Nucleotide composition and CpG and CpNpG content of ITS1, ITS2, and the 5.8S rRNA in representatives of the phylogenetic branches melanthiales-liliales and melanthiales-asparagales (Angiospermae,Monocotyledones) reflect the specifics of their evolution

The nucleotide composition and the contents of CpG and CpNpG in internal transcribed spacers 1 and 2 (ITS1 and ITS2) and the 5.8S rRNA gene of the nuclear genome were studied in two phylogenetic lineages of monocotyledonous angiosperms. The evolutionary advance of taxa by morphological characters proved to positively correlate with an increase in the contents of C, CpG, and CpNpG, contrasting the views that genome evolution in vertebrate and higher plants tends to decrease or, at least, preserve the amount of CpG and CpNpG, potentially subject to methylation, in nuclear DNA. Cryptaffinity taxa, which are intermediates between morphologically distinct taxonomic groups, displayed higher contents of CpG and CpNpG as compared with neighboring taxa. Changes in the contents of these elements in the regions of cryptaffinity taxa are intricate, suggesting a reciprocating character for their accumulation. Cryptaffinity taxa and their close phylogenetic relatives from the ancestral and descendant groups were assumed to reflect the key macroevolutionary changes and to correspond to saltatory periods separating the periods of gradual evolution.     

Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation

A cytosine DNA methyltransferase containing a chromodomain, Zea methyltransferase2 (Zmet2), was cloned from maize. The sequence of ZMET2 is similar to that of the Arabidopsis chromomethylases CMT1 and CMT3, with C-terminal motifs characteristic of eukaryotic and prokaryotic DNA methyltransferases. We used a reverse genetics approach to determine the function of the Zmet2 gene. Plants homozygous for a Mutator transposable element insertion into motif IX had a 13% reduction in methylated cytosines. DNA gel blot analysis of these plants with methylation-sensitive restriction enzymes and bisulfite sequencing of a 180-bp knob sequence showed reduced methylation only at CpNpG sites. No reductions in methylation were observed at CpG or asymmetric sites in heterozygous or homozygous mutant plants. Our research shows that chromomethylase Zmet2 is required for in vivo methylation of CpNpG sequences.     

Global associations between terrestrial producer and vertebrate consumer diversity

In both ecology and conservation, often a strong positive association is assumed between the diversity of plants as primary producers and that of animals, specifically primary consumers. Such a relationship has been observed at small spatial scales, and a begetting of diversity by diversity is expected under various scenarios of co-evolution and co-adaptation. But positive producer-consumer richness relationships may also arise from similar associations with past opportunities for diversification or contemporary environmental conditions, or from emerging properties of plant diversity such as vegetation complexity or productivity. Here we assess whether the producer-consumer richness relationship generalizes from plot to regional scale and provide a first global test of its strength for vascular plants and endothermic vertebrates. We find strong positive richness associations, but only limited congruence of the most diverse regions. The richness of both primary and higher-level consumers increases with plant richness at similar strength and rate. Environmental conditions emerge as much stronger predictors of consumer richness, and after accounting for environmental differences little variation is explained by plant diversity. We conclude that biotic interactions and strong local associations between plants and consumers only relatively weakly scale up to broad geographical scales and to functionally diverse taxa, for which environmental constraints on richness dominate.     

北京维管植物三十年之变化

植物名称是人类对植物研究与利用等活动的基础。植物名称的变化可能成为不同行业之间交流的障碍, 错误或含混的植物名称可能会造成不便甚至损失。北京作为中国的首都, 在生物多样性保护与生态文明建设的背景下, 对于植物多样性信息变化的管理水平和能力要求更高。及时并准确地更新植物名称的变化及其过程, 对于植物学工作者、园林工作者和与植物相关产业从业者都十分重要。本文基于过去30年间(1992‒2021年)北京各类维管植物的名称信息, 记录了自1993年《北京植物志》(1992年修订版)以来的维管植物名称的变化过程: 包括34个新类群、175个新记录、509个新异名, 49个错误鉴定, 以及50个存疑类群。过去30年间, 北京的维管植物发生了很大的变化。本文结果可作为北京维管植物多样性监测和保护的重要参考。     

