Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes

Short interspersed nuclear elements (SINEs) are non-long terminal repeat retrotransposons that are highly abundant, heterogeneous, and mostly not annotated in eukaryotic genomes. We developed a tool designated SINE-Finder for the targeted discovery of tRNA-derived SINEs. We analyzed sequence data of 16 plant genomes, including 13 angiosperms and three gymnosperms and identified 17,829 full-length and truncated SINEs falling into 31 families showing the widespread occurrence of SINEs in higher plants. The investigation focused on potato (Solanum tuberosum), resulting in the detection of seven different SolS SINE families consisting of 1489 full-length and 870 5' truncated copies. Consensus sequences of full-length members range in size from 106 to 244 bp depending on the SINE family. SolS SINEs populated related species and evolved separately, which led to some distinct subfamilies. Solanaceae SINEs are dispersed along chromosomes and distributed without clustering but with preferred integration into short A-rich motifs. They emerged more than 23 million years ago and were species specifically amplified during the radiation of potato, tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum). We show that tobacco TS retrotransposons are composite SINEs consisting of the 3' end of a long interspersed nuclear element integrated downstream of a nonhomologous SINE family followed by successfully colonization of the genome. We propose an evolutionary scenario for the formation of TS as a spontaneous event, which could be typical for the emergence of SINE families.     

Identification and characterization of a new member of the SINE Au retroposon family (GmAu1) in the soybean, Glycine max (L.) Merr., genome and its potential application

A plant short interspersed element (SINE) was identified in Glycine max after re-sequencing of the soybean sequence characterized amplified region (SCAR) markers. Detailed analysis revealed that this newly recognized SINE element consisted of a tRNA-related region, a tRNA non-related region, direct flanking repeat sequences, and a short stretch of Ts at the 3′-terminal region. These features are similar to previously characterized SINEs. To investigate the evolution of the SINE retroposon, BLASTN was used to search against genome sequences of other plants. Since it is homologous with the retroposon Au in Aegilops umbellulata (wheat) and its homology in soybean, the SINE is named as GmAu1. Genome analysis of the Glycine max var. Willimas 82 uncovered more than 847 copies of GmAu1 per haploid genome of soybean. Examination of the regions flanking the inserted GmAu1 sequences indicated a preference for introns over exons or other noncoding regions. Considering the flanking insertion sequences, 146 primers were designed in order to detect insertion mutations by a PCR-based method. Seventy-seven primers displayed polymorphism and were used to develop corresponding GmAu1-based SCAR markers. The retroposon GmAu1 and its related SCAR markers identified in this study will prove valuable to future investigations into the genetic mapping, phylogeny, and evolution of the Glycine genus.     

The evolution of embryo size in angiosperms and other seed plants: implications for the evolution of seed dormancy

Abstract.— Seed dormancy plays an important role in germination ecology and seed plant evolution. Morphological seed dormancy is caused by an underdeveloped embryo that must mature prior to germination. It has been suggested that the presence of an underdeveloped embryo is plesiomorphic among seed plants and that parallel directional change in embryo morphology has occurred separately in gymnosperms and in angiosperms. We test these hypotheses using original data on embryo morphology of key basal taxa, a published dataset, and the generalized least squares (GLS) method of ancestral character state reconstruction. Reconstructions for embryo to seed ratio (E:S) using family means for 179 families showed that E:S has increased between the ancestral angiosperm and almost all extant angiosperm taxa. Species in the rosid clade have particularly large embryos relative to the angiosperm ancestor. Results for the gymnosperms show a similar but smaller increase. There were no statistically significant differences in E:S between basal taxa and any derived group due to extremely large standard errors produced by GLS models. However, differences between reconstructed values for the angiosperm ancestor and more highly nested nodes are large and these results are robust to topological and branch-length manipulations. Our analysis supports the idea that the underdeveloped embryo is primitive among seed plants and that there has been a directional change in E:S within both angiosperms and gymnosperms. Our analysis suggests that dormancy enforced by an underdeveloped embryo is plesiomorphic among angiosperms and that nondormancy and other dormancy types probably evolved within the angiosperms. The shift in E:S was likely a heterochronic change, and has important implications for the life history of seed plants.     

