蜈蚣衣科SSU rDNA中I型内含子的初步研究

本文结合来自GenBank中的地衣型真菌SSU rDNA中Ⅰ型内含子的相关信息,对取自蜈蚣衣属(Physcia)两个种——斑面蜈蚣衣(Physcia aipolia)、蜈蚣衣(Physcia stellaris),和黑蜈蚣衣属(Phaeophyscia)一个种——毛边黑蜈蚣衣(Phaeophyscia hispidula)共10个样品的SSU rDNA中Ⅰ型内含子的分布模式进行了研究。结果表明,在这些地衣型真菌的SSU rDNA中具有多个Ⅰ型内含子;而内含子插入位点的分布并不具有种的特异性和地理特异性。这种分布模式暗示这些Ⅰ型内含子仍然处于“插入-删除”的平衡状态,而且在此过程中,有性生殖可能比基因的水平转移发挥了更重要的作用。     

蜈蚣衣科地衣1个中国新记录属——金奥克衣属

以采自新疆地区的地衣标本为试验材料,通过观察和研究该地衣形态解剖特征、次生代谢产物以及构建核糖体DNA内转录间隔区(internal transcribed spacer,ITS)系统发育树,研究鉴定该地衣标本为蜈蚣衣科(Physciaceae)1个中国新记录属:金奥克衣属[Oxnerella(S.Y.Kondr.,Lo″k?s&Hur)]及中国新记录种双裂金奥克衣[O.safavidiorum(S.Y.Kondr.,Zarei-Darki,Lo″k?s&Hur)],该种含有柔扁枝衣酸,文中提供了该种形态解剖图,并讨论了其与相似物种的关系。     

地衣的ITS序列系统发育分析和DNA条形码的初探

目的:构建出地衣植物核糖体rDNA(nrDNA)的ITS序列的系统发育树并探讨地衣植物的DNA条形码.方法:以黑龙江五大连池风景区的地衣植物为材料,采用特异性引物对地衣植物的ITS序列进行Pcr扩增,直接对其Pcr产物进行测序,利用MEGA4.0软件建立地衣植物的ITS序列的系统发育树.结果:根据系统发育分析得出一致性指数CI和维持性指数RI分别为0 5356和0.6602,相同属地衣的样本间即种内的遗传距离 和不同属的样本间即种间的遗传距离(K-2-P)平均值分别为0.030和0.600,种间距离大于种内距离.结论:根据地衣植物样本间的遗传距离(K-2-P)的分析,得出核糖体rDNA的ITS基因对地衣近缘属的分类鉴定上具有一定的参考价值,建议作为地衣分类鉴定的条形码的测试片段.     

中国蜈蚣衣科地衣多样性及区系研究

该研究通过对山西管涔山和五鹿山等区域采集的蜈蚣衣科地衣300余份标本的鉴定分析,结合已有报道,从物种多样性、空间分布特点、生境类型及区系成分等方面对蜈蚣衣科地衣进行研究,以明确中国蜈蚣衣科地衣物种组成及区系特点。结果表明：(1)中国蜈蚣衣科地衣共有7属197种54变种,饼干衣属(Rinodina)占绝对优势,约占蜈蚣衣科地衣总种数的30.5%。(2)中国蜈蚣衣科地衣多分布于新疆,蜈蚣衣属(Physcia)是该科中分布最广泛的属,但其中有26.4%的物种仅分布于单一地区。(3)蜈蚣衣科地衣生境类型多样,有树生、石生、藓丛生、土生和多生境5种,以多生境地衣为主(48.5%)。(4)中国蜈蚣衣科地衣的地理成分复杂,同时伴随多种区系成分,但以温带性质显著(占43.1%),东亚特色明显。(5)仅分布于中国的蜈蚣衣科地衣共4属10种,且主要分布于中国东北、西北和西南地区。     

新疆蜈蚣衣科3属地衣生态分布与地理区系成分分析

根据多年的实地调查资料和相关研究资料,对新疆的黑蜈蚣衣属（Phaeophyscia）、蜈蚣衣属（Physcia）和大孢蜈蚣衣属（Physconia）地衣的种类及分布区、区系特征和垂直分布特征进行了初步分析。结果表明,分布在新疆的蜈蚣衣科地衣共有37种,分属6种地理成分和6种生态类型,主要分布在新疆的天山和阿勒泰山。研究结果还显示,分布在阿勒泰山和天山的蜈蚣衣科种类的垂直分布有明显差异。     