北京维管植物编目和分布数据集

区域性维管植物编目对于该区域内植物多样性保护及植物资源可持续利用具有重要意义。北京作为中国首都, 尽管编目工作早在20世纪60年代就得以开展, 但近30年来没有进行系统更新。现有数据零散、不系统, 相关编目进展甚至已经落后于周边地区。本文在《北京植物志(1992年修订版)》的基础上, 结合多年实际野外调查, 通过系统检索文献资料对现有编目数据进行查漏补缺(补充新分类群、新记录)、修订名称(基于新分类修订成果)、更新分类系统(采用基于分子数据的新分类系统), 并添加物种等级、分布状态、生长状态、室内/室外、分布区、了解程度及保护状况等相关信息, 最终完成北京维管植物编目和分布数据集(分为本土植物和外来植物两个表单, 其中外来植物主要基于志书和文献记载)。截至2021年12月31日, 该数据集共有数据2,883条(本土1,680条, 外来1,203条), 其中包含北京本土野生维管植物134科611属1,597个类群(1,440种3天然杂交种46亚种97变种11变型), 与《北京植物志(1992年修订版)》相比增加3科26属173种4亚种28变种11变型, 其中列入《国家重点保护野生植物名录(2021)》的有16种(一级仅1种), 列入《北京市重点保护野生植物名录(2008)》的有90种3亚种4变种; 收录外来维管植物137科581属1,184个类群(含992种及其他种下等级), 其中栽培植物854种19杂交种15亚种29变种2变型87栽培品种38栽培群, 逸生植物132种1亚种, 归化植物77种2变种, 入侵植物27种。编目数据显示, 北京本土野生维管植物多样性整体上并不高, 主要以广泛分布的常见种为主, 特有种、狭域种以及珍稀濒危种数量不多; 同时, 北京存在大量的外来植物(许多种类在《北京植物志》各版中已经收录), 这些植物也是北京维管植物多样性的重要组成部分, 但现有数据尚不完整。     

Effect of CpG methylation on gene expression in transfected plant protoplasts

Activity of the cat gene driven by the cauliflower mosaic virus 35S promoter has been assayed by transfecting petunia protoplasts with the pUC8CaMVCAT plasmid. In vitro methylation of this plasmid with M.HpaII (methylates C in CCGG sites) and M.HhaI (methylates GCGC sites) did not affect bacterial chloramphenicol acetyltransferase (CAT) activity. It should be noted, however, that no HpaII or HhaI sites are present in the promoter sequence. In contrast, in vitro methylation of the plasmid with the spiroplasma methylase M.SssI, which methylates all CpG sites, resulted in complete inhibition of CAT activity. The promoter sequence contains 16 CpG sites and 13 CpNpG sites that are known to be methylation sites in plant DNA. In the light of this fact, and considering the results of the experiments presented here, we conclude that methylation at all CpG sites leaving CpNpG sites unmethylated is sufficient to block gene activity in a plant cell. Methylation of CpNpG sites in plant cells may, therefore, play a role other than gene silencing.     

Steppe-like grassland as a refuge of the wild edible and medicinal plant species in anthropogenic landscape in northeastern Croatia

Habitat fragmentation and modification have been recognized as the most serious threats to biodiversity. In Croatia, the intensive human activities resulted in the landscape transformation, reduction of grassland areas and loss of species number. Increasingly threatened are the wild edible and medicinal plants which contribute remarkably to the biodiversity of different grassland types. In northeastern Croatia, one of the last remnants of the steppe-like grassland remained preserved in a very complex anthropogenic landscape. We examined the diversity of vascular plants occurring on this small habitat patch. Among the relatively high number of plant taxa (in a total of 177) found during the two years of investigations, most could be used both for human nutrition (28 taxa), and for the treatment of a wide range of diseases (60 taxa), while some taxa have nutritional value for livestock (17 taxa). All 23 recorded taxa with edible and medicinal properties are threatened in Croatia, 21 are threatened across Europe, and two are Red Listed taxa. Our results showed that small and isolated steppe-like grassland represents an important refuge for variety of valuable plant species in intensively used landscapes. Accordingly, such small habitats should be, at least locally, effectively protected.     