21科41种(变种)植物叶片几丁质酶系的研究

对广州地区常见的21科41种（变种）植物叶片几丁质酶系研究的结果表明,所有受试植物都具有几丁质酶活性。几丁质酶不仅存在于被子植物的双子叶植物和单子叶植物中,而且也存在于裸子植物及蕨类植物中。几丁质酶活性及比活性均较高的有蕹菜、葱、蕨类植物、蒜、茄科植物、玉米、菜豆、番木瓜等。植物一般都具有两种几丁质酶:外切酶和内切酶。几丁质外切酶活性及比活性均较高的有蕨类植物、葱、茄科植物等。几丁质内切酶活性及比活性均较高的有蕹菜、裸子植物等。不同植物几丁质外切酶与内切酶的比例相差较大。有些植物的几丁质酶系以外切酶为主,如茄科植物、大部分豆科植物、番木瓜等;有些植物以内切酶为主,如裸子植物、伞形科植物、蕹菜等;有些植物的外切酶与内切酶含量相差不大。     

Ferulic acid is bound to the primary cell walls of all gymnosperm families

Unlignified primary cell walls containing ester-linked ferulic acid fluoresce blue in ultraviolet radiation which changes to green with increased intensity on treatment with ammonium hydroxide. Using this fluorescence behaviour, we detected ester-linked ferulic acid in the primary cell walls of all 41 species of gymnosperms we examined. These species were in 17 families representing all four extant classes of gymnosperms. In addition, we obtained cell-wall preparations containing >95% primary cell walls from nine gymnosperm species in nine families, representing all four extant classes. These preparations were analysed for ester-linked monomeric phenolic acids. We found ferulic acid (mostly trans) (88-1,561μg/g cell walls) in all of the preparations and p-coumaric acid (mostly trans) (0-106μg/g cell walls) in all except one of them. Ferulic acid ester-linked to primary cell walls has previously been found in angiosperms: in the commelinoid monocotyledons and in the dicotyledon order Caryophyllales, both monophyletic groups. From the present results, we postulate that the extant classes of gymnosperms are monophyletic and no class is sister to the angiosperms.     

A SINE Family Widely Distributed in the Plant Kingdom and its Evolutionary History

The distribution and evolution of Au SINE in plants were examined. Au SINE is a short interspersed element first identified in Aegilops umbellulata, a close relative of wheat. The Au SINE was previously found in species such as wheat, maize, tobacco, and tomato, but not in rice. In this study, we first searched public databases, and next examined the presence of Au in a broad range of plant species by PCR using internal primers of Au. Although Au is likely to be absent from many species including rice, it was identified in many Gramineae, Solanaceae, and Fabaceae species, and also in a basal angiosperm species, Asimina triloba. Phylogenetic studies suggest that Au SINE originated before the divergence of monocots and eudicots. Au SINE sequences of Asimina, Triticum, Zea, Nicotiana, Lotus, Medicago, and Glycine were aligned and compared. Although sequences of Au were highly conserved among distantly related species, every Au element in Glycine had a 16 bp deletion and its 3′ end differed from sequences of other species. This type of Au could only be found in G. max, and not in other species including other Fabaceae species such as M.␣truncatula and L. japonicus. This is the first report of a plant SINE family present in multiple lineages, and the evolution of Au SINE in the plant kingdom, especially in Gramineae and Fabaceae is discussed. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