中国新疆博格达山周边地区大型地衣物种多样性及分布特征

本研究对中国新疆博格达山周边地区大型地衣进行地衣分类学和生态学结合的综合研究,通过分析大型地衣物种多样性和分布特征,探讨影响地衣分布的环境变量与生态因子。研究结果表明:(1)分布在博格达山周边地区的大型地衣共有43种,隶属于6目、11科、15属,其中茶渍目和黄枝衣目大型地衣占优势,分别占该地区大型地衣科、属、种总数的55%、67%、81%。(2)博格达山周边地区的大型地衣组成5个样点组,分别是蓝灰蜈蚣衣+裂片石黄衣组、细片石黄衣+亚灰大孢蜈蚣衣组、长缘毛蜈蚣衣+菊叶黄梅组、地卷+暗裂芽黑蜈蚣衣组、黑蜈蚣衣+枪石蕊组,样点组的分布与环境因子密切相关。(3)在影响大型地衣分布的环境因素中海拔对地衣种类分布的影响较显著。本研究为更准确地确定博格达山区大型地衣分布规律提供科学依据。     

中国褐鳞叶衣属和鳞藓衣属地衣5个新记录种

报道了褐鳞叶衣属Fuscopannaria和鳞藓衣属Psoroma的5个中国地衣型真菌新记录种:蓝缘褐鳞叶衣F. coerulescens、裂叶褐鳞叶衣F. dissecta、泰国褐鳞叶衣F. siamensis、雅褐鳞叶衣F. venusta和鳞藓衣P. hypnorum。此二属的区别在于褐鳞叶衣属地衣体无下皮层,子实层半淀粉质,光合共生物为蓝细菌;而鳞藓衣属地衣体具下皮层,子实层淀粉质,光合共生物为绿藻。蓝缘褐鳞叶衣是典型的鳞叶状地衣,其疣状次生小裂片上覆有白色萜类结晶;裂叶褐鳞叶衣的鳞片深裂,边缘上仰,具白边;泰国褐鳞叶衣具周缘裂片,次生小裂片扁平小叶状或指状;雅褐鳞叶衣的鳞片向末端繁复分支,边缘具裂芽。鳞藓衣的主要特征为地衣体具衣瘿,孢子外壁具有疣状突起。文中提供了中国新记录种的图片,并给出了此二属地衣型真菌的中国物种检索表。     

中国蜈蚣衣科（子囊菌门）IV．——黑蜈蚣衣属一新种

本文描述黑蜈蚣衣属一新种即湖南黑蜈蚣衣(Phaeophyscia hunana)。新种以其短而窄的裂片,上表面疣状和具小裂片,以及红色髓层并含有skyrin和一未知地衣物质而区别于本属地衣其它种。     

中国蜈蚣衣科(子囊菌门)IV. 黑蜈蚣衣属一新种

本文描述黑蜈蚣衣属一新种即湖南黑蜈蚣衣(Phaeophyscia hunana).新种以其短而窄的裂片,上表面疣状和具小裂片,以及红色髓层并含有skyrin和一未知地衣物质而区别于本属地衣其它种.     

中国蜈蚣衣科(子囊菌门)IV. 黑蜈蚣衣属一新种

本文描述黑蜈蚣衣属一新种即湖南黑蜈蚣衣(Phaeophyscia hunana)。新种以其短而窄的裂片,上表面疣状和具小裂片,以及红色髓层并含有skyrin和一未知地衣物质而区别于本属地衣其它种。     

Nuclear-encoded rDNA group I introns: origin and phylogenetic relationships of insertion site lineages in the green algae