Genomic imprinting in plants and mammals: how life history constrains convergence

In both flowering plants and mammals, DNA methylation is involved in silencing alleles of imprinted genes, but surprising differences in imprinting control are emerging between the two taxa which may be traced to differences in their life cycles. Imprinted gene expression in plants occurs in the endosperm, a separate fertilisation product which transmits nutrients to the embryo and does not contribute a genome to the next generation. Regulation of expression of the known imprinted genes in Arabidopsis involves a cascade of gene expression beginning in the gametophyte, a haploid life phase interposed between the meiotic products and the gametes, which evolved from free-living organisms that constitute the dominant life phase of lower plants. Although the gametophytes of flowering plants are highly reduced they still express large numbers of genes, perhaps reflecting their evolutionary legacy, and which may now be recruited for control of imprinting. Strikingly, the genes at the top of the expression cascade appear to be specifically activated by demethylation, rather than targeted for silencing. Unlike in mammals, there is no evidence for global resetting of methylation in plants, and although imprinting involves the activity of a maintenance methyltransferase, de novo methyltransferases do not appear to be required. Plants do not set aside a germline; instead the cells that undergo meiosis to produce gametophytes differentiate in the adult plant during flower development. Both the late differentiation of the lineage producing germ cells, and the extent of gene expression during the haploid phase, may be incompatible with global resetting of methylation. Resetting may be unnecessary in any case because the adult plant expresses imprinted loci either biallelically or not at all, suggesting there is no chromosomal memory of parent-of-origin in the lineage that produces the gametophytes. Thus several features of the plant life cycle may account for the different strategies used by plants and animals to regulate parent-specific gene expression.     

Novel pattern of DNA methylation in Neurospora crassa transgenic for the foreign gene hph.

It has previously been reported that multiple copies of the hph gene integrated into the genome of Neurospora crassa are methylated at Hpa II sites (CCGG) during the vegetative life cycle of the fungus, while hph genes integrated as single copies are not methylated. Furthermore, methylation is correlated with silencing of the gene. We report here the methylation state of cytosine residues of the major part of the promoter region of the hph gene integrated into the genome of the multiple copy strain HTA5.7 during the vegetative stage of the life cycle. Cytosine methylation is sequence dependent, but the sequence specificity is complex and is different from the sequence specificity known for mammals and plants (CpG and CpNpG). The pattern of DNA methylation reported here is very different from that measured after meiosis in Neurospora or in Ascobulus . After the sexual cycle in those two fungi all the cytosines of multiple stretches of DNA are heavily methylated. This indicates that the still unknown methyltransferase in Neurospora has a different specificity in the sexual and the vegetative stages of the life cycle or that there are different methyltransferases. The pattern of methylation reported here is also different from the pattern of cytosine methylation of transgenes of Petunia , the only pattern published until now in plants that has DNA methylation at cytosines which are not in the canonical sequences CpG and CpNpG.     