The cellular and molecular biology of conifer embryogenesis

Gymnosperms and angiosperms are thought to have evolved from a common ancestor c. 300 million yr ago. The manner in which gymnosperms and angiosperms form seeds has diverged and, although broad similarities are evident, the anatomy and cell and molecular biology of embryogenesis in gymnosperms, such as the coniferous trees pine, spruce and fir, differ significantly from those in the most widely studied model angiosperm Arabidopsis thaliana. Molecular analysis of signaling pathways and processes such as programmed cell death and embryo maturation indicates that many developmental pathways are conserved between angiosperms and gymnosperms. Recent genomics research reveals that almost 30% of mRNAs found in developing pine embryos are absent from other conifer expressed sequence tag (EST) collections. These data show that the conifer embryo differs markedly from other gymnosperm tissues studied to date in terms of the range of genes transcribed. Approximately 72% of conifer embryo-expressed genes are found in the Arabidopsis proteome and conifer embryos contain mRNAs of very similar sequence to key genes that regulate seed development in Arabidopsis. However, 1388 loblolly pine (Pinus taeda) embryo ESTs (11.4% of the collection) are novel and, to date, have been found in no other plant. The data imply that, in gymnosperm embryogenesis, differences in structure and development are achieved by subtle molecular interactions, control of spatial and temporal gene expression and the regulating agency of a few unique proteins.     

Characterization of novel Alu- and tRNA-related SINEs from the tree shrew and evolutionary implications of their origins

We characterized two novel 7SL RNA-derived short interspersed nuclear element (SINE) families (Tu types I and II) and a novel tRNA-derived SINE family (Tu type III) from the tree shrew (Tupaia belangeri). Tu type I contains a monomer unit of a 7SL RNA-derived Alu-like sequence and a tRNA-derived region that includes internal RNA polymerase III promoters. Tu type II has a similar hybrid structure, although the monomer unit of the 7SL RNA-derived sequence is replaced by a dimer. Along with the primate Alu, the galago Alu type II, and the rodent B1, these two families represent the fourth and fifth 7SL RNA-derived SINE families to be identified. Furthermore, comparison of the Alu domains of Tu types I and II with those of other 7SL RNA-derived SINEs reveals that the nucleotides responsible for stabilization of the Alu domain have been conserved during evolution, providing the possibility that these conserved nucleotides play an indispensable role in retropositional activity. Evolutionary relationships among these 7SL RNA-derived SINE families, as well as phylogenetic relationships of their host species, are discussed.     

Accessory costs of seed production and the evolution of angiosperms

Accessory costs of reproduction frequently equal or exceed direct investment in offspring, and can limit the evolution of small offspring sizes. Early angiosperms had minimum seed sizes, an order of magnitude smaller than their contemporaries. It has been proposed that changes to reproductive features at the base of the angiosperm clade reduced accessory costs thus removing the fitness disadvantage of small seeds. We measured accessory costs of reproduction in 25 extant gymnosperms and angiosperms, to test whether angiosperms can produce small seeds more economically than gymnosperms. Total accessory costs scaled isometrically to seed mass for angiosperms but less than isometrically for gymnosperms, so that smaller seeds were proportionally more expensive for gymnosperms to produce. In particular, costs of abortions and packaging structures were significantly higher in gymnosperms. Also, the relationship between seed:ovule ratio and seed size was negative in angiosperms but positive in gymnosperms. We argue that the carpel was a key evolutionary innovation reducing accessory costs in angiosperms by allowing sporophytic control of pre- and postzygotic mate selection and timing of resource allocation. The resulting reduction in costs of aborting unfertilized ovules or genetically inferior embryos would have lowered total reproductive costs enabling early angiosperms to evolve small seed sizes and short generation times.     