Group I introns are widespread in eukaryotic organelles and nuclear- encoded ribosomal DNAs (rDNAs). The green algae are particularly rich in rDNA group I introns. To better understand the origins and phylogenetic relationships of green algal nuclear-encoded small subunit rDNA group I introns, a secondary structure-based alignment was constructed with available intron sequences and 11 new subgroup ICI and three new subgroup IB3 intron sequences determined from members of the Trebouxiophyceae (common phycobiont components of lichen) and the Ulvophyceae. Phylogenetic analyses using a weighted maximum-parsimony method showed that most group I introns form distinct lineages defined by insertion sites within the SSU rDNA. The comparison of topologies defining the phylogenetic relationships of 12 members of the 1512 group I intron insertion site lineage (position relative to the E. coli SSU rDNA coding region) with that of the host cells (i.e., SSU rDNAs) that contain these introns provided insights into the possible origin, stability, loss, and lateral transfer of ICI group I introns. The phylogenetic data were consistent with a viral origin of the 1512 group I intron in the green algae. This intron appears to have originated, minimally, within the SSU rDNA of the common ancestor of the trebouxiophytes and has subsequently been vertically inherited within this algal lineage with loss of the intron in some taxa. The phylogenetic analyses also suggested that the 1512 intron was laterally transferred among later-diverging trebouxiophytes; these algal taxa may have coexisted in a developing lichen thallus, thus facilitating cell- to-cell contact and the lateral transfer. Comparison of available group I intron sequences from the nuclear-encoded SSU rDNA of phycobiont and mycobiont components of lichens demonstrated that these sequences have independent origins and are not the result of lateral transfer from one component to the other.      

Divergent Histories of rDNA Group I Introns in the Lichen Family Physciaceae

The wide but sporadic distribution of group I introns in protists, plants, and fungi, as well as in eubacteria, likely resulted from extensive lateral transfer followed by differential loss. The extent of horizontal transfer of group I introns can potentially be determined by examining closely related species or genera. We used a phylogenetic approach with a large data set (including 62 novel large subunit [LSU] rRNA group I introns) to study intron movement within the monophyletic lichen family Physciaceae. Our results show five cases of horizontal transfer into homologous sites between species but do not support transposition into ectopic sites. This is in contrast to previous work with Physciaceae small subunit (SSU) rDNA group I introns where strong support was found for multiple ectopic transpositions. This difference in the apparent number of ectopic intron movements between SSU and LSU rDNA genes may in part be explained by a larger number of positions in the SSU rRNA, which can support the insertion and/or retention of group I introns. In contrast, we suggest that the LSU rRNA may have fewer acceptable positions and therefore intron spread is limited in this gene. Reviewing Editor: Dr. W. Ford Doolittle     

Positions of multiple insertions in SSU rDNA of lichen-forming fungi

Lichen-forming fungi, in symbiotic associations with algae, frequently have nuclear small subunit ribosomal DNA (SSU rDNA) longer than the 1,800 nucleotides typical for eukaryotes. The lichen-forming ascomycetous fungus Lecanora dispersa contains insertions at eight distinct positions of its SSU rDNA; the lichen-forming fungi Calicium tricolor and Porpidia crustulata each contain one insertion. Insertions are not limited to fungi that form lichens; the lichen ally Mycocalicium albonigrum also contains two insertions. Of the 11 insertion positions now reported for lichen-forming fungi and this ally, 6 positions are known only from lichen-forming fungi. Including the 4 newly reported in this study, insertions are now known from at least 17 positions among all reported SSU rDNA sequences. Insertions, most of which are Group I introns, are reported in fungal and protistan lineages and occur at corresponding positions in genomes as phylogenetically distant as the nuclei of fungi, green algae, and red algae. Many of these positions are exposed in the mature rRNA tertiary structure and may be subject to independent insertion of introns. Insertion of introns, accompanied by their sporadic loss, accounts for the scattered distribution of insertions observed within the SSU rDNA of these diverse organisms.      

Evolutionary dynamics of multiple group I introns in nuclear ribosomal RNA genes of endoparasitic fungi of the genus Cordyceps

A large number of group I introns were discovered in coding regions of small and large subunits of nuclear ribosomal RNA genes (SSU rDNA and LSU rDNA) in ascomycetous fungi of the genus CORDYCEPS: From 28 representatives of the genus, we identified in total 69 group I introns which were inserted at any of four specific sites in SSU rDNA and four specific sites in LSU rDNA. These group I introns reached sizes of up to 510 bp, occurred in up to eight sites in the same organism, and belonged to either subgroup IB3 or subgroup IC1 based on their sequence and structure. Introns inserted at the same site were closely related to each other among Cordyceps fungi, whereas introns inserted at different sites were phylogenetically distinct even in the same species. Mapped on the host phylogeny, the group I introns were generally not restricted to a particular lineage, but, rather, widely and sporadically distributed among distinct lineages. When the phylogenetic relationships of introns inserted at the same site were compared with the phylogeny of their hosts, the topologies were generally significantly congruent to each other. From these results, the evolutionary dynamics of multiple group I introns in Cordyceps fungi was inferred as follows: (1) most of the group I introns were already present at the eight sites in SSU and LSU rDNAs of the ancestor of the genus Cordyceps; (2) the introns have principally been immobile and vertically transmitted throughout speciation and diversification of Cordyceps fungi, which resulted in the phylogenetic congruence between the introns at the same site and their hosts; (3) in the course of vertical transmission, the introns have repeatedly been lost in a number of lineages independently, which has led to the present sporadic phylogenetic distribution of the introns; and (4) a few acquisitions of new introns, presumably through horizontal transmission, were identified in the evolutionary history of the genus Cordyceps, while no transpositions were detected. Losses of group I introns in SSU rDNA have occurred at least 27 times in the evolutionary course of the 28 Cordyceps members.     