HYPERMETHYLATION AT CPG-MOTIFS IN THE DINOFLAGELLATES AMPHIDINIUM CARTERAE (DINOPHYCEAE) AND SYMBIODINIUM MICROADRIATICUM (DINOPHYCEAE): EVIDENCE FROM RESTRICTION ANALYSES, 5-AZACYTIDINE AND ETHIONINE TREATMENT

Because of their peculiar chromatin features and phylogenetic position, dinoflagellates are potentially uniquely informative with respect to possible roles and evolution of DNA methylation systems. Here we report that DNA from Amphidinium carterae Hulburt and Symbiodinium microadriaticum Freudenthal was not significantly digested by a range of CpG methylation-sensitive endonucleases. Corresponding methylation-insensitive isoschizomers cleaved all DNA preparations. Treatment with the methylation inhibitors 5-azacytidine and ethionine resulted in major increases in digestibility of dinoflagellate DNA by CpG methylation-sensitive enzymes. The 5-azacytidine effect was not confined to heterochromatin. Our studies indicate that at least in some dinoflagellates, a high proportion of CpG motifs and a significant number of CpNpG motifs are normally methylated, implying methyltransferase substrate specificities similar to those of higher plants.     

Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins

Cytosine methylation at symmetrical CpG and CpNpG sequences plays a key role in the epigenetic control of plant growth and development; yet, the way by which the methylation signal is interpreted into a functional state has not been elucidated. In animals, the methylation signal is recognized by methyl-CpG-binding domain (MBD) proteins that specifically bind methylated CpG dinucleotides. In Arabidopsis thaliana, 12 putative MBD proteins were identified and classified into seven subclasses. Here, we characterized six MBD proteins representing four subclasses (II, III, IV, and VI) of the Arabidopsis MBD family. We found that AtMBD7 (subclass VI), a unique protein containing a double MBD motif, as well as AtMBD5 and AtMBD6 (subclass IV), bind specifically symmetrically methylated CpG sites. The MBD motif derived from AtMBD6, but not from AtMBD2, was sufficient for binding methylated CpG dinucleotides. AtMBD6 precipitated histone deacetylase (HDAC) activity from the leaf nuclear extract. The examined AtMBD proteins neither bound methylated CpNpG sequences nor did they display DNA demethylase activity. Our results suggest that AtMBD5, AtMBD6, and AtMBD7 are likely to function in Arabidopsis plants as mediators of the CpG methylation, linking DNA methylation-induced gene silencing with histone deacetylation.     

CpG + CpNpG analysis of protein-coding sequences from tomato

We develop codon-based models for simultaneously inferring the mutational effects of CpG and CpNpG methylation in coding regions. In a data set of 369 tomato genes, we show that there is very little effect of CpNpG methylation but a strong effect of CpG methylation affecting almost all genes. We further show that the CpNpG and CpG effects are largely uncorrelated. Our results suggest different roles of CpG and CpNpG methylation, with CpNpG methylation possibly playing a specialized role in defense against transposons and RNA viruses.     

Highly divergent methyltransferases catalyze a conserved reaction in tocopherol and plastoquinone synthesis in cyanobacteria and photosynthetic eukaryotes

Tocopherols are lipid-soluble compounds synthesized only by photosynthetic eukaryotes and oxygenic cyanobacteria. The pathway and enzymes for tocopherol synthesis are homologous in cyanobacteria and plants except for 2-methyl-6-phytyl-1,4-benzoquinone/2-methyl-6-solanyl-1,4-benzoquinone methyltransferase (MPBQ/MSBQ MT), which catalyzes a key methylation step in both tocopherol and plastoquinone (PQ) synthesis. Using a combined genomic, genetic, and biochemical approach, we isolated and characterized the VTE3 (vitamin E defective) locus, which encodes MPBQ/MSBQ MT in Arabidopsis. The phenotypes of vte3 mutants are consistent with the disruption of MPBQ/MSBQ MT activity to varying extents. The ethyl methanesulfonate-derived vte3-1 allele alters tocopherol composition but has little impact on PQ levels, whereas the null vte3-2 allele is deficient in PQ and alpha- and gamma-tocopherols. In vitro enzyme assays confirmed that VTE3 is the plant functional equivalent of the previously characterized MPBQ/MSBQ MT (Sll0418) from Synechocystis sp PCC6803, although the two proteins are highly divergent in primary sequence. Sll0418 orthologs are present in all fully sequenced cyanobacterial genomes, Chlamydomonas reinhardtii, and the diatom Thalassiosira pseudonana but absent from vascular and nonvascular plant databases. VTE3 orthologs are present in all vascular and nonvascular plant databases and in C. reinhardtii but absent from cyanobacterial genomes. Intriguingly, the only prokaryotic genomes that contain VTE3-like sequences are those of two species of archea, suggesting that, in contrast to all other enzymes of the plant tocopherol pathway, the evolutionary origin of VTE3 may have been archeal rather than cyanobacterial. In vivo analyses of vte3 mutants and the corresponding homozygous Synechocystis sp PCC6803 sll0418::aphII mutant revealed important differences in enzyme redundancy, the regulation of tocopherol synthesis, and the integration of tocopherol and PQ biosynthesis in cyanobacteria and plants.     

