Evolution of DNA amounts across land plants (embryophyta)

BACKGROUND AND AIMS: DNA C-values in land plants (comprising bryophytes, lycophytes, monilophytes, gymnosperms and angiosperms) vary approximately 1000-fold from approx. 0.11 to 127.4 pg. To understand the evolutionary significance of this huge variation it is essential to evaluate the phylogenetic component. Recent increases in C-value data (e.g. Plant DNA C-values database; release 2.0, January 2003; http://www.rbgkew.org.uk/cval/homepage.html) together with improved consensus of relationships between and within land plant groups makes such an analysis timely. METHODS: Insights into the distribution of C-values in each group of land plants were gained by superimposing available C-value data (4119 angiosperms, 181 gymnosperms, 63 monilophytes, 4 lycophytes and 171 bryophytes) onto phylogenetic trees. To enable ancestral C-values to be reconstructed for clades within land plants, character-state mapping with parsimony and MacClade was also applied. KEY RESULTS AND CONCLUSIONS: Different land plant groups are characterized by different C-value profiles, distribution of C-values and ancestral C-values. For example, the large ( approximately 1000-fold) range yet strongly skewed distribution of C-values in angiosperms contrasts with the very narrow 12-fold range in bryophytes. Further, character-state mapping showed that the ancestral genome sizes of both angiosperms and bryophytes were reconstructed as very small (i.e. < or =1.4 pg) whereas gymnosperms and most branches of monilophytes were reconstructed with intermediate C-values (i.e. >3.5, <14.0 pg). More in-depth analyses provided evidence for several independent increases and decreases in C-values; for example, decreases in Gnetaceae (Gymnosperms) and heterosperous water ferns (monilophytes); increases in Santalales and some monocots (both angiosperms), Pinaceae, Sciadopityaceae and Cephalotaxaceae (Gymnosperms) and possibly in the Psilotaceae + Ophioglossaceae clade (monilophytes). Thus, in agreement with several focused studies within angiosperm families and genera showing that C-values may both increase and decrease, it is apparent that this dynamic pattern of genome size evolution is repeated on a broad scale across land plants.     

First nuclear DNA C-values for 28 angiosperm genera

This paper reports first DNA C-values for 28 angiosperm genera. These include first DNA C-values for 25 families, of which 16 are monocots. Overall familial representation is 47.2 % for angiosperms, but is now much higher for monocots (75 %) and basal angiosperms (73.1 %) than for eudicots (38.7 %). Chromosome counts are reported for 22 taxa, including first records for six genera plus seven species. Unrepresented families will become increasingly enriched for monotypic taxa from obscure locations that are harder to access. Thus, completing familial representation for genome size for angiosperms may prove impossible in any short period, and progress towards this goal will become slower.     

Organization of the root apical meristem in angiosperms

Although flowers, leaves, and stems of the angiosperms have understandably received more attention than roots, the growing root tips, or root apical meristems (RAMs), are organs that could provide insight into angiosperm evolution. We studied RAM organization across a broad spectrum of angiosperms (45 orders and 132 families of basal angiosperms, monocots, and eudicots) to characterize angiosperm RAMs and cortex development related to RAMs. Types of RAM organization in root tips of flowering plants include open RAMs without boundaries between some tissues in the growing tip and closed RAMs with distinct boundaries between apical regions. Epidermis origin is associated with the cortex in some basal angiosperms and monocots and with the lateral rootcap in eudicots and other basal angiosperms. In most angiosperm RAMs, initials for the central region of the rootcap, or columella, are distinct from the lateral rootcap and its initials. Slightly more angiosperm families have exclusively closed RAMs than exclusively open RAMs, but many families have representatives with both open and closed RAMs. Root tips with open RAMs are generally found in angiosperm families considered sister to other families; certain open RAMs may be ancestral in angiosperms.     

Size is not everything: rates of genome size evolution,not C-value,correlate with speciation in angiosperms

Angiosperms represent one of the key examples of evolutionary success, and their diversity dwarfs other land plants; this success has been linked, in part, to genome size and phenomena such as whole genome duplication events. However, while angiosperms exhibit a remarkable breadth of genome size, evidence linking overall genome size to diversity is equivocal, at best. Here, we show that the rates of speciation and genome size evolution are tightly correlated across land plants, and angiosperms show the highest rates for both, whereas very slow rates are seen in their comparatively species-poor sister group, the gymnosperms. No evidence is found linking overall genome size and rates of speciation. Within angiosperms, both the monocots and eudicots show the highest rates of speciation and genome size evolution, and these data suggest a potential explanation for the megadiversity of angiosperms. It is difficult to associate high rates of diversification with different types of polyploidy, but it is likely that high rates of evolution correlate with a smaller genome size after genome duplications. The diversity of angiosperms may, in part, be due to an ability to increase evolvability by benefiting from whole genome duplications, transposable elements and general genome plasticity.     