Numerous group I introns with variable distributions in the ribosomal DNA of a lichen fungus.

The length of the small subunit ribosomal DNA (SSU rDNA) differs significantly among individuals from natural populations of the ascomycetous lichen complex Cladonia chlorophaea. The sequence of the 3' region of the SSU rDNA from two individuals, chosen to represent the shortest and longest sequences, revealed multiple insertions within a region that otherwise aligned with a 520-nucleotide sequence of the SSU rDNA in Saccharomyces cerevisiae. The high degree of variability in SSU rDNA size can be accounted for by different numbers of insertions; one individual had two group I introns and the second had five introns, two of which were clearly related to introns at identical positions in the other individual. Yet, introns in different positions, whether within an individual or between individuals, were not similar in sequence. The distribution of introns at three of the positions is consistent with either intron loss or acquisition, and clearly indicates the dynamic variability in this region of the nuclear genome. All seven insertions, which ranged in size from 210 to 228 nucleotides, had the conserved sequence and secondary structural elements of group I introns. The variation in distribution and sequence of group I introns within a short highly conserved region of rDNA presents a unique opportunity for examining the molecular evolution and mobility of group I introns within a systematics framework.     

Structural characteristics and possible horizontal transfer of group I introns between closely related plant pathogenic fungi.

We have characterized structural features and the distribution pattern of nuclear group I introns found in ribosomal DNA (rDNA) of closely related plant pathogenic fungi of the family Sclerotiniaceae. Sixteen introns, at two distinct positions in the small-subunit (SSU) and large-subunit (LSU) rDNA, were sequenced and analyzed among the 29 taxa included in the initial screening. Genera found to contain introns were Botrytis, Dumontinia, Encoelia, Grovesinia, Myriosclerotinia, and Sclerotinia. Secondary-structure analyses of the group I introns concluded that all belong to the common IC1 subclass. Interestingly, the SSU rDNA intron from Myriosclerotinia caricisampullacea contains an insertion-like sequence extension which may be a relic of an open reading frame. Incongruent branching patterns of intron-based and rDNA-based (internal transcribed spacer) phylogenetic trees suggest that the fungal host genomes and the group I introns do not share a common evolutionary history. A model to explain how horizontal intron transfers may have occurred among the closely related fungal taxa is proposed.     

A diverse population of introns in the nuclear ribosomal genes of ericoid mycorrhizal fungi includes elements with sequence similarity to endonuclease-coding genes

Ericoid mycorrhizal fungi form symbioses with the roots of members of the Ericales. Although only two genera have been identified in culture, the taxonomic diversity of ericoid symbionts is certainly wider. Genetic variation among 40 ericoid fungal isolates was investigated in this study. PCR amplification of the nuclear small-subunit ribosomal DNA (SSU rDNA) and of the internal transcribed spacer (ITS), followed by sequencing, led to the discovery of DNA insertions of various sizes in the SSU rDNA of most isolates. They reached sizes of almost 1,800 bp and occurred in up to five different insertion sites. Their positions and sizes were generally correlated with morphological and ITS-RFLP grouping of the isolates, although some insertions were found to be optional among isolates of the same species, and insertions were not always present in all SSU rDNA repeats within an isolate. Most insertions were identified as typical group I introns, possessing the conserved motifs characteristic of this group. However, other insertions lack these motifs and form a distinct group that includes other fungal ribosomal introns. Alignments with almost 70 additional sequences from fungal nuclear SSU rDNA introns indicate that introns inserted at the same site along the rDNA gene are generally homologous, but they also suggest the possibility of some horizontal transfers. Two of the ericoid fungal introns showed strong homology with a conserved motif found in endonuclease genes from nuclear rDNA introns.     