Characterization of the level,target sites and inheritance of cytosine methylation in tomato nuclear DNA

The tomato nuclear genome was determined to have a G+C content of 37% which is among the lowest reported for any plant species. Non-coding regions have a G+C content even lower (32% average) whereas coding regions are considerably richer in G+C (46%).5-methyl cytosine was the only modified base detected and on average 23% of the cytosine residues are methylated. Immature tissues and protoplasts have significantly lower levels of cytosine methylation (average 20%) than mature tissues (average 25%). Mature pollen has an intermediate level of methylation (22%). Seeds gave the highest value (27%), suggesting de novo methylation after pollination and during seed development.Based on isoschizomer studies we estimate 55% of the CpG target sites (detected by Msp I/Hpa II) and 85% of the CpNpG target sites (detected by Bst NI/Eco RI)are methylated. Unmethylated target sites (both CpG and CpNpG) are not randomly distributed throughout the genome, but frequently occur in clusters. These clusters resemble CpG islands recently reported in maize and tobacco.The low G+C content and high levels of cytosine methylation in tomato may be due to previous transitions of 5mCT. This is supported by the fact that G+C levels are lowest in non-coding portions of the genome in which selection is relaxed and thus transitions are more likely to be tolerated. This hypothesis is also supported by the general deficiency of methylation target sites in the tomato genome, especially in non-coding regions.Using methylation isoschizomers and RFLP analysis we have also determined that polymorphism between plants, for cytosine methylation at allelic sites, is common in tomato. Comparing DNA from two tomato species, 20% of the polymorphisms detected by Bst NI/Eco RII could be attributed to differential methylation at the CpNpG target sites. With Msp I/Hpa II, 50% of the polymorphisms were attributable to methylation (CpG and CpNpG sites). Moreover, these polymorphisms were demonstrated to be inherited in a mendelian fashion and to co-segregate with the methylation target site and thus do not represent variation for transacting factors that might be involved in methylation of DNA. The potential role of heritable methylation polymorphism in evolution of gene regulation and in RFLP studies is discussed.     

表观遗传修饰介导的植物胁迫记忆

植物因其固着生长的方式, 已经进化出各类特殊的机制来适应多变的外界环境。为提高自身的存活率, 植物进化出一类胁迫记忆机制, 以适应环境和保护自己。表观遗传修饰不仅能调控植物的正常生长发育, 而且参与植物对各种非生物或生物胁迫的响应。近年的研究表明, 表观遗传修饰在植物胁迫记忆调控中也发挥重要作用。例如, DNA甲基化、组蛋白甲基化及乙酰化等表观遗传修饰参与并维持特定的胁迫记忆。该文主要对表观遗传修饰介导的植物胁迫记忆最新进展进行综述, 并展望未来的重点和热点研究方向。     