Nuclear DNA C-values Complete Familial Representation in Gymnosperms

The gymnosperms are a monophyletic yet diverse group of woodytrees with approx. 730 extant species in 17 families. A recentsurvey showed that DNA C-values were available for approx. 16%of species, but for only 12 of the 17 families. This paper completesfamilial representation reporting first C-values for the fiveremaining families: Boweniaceae, Stangeriaceae, Welwitschiaceae,Cephalotaxaceae and Sciadopityaceae. C-values for nine Ephedraand two Gnetum species are also reported. C-values are now availablefor 152 (21%) species. Analysis confirms that gymnosperms arecharacterized by larger C-values than angiosperms (modal 1Cof gymnosperms = 15.8 pg compared with 0.6 pg in angiosperms)although the range (1C = 2.25–32.20 pg) is smaller thanthat in angiosperms (1C = 0.05–127.4 pg). Given completefamilial coverage for C-values and increasing consensus in gymnospermphylogeny, the phylogenetic component of C-value variation wasalso investigated by comparing the two datasets. This analysisrevealed that ancestral gymnosperms (represented by cycads and/orGinkgo; mean genome size = 14.71 pg) probably had larger genomes thanancestral angiosperms. Copyright 2001 Annals of Botany Company Gymnosperm DNA amounts, C-values, phylogeny, ancestral genome size, Cycadales, Ginkgo, Gnetales, conifers, Pinaceae     

The origin and diversification of angiosperms

The angiosperms, one of five groups of extant seed plants, are the largest group of land plants. Despite their relatively recent origin, this clade is extremely diverse morphologically and ecologically. However, angiosperms are clearly united by several synapomorphies. During the past 10 years, higher-level relationships of the angiosperms have been resolved. For example, most analyses are consistent in identifying Amborella, Nymphaeaceae, and Austrobaileyales as the basalmost branches of the angiosperm tree. Other basal lineages include Chloranthaceae, magnoliids, and monocots. Approximately three quarters of all angiosperm species belong to the eudicot clade, which is strongly supported by molecular data but united morphologically by a single synapomorphy-triaperturate pollen. Major clades of eudicots include Ranunculales, which are sister to all other eudicots, and a clade of core eudicots, the largest members of which are Saxifragales, Caryophyllales, rosids, and asterids. Despite rapid progress in resolving angiosperm relationships, several significant problems remain: (1) relationships among the monocots, Chloranthaceae, magnoliids, and eudicots, (2) branching order among basal eudicots, (3) relationships among the major clades of core eudicots, (4) relationships within rosids, (5) relationships of the many lineages of parasitic plants, and (6) integration of fossils with extant taxa into a comprehensive tree of angiosperm phylogeny.     

A strong nucleotypic effect on the cell cycle regardless of ploidy level

Background and Aims: In published studies, positive relationships between nucleotypeand the duration of the mitotic cell cycle in angiosperms havebeen reported but the highest number of species analyzed wasapprox. 60. Here an analysis is presented of DNA C-values andcell cycle times in root apical meristems of angiosperms comprising110 measurements, including monocots and eudicots within a settemperature range, and encompassing an approx. 290-fold variationin DNA C-values. Methods: Data for 110 published cell cycle times of seedlings grown attemperatures between 20–25 °C were compared with DNAC-values (58 values for monocots and 52 for eudicots). Regressionanalyses were undertaken for all species, and separately formonocots and eudicots, diploids and polyploids, and annualsand perennials. Cell cycle times were plotted against the nuclearDNA C-values. Key Results: A positive relationship was observed between DNA C-value andcell cycle time for all species and for eudicots and monocotsseparately, regardless of the presence or absence of polyploidvalues. In this sample, among 52 eudicots the maximum cell cyclelength was 18 h, whereas the 58 monocot values ranged from 8–120h. There was a striking additional increase in cell cycle durationin perennial monocots with C-values greater than 25 pg. Indeed,the most powerful relationship between DNA C-value and cellcycle time and the widest range of cell cycle times was in perennialsregardless of ploidy level. Conclusions: DNA replication is identified as a rate limiting step in thecell cycle, the flexibility of DNA replication is explored,and we speculate on how the licensing of initiation points ofDNA replication may be a responsive component of the positivenucleotypic effect of C-value on the duration of the mitoticcell cycle.     

