Chloroplast DNA variation and phylogeny of theRanunculaceae

Restriction site mapping of chloroplast DNA from 31 species representing 26 genera of theRanunculaceae was performed using eleven restriction endonucleases. The chloroplast genome varies in length from approximately 152 to 160 kb. Length variants are frequent in theRanunculaceae and range from usually less than 300 bp to rarely 1.5 kb. The inverted repeat is extended into the large single copy (LSC) region by 4–4.5 kb inAnemone, Clematis, Clematopsis, Hepatica, Knowltonia, andPulsatilla. Several inversions are present in the LSC-region of the cpDNA in all these genera and inAdonis. The frequency of restriction site mutations varies within the chloroplast genome in theRanunculaceae between 4 and 32 mutations per kilobase, and is lowest in the inverted repeat and the regions containing the ATPase-genes and the genespsaA, psaB, psbA, rpoB, andrbcL. A total of 547 phylogenetically informative restriction sites was utilized in cladistic analyses of the family using Wagner, Dollo, and weighted parsimony. These three parsimony analyses result in different tree topologies. Four, six, and one equally most parsimonious trees were obtained with Wagner, Dollo, and weighted parsimony, respectively. The amount of support for the monophyletic groups was evaluated using bootstrapping and decay analysis. All three parsimony methods suggest thatHydrastis is the sister group to the remainder of theRanunculaceae, and that theAnemone-Clematis group, which shares several derived cpDNA rearrangements, is monophyletic. Only a few of the traditional groups in theRanunculaceae are supported by cpDNA restriction side data. Only Dollo parsimony provides support for the hypothesis thatThalictroideae andRanunculoideae are monophyletic.     

Fine structure and 18S rDNA phylogeny of a marine araphid pennate diatom Plagiostriata goreensis gen. et sp. nov. (Bacillariophyta)

A marine araphid pennate diatom Plagiostriata goreensis is described from the sand grains of Goree Island, Dakar, Republic of Senegal, based on observations of fine structure of its frustule. The most striking feature of the species is its striation, which is angled at approximately 60° across the robust sternum. The other defining features of the species are its one highly reduced rimoportula and apical pores located at both ends of the valve margin. In the 18S rDNA phylogeny, the species appears as a member of a ‘small‐celled clade’ of araphid pennate diatoms that consist of Nanofrustulum, Opephora and Staurosira. The results of the phylogenetic analyses suggest that the distinct characters of the diatom; namely, oblique striae and apical pores, may have been acquired independently. However, it remains unclear whether the rimoportula of P. goreensis is a reduced state or P. goreensis acquired its morphologically curious rimoportula independently after the loss of an ancient rimoportula at the root of the small‐celled clade.     

The Effects of Proteins and Phospholipids on the Mobility of Wheat Doughs

Penicillium strains (n=394) preserved at NBRC (the NITE Biological Resource Center) were compared as to groupings (11 species-clusters) based on phylogeny and the production of bioactive compounds. The strains in two clusters, of which P. chrysogenum and P. citrinum are representative, showed higher rates of positive strains with multi-biological activities.     

Perenniporia cinereofusca sp. nov. (Polyporales,Basidiomycota) evidenced by morphological characters and phylogenetic analysis

A new Perenniporia species, P. cinereofusca, is described based on morphological and molecular characters. It is characterized by an annual growth habit, resupinate basidiocarps with gray to pale brown pore surface, tissues becoming black in 5% potassium hydroxide (KOH), a dimitic hyphal system with weakly dextrinoid skeletal hyphae and hyaline to pale yellowish, distinctly thick-walled and indextrinoid basidiospores (6.5–7.7 × 5.3–6.3 μm), and presence of dendrohyphidia and large rhomboid crystals. Both morphological and molecular evidence confirmed the placement of the new species in Perenniporia sensu stricto and showed its relationships with similar species in the genus.     

A workflow of massive identification and application of intron markers using snakes as a model

Relative to the commonly used mitochondrial and nuclear protein‐coding genes, the noncoding intron sequences are a promising source of informative markers that have the potential to resolve difficult phylogenetic nodes such as rapid radiations and recent divergences. Yet many issues exist in the use of intron markers, which prevent their extensive application as conventional markers. We used the diverse group of snakes as an example to try paving the way for massive identification and application of intron markers. We performed a series of bioinformatics screenings which identified appropriate introns between single‐copy and conserved exons from two snake genomes, adding particular constraints on sequence length variability and sequence variability. A total of 1,273 candidate intron loci were retrieved. Primers for nested polymerase chain reaction (PCR) were designed for over a hundred candidates and tested in 16 snake representatives. 96 intron markers were developed that could be amplified across a broad range of snake taxa with high PCR successful rates. The markers were then applied to 49 snake samples. The large number of amplicons was subjected to next‐generation sequencing (NGS). An analytic strategy was developed to accurately recover the amplicon sequences, and approximately, 76% of the marker sequences were recovered. The average p‐distances of the intron markers at interfamily, intergenus, interspecies, and intraspecies levels were .168, .052, .015, and .004, respectively, suggesting that they were useful to study snake relationships of different evolutionary depths. A snake phylogeny was constructed with the intron markers, which produced concordant results with robust support at both interfamily and intragenus levels. The intron markers provide a convenient way to explore the signals in the noncoding regions to address the controversies on the snake tree. Our improved strategy of genome screening is effective and can be applied to other animal groups. NGS coupled with appropriate sequence processing can greatly facilitate the extensive application of molecular markers.     