Exploring the plant transcriptome through phylogenetic profiling

Publicly available protein sequences represent only a small fraction of the full catalog of genes encoded by the genomes of different plants, such as green algae, mosses, gymnosperms, and angiosperms. By contrast, an enormous amount of expressed sequence tags (ESTs) exists for a wide variety of plant species, representing a substantial part of all transcribed plant genes. Integrating protein and EST sequences in comparative and evolutionary analyses is not straightforward because of the heterogeneous nature of both types of sequence data. By combining information from publicly available EST and protein sequences for 32 different plant species, we identified more than 250,000 plant proteins organized in more than 12,000 gene families. Approximately 60% of the proteins are absent from current sequence databases but provide important new information about plant gene families. Analysis of the distribution of gene families over different plant species through phylogenetic profiling reveals interesting insights into plant gene evolution, and identifies species- and lineage-specific gene families, orphan genes, and conserved core genes across the green plant lineage. We counted a similar number of approximately 9,500 gene families in monocotyledonous and eudicotyledonous plants and found strong evidence for the existence of at least 33,700 genes in rice (Oryza sativa). Interestingly, the larger number of genes in rice compared to Arabidopsis (Arabidopsis thaliana) can partially be explained by a larger amount of species-specific single-copy genes and species-specific gene families. In addition, a majority of large gene families, typically containing more than 50 genes, are bigger in rice than Arabidopsis, whereas the opposite seems true for small gene families.     

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     

Comparative evolution history of SINEs in Arabidopsis thaliana and Brassica oleracea: evidence for a high rate of SINE loss

Brassica oleracea and Arabidopsis thaliana belong to the Brassicaceae(Cruciferae) family and diverged 16 to 19 million years ago. Although the genome size of B. oleracea (approximately 600 million base pairs) is more than four times that of A. thaliana (approximately 130 million base pairs), their gene content is believed to be very similar with more than 85% sequence identity in the coding region. Therefore, this important difference in genome size is likely to reflect a different rate of non-coding DNA accumulation. Transposable elements (TEs) constitute a major fraction of non-coding DNA in plant species. A different rate in TE accumulation between two closely related species can result in significant genome size variations in a short evolutionary period. Short interspersed elements (SINEs) are non-autonomous retroposons that have invaded the genome of most eukaryote species. Several SINE families are present in B. oleracea and A. thaliana and we found that two of them (called RathE1 and RathE2) are present in both species. In this study, the tempo of evolution of RathE1 and RathE2 SINE families in both species was compared. We observed that most B. oleracea RathE2 SINEs are "young" (close to the consensus sequence) and abundant while elements from this family are more degenerated and much less abundant in A. thaliana. However, the situation is different for the RathE1 SINE family for which the youngest elements are found in A. thaliana. Surprisingly, no SINE was found to occupy the same (orthologous) genomic locus in both species suggesting that either these SINE families were not amplified at a significant rate in the common ancestor of the two species or that older elements were lost and only the recent (lineage-specific) insertions remain. To test this latter hypothesis, loci containing a recently inserted SINE in the A. thaliana col-0 ecotype were selected and characterized in several other A. thaliana ecotypes. In addition to the expected SINE containing allele and the pre-integrative allele (i.e. the "empty" allele), we observed in the different ecotypes, alleles with truncated portions of the SINE (up to the complete loss of the element) and of the immediate genomic flanking sequences. The absence of SINEs in orthologous positions between B. oleracea and A. thaliana and the presence in recently diverged A. thaliana ecotypes of alleles containing severely truncated SINEs suggest a very high rate of SINE loss in these species.     

The occurrence of polyprenols in seeds and leaves of woody plants

The contents of the heterogenous group of polyisoprenoids was found about two orders of magnitude lower in seeds than the amount of polyprenols and/or their carboxylic esters accumulated during vegetation season in leaves. In contrast to leaves, no seeds were found containing more than 0.5 mg of these lipids per gram of dry tissue. Almost 50% had less than 0.01 mg/g - the amount which is the limit of detection by the procedure used in this work. In gymnosperms (10 representatives of Cupressaceae, Pinaceae and Taxaceae) the polyprenol spectra in seeds and in needles were similar. In angiosperms (25 representatives of 13 botanical families) the polyisoprenoid mixture in seeds resembled the minor, additional subfamily found in leaves.     