Nuclear DNA Amounts in Pteridophytes

DNA amounts (C-value and genome size) are much-used biodiversitycharacters. A workshop held at Kew in 1997 identified majorgaps in our knowledge of plant DNA amounts, recommending targetsfor new work to fill them. Murray reviewed non-angiosperm plantsnoting that representation of pteridophyte species (approx.0.42%) was poor, while locating C-value data for them was verydifficult. The workshop confirmed the need to make data forother groups besides angiosperms accessible for reference purposes.This paper pools DNA C-values for 48 pteridophyte species fromeight original sources into one reference source, and fulfilsa key workshop recommendation for this group. Comparing thesedata shows that nuclear 1C-values in pteridophytes vary approx.1000-fold, from 0.055 pg in Selaginella species to about 55pg in Ophioglossum petiolatum. Genome size estimates for 25pteridophytes vary approx. 200-fold from 0.055 to 10.7 pg, andthe mean genome sizes in diploids and polyploids (5.15 and 4.59pg, respectively) are not significantly different. Wider comparisonsshow that ranges of genome sizes in the major groups of landplants are very different. Those in bryophytes and pteridophytesare narrow compared with those in gymnosperms and angiosperms.The data indicate that the origin of land plants possibly involveda first major increase in genome size in the evolution of vascularplants, while a second such increase occurred later in gymnosperms.C-values for pteridophytes remain very few, but conversely opportunitiesfor new work on them are many. Copyright 2001 Annals of BotanyCompany Pteridophyte DNA amounts, DNA C-values, nuclear genome sizes     

Genome size variation in Macaronesian angiosperms: forty percent of the Canarian endemic flora completed

Genome sizes for 127 Macaronesian endemic angiosperms from 69 genera and 32 families were estimated using propidium iodide flow cytometry. Only about 30-fold variation in 1C-values was found, ranging from 0.32 pg in Echium bonnetii to 9.52 pg in Scilla dasyantha. Taxa with very small DNA amounts (1C 1.4 pg) were the most dominant group (71.7%), whereas the frequency of other categories was much lower (18.9% and 9.4% in taxa with small (1.41–3.50 pg) and intermediate 1C-values (3.51–14.00 pg), respectively). Comparisons of average C- and Cx-values between Macaronesian endemics and non-Macaronesian representatives always revealed significantly smaller amounts in the former group at various taxonomic levels (genus, family, major phylogenetic lineage). Potential relationship between nuclear DNA content and insular burst of speciation is suggested owing to the marked prevalence of very small genomes among angiosperms that underwent rapid adaptive radiation. Merging all the genome size data on Macaronesian angiosperms available shows that this flora represents the best covered plant assemblage from the phytogeographic point of view.     

Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae)

We have determined the complete chloroplast genome sequences of four early-diverging lineages of angiosperms, Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae), to examine the organization and evolution of plastid genomes and to estimate phylogenetic relationships among angiosperms. For the most part, the organization of these plastid genomes is quite similar to the ancestral angiosperm plastid genome with a few notable exceptions. Dioscorea has lost one protein-coding gene, rps16; this gene loss has also happened independently in four other land plant lineages, liverworts, conifers, Populus, and legumes. There has also been a small expansion of the inverted repeat (IR) in Dioscorea that has duplicated trnH-GUG. This event has also occurred multiple times in angiosperms, including in monocots, and in the two basal angiosperms Nuphar and Drimys. The Illicium chloroplast genome is unusual by having a 10 kb contraction of the IR. The four taxa sequenced represent key groups in resolving phylogenetic relationships among angiosperms. Illicium is one of the basal angiosperms in the Austrobaileyales, Chloranthus (Chloranthales) remains unplaced in angiosperm classifications, and Buxus and Dioscorea are early-diverging eudicots and monocots, respectively. We have used sequences for 61 shared protein-coding genes from these four genomes and combined them with sequences from 35 other genomes to estimate phylogenetic relationships using parsimony, likelihood, and Bayesian methods. There is strong congruence among the trees generated by the three methods, and most nodes have high levels of support. The results indicate that Amborella alone is sister to the remaining angiosperms; the Nymphaeales represent the next-diverging clade followed by Illicium; Chloranthus is sister to the magnoliids and together this group is sister to a large clade that includes eudicots and monocots; and Dioscorea represents an early-diverging lineage of monocots just internal to Acorus.     