太平洋克拉里昂-克利伯顿断裂带嘴刺目线虫多样性

从太平洋深海克拉里昂-克利伯顿断裂带(Clarion-Clipperton fracture zone,简称CC区)4个站位采集的深海沉积物样品中检出26条嘴刺目(Enoplida)线虫个体。综合应用形态学和分子生物学方法,共鉴定嘴刺目线虫6科8属,其中尖口线虫科(Oxystominidae)个体数量最多,占总数的57.7%,其次为前感线虫科(Anticomidae,19.2%)、光皮线虫科(Phanodermatidae,7.7%)、钩线虫科(Oncholaimidae,7.7%)、烙线虫科(Ironidae,3.8%)和矛线虫科(Enchelidiidae,3.8%)。科、属组成与相邻站点同期采样所获的线虫近似,而丰度组成比例有所差异。分子生物学方法获得了线虫rRNA基因序列16条,经Gen Bank数据库比对,其与已有的序列相似性范围为94%—99%,以此为依据可确定到科的水平和大部分属的水平(84.6%)。DNA条形码比对结果和形态学鉴定结果有较高一致性,表明分子条形码技术可作为深海线虫鉴定的有效手段。系统发育分析结果显示,基于18S和28S rRNA基因序列,采用不同方法构建系统发育树,其分支结构基本一致;钩线虫科和矛线虫科聚类在一起,光皮线虫科和前感线虫科聚类在一起,显示出彼此间较近的遗传关系。     

Hesperotestudo (Testudines: Testudinidae) from the Pleistocene of Bermuda, with comments on the phylogenetic position of the genus

A recently discovered fossil land tortoise (Testudines: Testudinidae) is described from the Pleistocene of Bermuda. Its morphology is sufficiently well preserved to allow assignment to the extinct North American genus Hesperotestudo. However, several features of this tortoise are unique and it is named Hesperotestudo bermudae sp. nov. A review of the phylogenetic relationships of the better known genera of the Testudinidae suggests that the affinities of Hesperotestudo lie with other North American tortoises (Gopherus) and not with Geochelone or other testudinines; thus, Hesperotestudo is reassigned to the Xerobatinae. This is at least the fifth documentation of a testudinid dispersing over open ocean to an oceanic island (the first for Hesperotestudo) and it corroborates the hypothesis that members of this family are well suited to over-water dispersal.     

中国鬼伞类真菌的分类

鬼伞类真菌涉及蘑菇科的鬼伞属Coprinus以及小脆柄菇科的小鬼伞属Coprinellus、拟鬼伞属Coprinopsis、近地伞属Parasola、刺毛鬼伞属Tulosesus和心孢鬼伞属Narcissea。基于标本研究和文献记载,确认我国该类真菌57种：小鬼伞属9种,刺毛鬼伞属10种,心孢鬼伞属3种,拟鬼伞属25种,近地伞属8种,鬼伞属2种。本文记载1个新组合——速亡型心孢鬼伞Narcissea ephemeroides,中国新记录种11个：黄鳞小鬼伞Coprinellus ellisii、甜味小鬼伞Coprinellus saccharinus、锐突拟鬼伞Coprinopsis acuminata、非洲雪白拟鬼伞Coprinopsis afronivea、美丽拟鬼伞Coprinopsis bellula、钟孢拟鬼伞Coprinopsis mitraespora、麻醉拟鬼伞Coprinopsis narcotica、厚壁拟鬼伞Coprinopsis pachyderma、近雪白拟鬼伞Coprinopsis pseudonivea、施罗特近地伞Parasola schroeteri和刺毛近地伞Parasola setulosa。编制了中国鬼伞类真菌分种检索表,对新组合和中国新记录种进行形态学描述,并提供线条图。结合ITS和LSU序列片段,采用了最大似然法和贝叶斯分析法建立系统发育树,反映各类群之间的系统演化关系。     

A comparative whole genome analysis of Helicobacter pylori from a human dense South Asian setting

Helicobacter pylori, a Gram-negative bacterium, is associated with a wide range of gastric diseases such as gastritis, duodenal ulcer, and gastric cancer. The prevalence of H pylori and risk of disease vary in different parts of the world based on the prevailing bacterial lineage. Here, we present a contextual and comparative genomics analysis of 20 clinical isolates of H pylori from patients in Bangladesh. Despite a uniform host ethnicity (Bengali), isolates were classified as being part of the HpAsia2 (50%) or HpEurope (50%) population. Out of twenty isolates, eighteen isolates were cagA positive, with two HpEurope isolates being cagA negative, three EPIYA motif patterns (AB, AB-C, and ABC-C) were observed among the cagA-positive isolates. Three vacA genotypes were observed with the s1m1i1dic1 genotype observed in 75% of isolates; the s1m2i1d1c2 and s2m2i2d2c2 genotypes were found to be 15% and 10% of isolates, respectively. The non-virulent genotypes s2m2i2d2c2 was only observed in HpEurope population isolates. Genotypic analysis of oipA gene, present in all isolates, revealed five different patterns of the CT repeat; all HpAsia2 isolates were in “ON” while 20% of HpEurope isolates were genotypically “OFF.” The three blood group antigen binding adhesins encoded genes (bab genes) examined and we observed that the most common genotype was (babA/babB/-) found in eight isolates, notably six were HpAsia2 isolates. The babA gene was found in all HpAsia2 isolates but present in only half of the HpEurope isolates. In silico antibiotic susceptibility analysis revealed that 40% of the strains were multi-drug resistant. Mutations associated with resistance to metronidazole, fluoroquinolone, and clarithromycin were detected 90%, 45%, and 5%, respectively, in H pylori strain. In conclusion, it is evident that two populations of H pylori with similar antibiotic profiles are predominant in Bangladesh, and it appears that genotypically the HpAisa2 isolates are potentially more virulent than the HpEurope isolates.