Was the ANITA rooting of the angiosperm phylogeny affected by long-branch attraction? Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya

Five groups of basal angiosperms, Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya (ANITA), were identified in several recent studies as representing a series of the earliest-diverging lineages of the angiosperm phylogeny. All of these studies except one employed a multigene analysis approach and used gymnosperms as the outgroup to determine the ingroup topology. The high level of divergence between gymnosperms and angiosperms, however, has long been implicated in the difficulty of reconstructing relationships at the base of angiosperm phylogeny using DNA sequences, for fear of long-branch attraction (LBA). In this study, we replaced the gymnosperm sequences from the five-gene matrix (mitochondrial atp1 and matR, plastid atpB and rbcL, and nuclear 18S rDNA) used in our earlier study with four categories of divergent sequences--random sequences with equal base frequencies or equally AT- and GC-rich contents, homopolymers and heteropolymers, misaligned gymnosperm sequences, and aligned lycopod and bryophyte sequences--to evaluate whether the gymnosperms were an appropriate outgroup to angiosperms in our earlier study that identified the ANITA rooting. All 24 analyses performed rooted the angiosperm phylogeny at either Acorus or Alisma (or Alisma-Triglochin-Potamogeton in one case due to use of a slightly different alignment) and placed the monocots as a basal grade, producing genuine LBA results. These analyses demonstrate that the identification of ANITA as the basalmost extant angiosperms was based on historical signals preserved in the gymnosperm sequences and that the gymnosperms were an appropriate outgroup with which to root the angiosperm phylogeny in the multigene sequence analysis. This strategy of evaluating the appropriateness of an outgroup using artificial sequences and a series of outgroups with increments of divergence levels can be applied to investigations of phylogenetic patterns at the bases of other major clades, such as land plants, animals, and eukaryotes.     

Phylogeny of the Botryosphaeriaceae reveals patterns of host association

Three anamorph genera of the Botryosphaeriaceae namely Diplodia, Lasiodiplodia and Dothiorella have typically dark, ovoid conidia with thick walls, and are consequently difficult to distinguish from each other. These genera are well-known pathogens of especially pine species. We generated a multiple gene genealogy to resolve the phylogenetic relationships of Botryosphaeriaceae with dark conidial anamorphs, and mapped host associations based on this phylogeny. The multiple gene genealogy separated Diplodia, Lasiodiplodia and Dothiorella and it revealed trends in the patterns of host association. The data set was expanded to include more lineages of the Botryosphaeriaceae, and included all isolates from different host species for which ITS sequence data are available. Results indicate that Diplodia species occur mainly on gymnosperms, with a few species on both gymnosperms and angiosperms. Lasiodiplodia species occur equally on both gymnosperms and angiosperms, Dothiorella species are restricted to angiosperms and Neofusicoccum species occur mainly on angiosperms with rare reports on Southern Hemisphere gymnosperms. Botryosphaeria species with Fusicoccum anamorphs occur mostly on angiosperms with rare reports on gymnosperms. Ancestral state reconstruction suggests that a putative ancestor of the Botryosphaeriaceae most likely evolved on the angiosperms. Another interesting observation was that both host generalist and specialist species were observed in all the lineages of the Botryosphaeriaceae, with little evidence of host associated co-evolution.     

Sexual systems in gymnosperms: A review

The aim of this study was to update figures for the presence of dioecy among the gymnosperms and investigate its correlation with climate, growth form, pollination and seed dispersal syndromes, and risk of extinction. Dioecy was found in almost 65% of contemporary gymnosperm species, a higher percentage than previous estimates. It dominates in 8 of the 12 families. As in angiosperms, dioecious gymnosperms are particularly common in climbers and are more commonly found in tropical climates. Analysis of the degree of threat using IUCN red list categories showed that the proportion of threatened species is higher in dioecious than in monoecious species only in temperate climate. The high sensitivity of dioecious species to environmental changes associated with human activity in temperate climate may explain this phenomenon. The monophyly of extant gymnosperms and the relatively small number of species (about 1000) create the possibility of treating them as a model group in investigating the evolution of sexual systems.     