被子植物系统发育深层关系研究: 进展与挑战

被子植物系统发育学是研究被子植物及其各类群间亲缘关系与进化历史的学科。从20世纪90年代起, 核苷酸和氨基酸序列等分子数据开始被广泛运用于被子植物系统发育研究, 经过20多年的发展, 从使用单个或联合少数几个细胞器基因, 到近期应用整个叶绿体基因组来重建被子植物的系统发育关系, 目、科水平上的被子植物系统发育框架已被广泛接受。在这个框架中, 基部类群、主要的5个分支(即真双子叶植物、单子叶植物、木兰类、金粟兰目和金鱼藻目)、每个分支所包含的目以及几个大分支包括的核心类群等都具有高度支持。与此同时, 细胞器基因还存在一些固有的问题, 例如单亲遗传、系统发育信息量有限等, 因此近年来双亲遗传的核基因在被子植物系统发育研究中的重要性逐渐得到关注, 并在不同分类阶元的研究中都取得了一定进展。但是, 被子植物系统发育中仍然存在一些难以确定的关系, 例如被子植物5个分支之间的关系、真双子叶植物内部某些类群的位置等。本文简述了20多年来被子植物系统发育深层关系的主要研究进展, 讨论了被子植物系统发育学常用的细胞器基因和核基因的选用, 已经确定和尚未确定系统发育位置的主要类群, 以及研究中尚存在的问题和可能的解决方法。     

Smallest angiosperm genomes found in lentibulariaceae, with chromosomes of bacterial size

Nuclear holoploid genome sizes (C-values) have been estimated to vary about 800-fold in angiosperms, with the smallest established 1C-value of 157 Mbp recorded in Arabidopsis thaliana. In the highly specialized carnivorous family Lentibulariaceae now three taxa have been found that exhibit significantly lower values: Genlisea margaretae with 63 Mbp, G. aurea with 64 Mbp, and Utricularia gibba with 88 Mbp. The smallest mitotic anaphase chromatids in G. aurea have 2.1 Mbp and are thus of bacterial size (NB: E. coli has ca. 4 Mbp). Several Utricularia species range somewhat lower than A. thaliana or are similar in genome size. The highest 1C-value known from species of Lentibulariaceae was found in Genlisea hispidula with 1510 Mbp, and results in about 24-fold variation for Genlisea and the Lentibulariaceae. Taking into account these new measurements, genome size variation in angiosperms is now almost 2000-fold. Genlisea and Utricularia are plants with terminal positions in the phylogeny of the eudicots, so that the findings are relevant for the understanding of genome miniaturization. Moreover, the Genlisea-Utricularia clade exhibits one of the highest mutational rates in several genomic regions in angiosperms, what may be linked to specialized patterns of genome evolution. Ultrasmall genomes have not been found in Pinguicula, which is the sister group of the Genlisea-Utricularia clade, and which does not show accelerated mutational rates. C-values in Pinguicula varied only 1.7-fold from 487 to 829 Mbp.     

Phytochrome gene expression and phylogenetic analysis in the short-day plant Pharbitis nil (Convolvulaceae): Differential regulation by light and an endogenous clock

To investigate the role of distinct phytochrome pools in photoperiodic timekeeping, we characterized four phytochrome genes in the short-day plant Pharbitis nil. Each PHY gene had different photosensory properties and sensitivity to night break that inhibits flowering. During extended dark periods, PHYE, PHYB, and PHYC mRNA accumulation exhibited a circadian rhythmicity indicative of control by an endogenous clock. Phylogenetic analysis recovered four clades of angiosperm phytochrome genes, phyA, phyB, phyC, and phyE. All except the phyE clade included sequences from both monocots and eudicots. In addition, phyA is sister to phyC and phyE sister to phyB, with gymnosperm sequences sister to either the phyA-phyC clade or to the phyB-phyE clade. These results suggest that a single duplication occurred in an ancestral seed plant before the divergence of extant gymnosperms from angiosperms and that two subsequent duplications occurred in an ancestral angiosperm before the divergence of monocots from eudicots. Thus in P. nil, a multigene family with different patterns of mRNA abundance in light and darkness contributes to the total phytochrome pool: one pool is light labile (phyA), whereas the other is light stable (phyB and phyE). In addition, PHYC mRNA represents a third phytochrome pool with intermediate photosensory properties.     