表观遗传修饰介导的植物胁迫记忆

植物因其固着生长的方式, 已经进化出各类特殊的机制来适应多变的外界环境。为提高自身的存活率, 植物进化出一类胁迫记忆机制, 以适应环境和保护自己。表观遗传修饰不仅能调控植物的正常生长发育, 而且参与植物对各种非生物或生物胁迫的响应。近年的研究表明, 表观遗传修饰在植物胁迫记忆调控中也发挥重要作用。例如, DNA甲基化、组蛋白甲基化及乙酰化等表观遗传修饰参与并维持特定的胁迫记忆。该文主要对表观遗传修饰介导的植物胁迫记忆最新进展进行综述, 并展望未来的重点和热点研究方向。     

A Characterization of the Non-indigenous Flora of the Azores Archipelago

The 9 Azores islands are located in the North Atlantic Ocean, about 1500 km from Europe. The vascular plant flora, consisting of 1002 taxa, was characterized using a database. Biogeographic and historic criteria were used to categorize the taxa as indigenous (31%) and non-indigenous (69%). The proportion of non-indigenous vascular plant taxa is higher than in other island ecosystems. This might have resulted from the removal of native vegetation and the introduction of many cultivated and ornamental plants, and from the relatively large extension of the agricultural landscape. The introduced plants were largely subcosmopolitan therophytes and hemicryptophytes, mainly Dicotyledoneae and Monocotyledoneae. The families with highest absolute contributions were similar to those in other areas of the world (Poaceae, Asteraceae, Fabaceae, Brassicaceae, Scrophulariaceae), but not all contributed as expected by their species richness worldwide. Many were introduced as ornamental or crop plants, but there were also many accidental introductions of weeds (about 55% of non-indigenous taxa). Considering the 9 islands, the percentage of introductions was positively correlated with human population density and island surface below 300 m, and negatively correlated with island surface allocated to natural areas.     

Methyl-CpG-binding domain (MBD) proteins in plants

Cytosine methylation is the most prevalent epigenetic modification of plant nuclear DNA, which occurs in symmetrical CpG or CpNpG as well as in non-symmetrical contexts. Intensive studies demonstrated the central role played by cytosine methylation in genome organization, gene expression and in plant growth and development. However, the way by which the methyl group is interpreted into a functional state has only recently begun to be explored with the isolation and characterization of methylated DNA binding proteins capable of binding 5-methylcytosine. These proteins belong to an evolutionary conserved protein family initially described in animals termed methyl-CpG-binding domain (MBD) proteins. Here, we highlight recent advances and present new prospects concerning plant MBD proteins and their possible role in controlling chromatin structure mediated by CpG methylation.     

世界维管植物新分类群2021年年度报告

2021年全球共发表维管植物新分类群2,219个, 包括新亚科1个、新族7个、新亚族7个、新属68个、新亚属7个、新组15个、新亚组8个、新系10个、新种1,979个、新亚种46个、新变种59个和新变型12个; 这些新分类群隶属于185科881属, 兰科、菊科和茜草科是本年度最受关注的类群。2,219个维管植物新分类群由来自全球的1,942位学者发表在165个期刊和14部专著中, 其中有42位作者发表了11个以上的新分类群。值得关注的是, Phytotaxa和PhytoKeys是2021年发表维管植物新分类群的主要期刊, 分别发表586个和112个。本年度发表的2,096个新种及种下单元中, 被子植物门1,940个、蕨类植物门147个、裸子植物门9个, 其中兰科植物最多, 共227个。2021年发表的新种及种下单元来自世界115个国家和地区。亚洲和南美洲是新种及种下单元发现的热点地区, 分别发现837个和571个。中国、巴西和马达加斯加是2021年贡献维管植物新种及种下单元最多的前3个国家, 分别发现283、269和169个。考虑到在2021年2月1日之后IPNI对2020年发表的维管植物新种增加了797个, 我们估计在2022年4月16日之后, 各数据库中2021年发表的新种及种下单元会增加700个左右。这将使2021年发表的新种(和种下分类群)数量增加到大约2,800个, 这与2001年以来每年发表的维管植物新种数量相当。