Changes in hydraulic traits of nine vascular plants from different evolutionary lineages北大核心CSCD

Aims As vascular plants evolve from ferns to gymnosperms and angiosperms, their physiological structures and functions are assumed more adaptable to arid environment. Whether the three plant groups from early to late evolved lineages have improved their water transport and use efficiency has been studied on the basis of the morphological structure of leaf veins and stomata.Moreover, the water transportation rate was directly measured in the angiosperms. Therefore, we measured structural and functional traits related to water relations in all three plant groups simultaneously, to test the hypothesis on the evolutionary process of plant hydraulics. Methods We selected three species in each group grown in South China Botanical Garden, Guangzhou, China, including ferns (Dicranopteris pedata, Cyclosorus parasiticus and Blechnum orientale), gymnosperms (Podocarpus macrophyllus, Podocarpus nagi and Taxodium distichum) and angiosperms (Manglietia fordiana var. hainanensis, Sindora tonkinensis and Bauhinia purpurea). Important findings Sapwood and leaf specific hydraulic conductivities (KS and KL, respectively), and leaf conductance (Kleaf) significantly increased from ferns, gymnosperms to angiosperms. However, no significant trends were found in transpiration rate (E) and intrinsic water use efficiency. Meanwhile, neither the size and density of stomata nor wood density showed significant difference among three plant groups. The hydraulic functional traits (KS, KL and Kleaf) had significantly positive correlations with each other, but had no relationships with the two measured structural traits. Phylogenetic independent contrasts analyses showed that the coordination between KS and Kleaf, and between KS and E were independent of the phylogeny. Based on the nine vascular species, this study demonstrated that water transport related traits are improved as vascular plants evolved, and the co-evolution between water transport and transpiration traits were identified. For further study, it is necessary to consolidate our data with investigations of more detailed water-transport structures in more species from different evolutionary lineages. © 2018 Editorial Office of Chinese Journal of Plant Ecology. All rights reserved.     

New SINE families from rice, OsSN, with poly(A) at the 3' ends

A database search of the sequences flanking a member of rice retrotransposon RIRE7 revealed that a 298-bp sequence in the region downstream of the member is a repetitive sequence interspersed in the genome of Oryza sativa cv. Nipponbare. Most of the repetitive sequences were flanked by a direct repeat of a target-site sequence, about 14 bp in length. The consensus sequence, 293 bp in length, had no regions encoding any proteins but had sequence motifs of an internal promoter of RNA polymerase III. These indicate that the sequence is a retroposon SINE, designated OsSN1 (Oryza sativa SINE1). OsSN1 is a new rice SINE, because it has no homology with any of the three p-SINE families previously identified from rice, and because it has a stretch of A at the 3' end, unlike p-SINE and any other Gramineae SINEs which have a stretch of T at the 3' end. The Nipponbare genome was found to have many members related to OsSN1, forming two additional new SINE families (designated OsSN2 and OsSN3). OsSN2 and OsSN3 are highly homologous to the 3' and 5' regions of OsSN1, respectively. This suggests that OsSN1 has a mosaic structure, which is generated by sequence exchange (or shuffling) between ancestral OsSN2 and OsSN3. Despite the absence of homology in the 3' regions between OsSN1 (or OsSN2) and OsSN3, a sequence, 5'-TTCTC-3', is commonly present in the region preceding the A stretch at the 3' end. This sequence together with the A stretch and a stem-loop structure found in the region near the A stretch are assumed to be important for retroposition. OsSN members were present in strains of Oryza species, as were p-SINE members. Some of the members showed insertion polymorphism at the respective loci among the rice strains. p-SINE had such polymorphic members, which are useful for classification and phylogenetic analysis of various strains of Oryza species. The polymorphic members of OsSN were more frequently found than those of p-SINE, and therefore, such members are likely to be useful for extensive taxonomic and phylogenetic studies on various rice strains.