Climate and growth form: the consequences for genome size in plants

The adaptive significance of nuclear DNA variation in angiosperms is still widely debated. The discussion mainly revolves round the causative factors influencing genome size and the adaptive consequences to an organism according to its growth form and environmental conditions. Nuclear DNA values are now known for 3874 angiosperm species (including 773 woody species) from over 219 families (out of a total of 500) and 181 species of woody gymnosperms, representing all the families. Therefore, comparisons have been made on not only angiosperms, taken as a whole, but also on the subsets of data based on taxonomic groups, growth forms, and environment. Nuclear DNA amounts in woody angiosperms are restricted to less than 23.54 % of the total range of herbaceous angiosperms; this range is further reduced to 6.8 % when woody and herbaceous species of temperate angiosperms are compared. Similarly, the tropical woody dicots are restricted to less than 50.5 % of the total range of tropical herbaceous dicots, while temperate woody dicots are restricted to less than 10.96 % of the total range of temperate herbaceous dicots. In the family Fabaceae woody species account for less than 14.1 % of herbaceous species. Therefore, in the total angiosperm sample and in subsets of data, woody growth form is characterized by a smaller genome size compared with the herbaceous growth form. Comparisons between angiosperm species growing in tropical and temperate regions show highly significant differences in DNA amount and genome size in the total angiosperm sample. However, when only herbaceous angiosperms were considered, significant differences were obtained in DNA amount, while genome size showed a non-significant difference. An atypical result was obtained in the case of woody angiosperms where mean DNA amount of tropical species was almost 25.04 % higher than that of temperate species, which is because of the inclusion of 85 species of woody monocots in the tropical sample. The difference becomes insignificant when genome size is compared. Comparison of tropical and temperate species among dicots and monocots and herbaceous monocots taken separately showed significant differences both in DNA amount and genome size. In herbaceous dicots, while DNA amount showed significant differences the genome size varies insignificantly. There was a non-significant difference among tropical and temperate woody dicots. In three families, i.e., Poaceae, Asteraceae, and Fabaceae the temperate species have significantly higher DNA amount and genome size than the tropical ones. Woody gymnosperms had significantly more DNA amount and genome size than woody angiosperms, woody eudicots, and woody monocots. Woody monocots also had significantly more DNA amount and genome size than woody eudicots. Lastly, there was no significant difference between deciduous and evergreen hardwoods. The significance of these results in relation to present knowledge on the evolution of genome size is discussed.     

Complete Sequence of the Duckweed (<Emphasis Type="Italic">Lemna minor</Emphasis>) Chloroplast Genome: Structural Organization and Phylogenetic Relationships to Other Angiosperms

The complete nucleotide sequence of the duckweed (Lemna minor) chloroplast genome (cpDNA) was determined. The cpDNA is a circular molecule of 165,955 bp containing a pair of 31,223-bp inverted repeat regions (IRs), which are separated by small and large single-copy regions of 89,906 and 13,603 bp, respectively. The entire gene pool and relative positions of 112 genes (78 protein-encoding genes, 30 tRNA genes, and 4 rRNA genes) are almost identical to those of Amborella trichopoda cpDNA; the minor difference is the absence of infA and ycf15 genes in the duckweed cpDNA. The inverted repeat is expanded to include ycf1 and rps15 genes; this pattern is unique and does not occur in any other sequenced cpDNA of land plants. As in basal angiosperms and eudicots, but not in other monocots, the borders between IRs and a large single-copy region are located upstream of rps19 and downstream of trnH, so that trnH is not included in IRs. The model of rearrangements of the chloroplast genome during the evolution of monocots is proposed as the result of the comparison of cpDNA structures in duckweed and other monocots. The phylogenetic analyses of 61 protein-coding genes from 38 plastid genome sequences provided strong support for the monophyly of monocots and position of Lemna as the next diverging lineage of monocots after Acorales. Our analyses also provided support for Amborella as a sister to all other angiosperms, but in the bayesian phylogeny inference based on the first two codon positions Amborella united with Nymphaeales.     

Phylogenetic analysis of the plant-specific zinc finger-homeobox and mini zinc finger gene families

Zinc finger-homeodomain proteins (ZHD) are present in many plants; however, the evolutionary history of the ZHD gene family remains largely unknown. We show here that ZHD genes are plant-specific, nearly all intronless, and related to MINI ZINC FINGER ( MIF ) genes that possess only the zinc finger. Phylogenetic analyses of ZHD genes from representative land plants suggest that non-seed plant ZHD genes occupy basal positions and angiosperm homologs form seven distinct clades. Several clades contain genes from two or more major angiosperm groups, including eudicots, monocots, magnoliids, and other basal angiosperms, indicating that several duplications occurred before the diversification of flowering plants. In addition, specific lineages have experienced more recent duplications. Unlike the ZHD genes, MIF s are found only from seed plants, possibly derived from ZHD s by loss of the homeodomain before the divergence of seed plants. Moreover, the MIF genes have also undergone relatively recent gene duplications. Finally, genome duplication might have contributed substantially to the expansion of family size in angiosperms and caused a high level of functional redundancy/overlap in these genes.