and to guide identification of true orthologs in divergent taxa. Here, we employed an integrated syntenic and phylogenomic analyses to reveal an ancient WGD that shaped the genomes of all commelinid monocots, including grasses, bromeliads, bananas (Musa acuminata), ginger, palms, and other plants of fundamental, agricultural, and/or horticultural interest. First, comprehensive phylogenomic analyses revealed 1421 putative gene families that retained ancient duplication shared by Musa (Zingiberales) and grass (Poales) genomes, indicating an ancient WGD in monocots. Intergenomic synteny blocks of Musa and Oryza were investigated, and 30 blocks were shown to be duplicated before Musa-Oryza divergence an estimated 120 to 150 million years ago. Synteny comparisons of four monocot (rice [Oryza sativa], sorghum [Sorghum bicolor], banana, and oil palm [Elaeis guineensis]) and two eudicot (grape [Vitis vinifera] and sacred lotus [Nelumbo nucifera]) genomes also support this additional WGD in monocots, herein called Tau (τ). Integrating synteny and phylogenomic comparisons achieves better resolution of ancient polyploidy events than either approach individually, a principle that is exemplified in the disambiguation of a WGD series of rho (ρ)-sigma (σ)-tau (τ) in the grass lineages that echoes the alpha (α)-beta (β)-gamma (γ) series previously revealed in the Arabidopsis thaliana lineage.     

Phylogenetic structure in the grass family (Poaceae): evidence from the nuclear gene phytochrome B

Phylogenetic analyses of partial phytochrome B (PHYB) nuclear DNA sequences provide unambiguous resolution of evolutionary relationships within Poaceae. Analysis of PHYB nucleotides from 51 taxa representing seven traditionally recognized subfamilies clearly distinguishes three early-diverging herbaceous "bambusoid" lineages. First and most basal are Anomochloa and Streptochaeta, second is Pharus, and third is Puelia. The remaining grasses occur in two principal, highly supported clades. The first comprises bambusoid, oryzoid, and pooid genera (the BOP clade); the second comprises panicoid, arundinoid, chloridoid, and centothecoid genera (the PACC clade). The PHYB phylogeny is the first nuclear gene tree to address comprehensively phylogenetic relationships among grasses. It corroborates several inferences made from chloroplast gene trees, including the PACC clade, and the basal position of the herbaceous bamboos Anomochloa, Streptochaeta, and Pharus. However, the clear resolution of the sister group relationship among bambusoids, oryzoids, and pooids in the PHYB tree is novel; the relationship is only weakly supported in ndhF trees and is nonexistent in rbcL and plastid restriction site trees. Nuclear PHYB data support Anomochlooideae, Pharoideae, Pooideae sensu lato, Oryzoideae, Panicoideae, and Chloridoideae, and concur in the polyphyly of both Arundinoideae and Bambusoideae.