USING RDNA GENES TO UNDERSTAND THE ORIGIN AND EVOLUTION OF SPLICEOSOMAL AND GROUP I INTRONS

Ribosomal DNA genes in lichen algae and lichen fungi are astonishingly rich in spliceosomal and group I introns. We use phylogenetic, secondary structure, and biochemical analyses to understand the evolution of these introns. Despite the widespread distribution of spliceosomal introns in nuclear pre-mRNA genes, their general mechanism of origin remains an open question because few proven cases of recent and pervasive intron origin have been documented. The lichen introns are valuable in this respect because they are undoubtedly of a "recent" origin and limited to the Euascomycetes. Our analyses suggest that rDNA spliceosomal introns have arisen through aberrant reverse-splicing (in trans) of free pre-mRNA introns into r RNAs. We propose that the spliceosome itself (and not an external agent; e.g. transposable elements, group II introns) has given rise to the introns. The rDNA introns are found most often between the flanking sequence G (78%) - intron-G (72%), and their clustered positions on secondary structures suggest that particular r RNA regions are preferred sites (i.e., proto-splice sites) for insertion. Mapping of intron positions on the newly available tertiary structures show that they are found most often in exposed regions of the ribosomes. This again is consistent with an intron origin through reverse-splicing. Remarkably, the distribution and phylogenetic relationships of most group I introns in nuclear rDNA genes are also consistent with a reverse-splicing origin. These data underline the value of lichens as a model system for understanding intron origin and stress the importance of RNA-level processes in the spread of these sequences in nuclear coding regions.     

Origin and evolution of chloroplast group I introns in lichen algae

The history of group I introns is characterized by repeated horizontal transfers, even among phylogenetically distant species. The symbiogenetic thalli of lichens are good candidates for the horizontal transfer of genetic material among distantly related organisms, such as fungi and green algae. The main goal of this study was to determine whether there were different trends in intron distribution and properties among Chlorophyte algae based on their phylogenetic relationships and living conditions. Therefore, we investigated the occurrence, distribution and properties of group I introns within the chloroplast LSU rDNA in 87 Chlorophyte algae including lichen and free‐living Trebouxiophyceae compared to free‐living non‐Trebouxiophyceae species. Overall, our findings showed that there was high diversity of group I introns and homing endonucleases (HEs) between Trebouxiophyceae and non‐Trebouxiophyceae Chlorophyte algae, with divergence in their distribution patterns, frequencies and properties. However, the differences between lichen Trebouxiophyceae and free‐living Trebouxiophyceae were smaller. An exception was the cL2449 intron, which was closely related to ω elements in yeasts. Such introns seem to occur more frequently in lichen Trebouxiophyceae compared to free‐living Trebouxiophyceae. Our data suggest that lichenization and maintenance of lichen symbiosis for millions of years of evolution may have facilitated horizontal transfers of specific introns/HEs between symbionts. The data also suggest that sequencing of more chloroplast genes harboring group I introns in diverse algal groups may help us to understand the group I intron/HE transmission process within these organisms.     

Patterns of Group I Intron Presence in Nuclear SSU rDNA of the Lichen Family Parmeliaceae

Group I introns are commonly reported within nuclear SSU ribosomal DNA of eukaryotic micro-organisms, especially in lichen-forming fungi. We have studied the primary and secondary structure of 70 new nuclear SSU rDNA group I introns of Parmeliaceae (Ascomycota: Lecanorales) and compared them with those available in databases, covering more than 60 species. The analyzed samples of Parmeliaceae fell into two groups, one having an intron at the 1506 site and another lacking this one but having another at the 1516 or 1521 position. Introns at the 1521 position seem to be transposed from 1516 sites. Introns at the 1516 position were similar in structure to ones previously reported at this site and known from other lecanoralean fungi, while those at the 1506 position showed structural differences and no similar introns are known from related fungi. The study of the distribution of group I introns within a large monophyletic ensemble of fungi has revealed an unexpected correlation between intron types and ecological and geographical parameters. The introns at the 1516 position occurred in mainly arctic, boreal, and temperate lichens, while those at position 1506 were present in mainly tropical and subtropical to oceanic mild-temperate taxa. Further, the 1516 introns occurred in genera with few distributed species that could represent older taxa, while the 1506 ones were mainly in species-rich genera that could be of recent speciation, as many species have wide distribution areas. The transition between two different environments has been accompanied by a change in introns gained and lost. [Reviewing Editor: Dr. Debashish Bhattacharya]