Whole‐genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations

Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 Branchiostoma individuals by whole‐genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size (N_e) of Branchiostoma population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long‐term population dynamics of Branchiostoma. The inferred ancestral N_e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10^?9) or third glaciation (mutation rate = 9 × 10^?9) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all Branchiostoma individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long‐term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.     

Production of phenolics and the emission of volatile organic compounds by perennial ryegrass (Lolium perenne L.)/Neotyphodium lolii association as a response to infection by Fusarium poae

Grasses very often form symbiotic associations with Neotyphodium/Epichloë endophytic fungi. These endophytes often allow the host grass to be protected from different pathogens. However, there is little known about the mechanisms of such endophyte influence on the host. Thus, the purpose of this research was to examine the effect of the N. lolii endophyte on the total production of phenolic compounds, VOCs emission and the resistance of three perennial ryegrass genotypes infected by pathogenic Fusarium poae. Analyses of total phenolics content were performed in control (not inoculated) and inoculated plants after 1, 2, 3, 4, 5, and 6 days (DAI) and for VOCs after 0, 3, 6 and 12 DAI. The presence of endophytes significantly reduced the disease index in two of the three genotypes relative to that in E−. Plants infected by N. lolii exhibited higher production of phenolics relative to the E− plants. The highest amounts of phenolics were observed on the second and sixth DAI. Genotype Nl22 showed the strongest effect of the endophyte on the production of phenolics, which increased by over 61%. Both the endophyte infected and non-infected plants emitted most abundantly two GLVs ((Z)-3-hexenal, (Z)-3-hexen-1-yl acetate), three terpenes (linalool, (Z)-ocimene, β-caryophyllene) and three shikimic acid pathway derivatives (benzyl acetate, indole, and methyl salicylate). The endophyte presence and the intervals of VOCs detection were a highly significant source of variation for all emitted volatiles (P < 0.001). The genotype of the perennial ryegrass significantly affected only the emission of methyl salicylate (P < 0.05) and β-caryophyllene (P < 0.05). Most of the VOCs ((Z)-3-hexen-1-yl acetate, (Z)-3-hexenal, linalool and methyl salicylate) reached their highest levels of emission on the sixth DAI, when averaged over genotypes and endophyte status. The results highlight the role of Neotyphodium spp. in the mediation of quadro-trophic interactions among plants, symbiotic endophytes, invertebrate herbivores and plant pathogenic fungi. Our results also confirm the fact that symbiotic plants can activate a defense reaction faster than non-symbiotic plants after a pathogen attack. Thus, N. lolii can be involved in the defense of perennial ryegrass against pathogens and potentially could be central to the host plants’ protection.     

Development and Application of Microsatellites in Candidate Genes Related to Wood Properties in the Chinese White Poplar (Populus tomentosa Carr.)

Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2–7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species.     

中国鲤形目鱼类的中轴骨骼数及其生态适应性

为探讨中国鲤形目鱼类中轴骨骼数及其与系统发育和生态习性的相关性,采用X光透视照相法对157种鲤科(Cyprinidae)、鳅科(Cobitidae)、平鳍鳅科(Balitoridae)鱼类的脊椎骨数、肋骨数、尾椎数进行了比较分析。结果显示,中国鲤形目鱼类的脊椎骨数在30-52枚之间,均值39.45?4.44;肋骨数在8-28对之间,均值15.27?3.08;尾椎数在14-34枚之间,均值21.08?2.89。依据脊椎骨数、肋骨数、尾椎数对鲤科各亚科进行聚类,显示鲤科12个亚科分为2大类：雅罗鱼类,包括雅罗鱼亚科、鲌亚科、鲴亚科、裂腹鱼亚科等4亚科;鲃类,包括鲢亚科、鮈亚科、鱼丹亚科、鲃亚科、野鲮亚科、鳅鮀亚科、鲤亚科、鱊亚科等8亚科。单因素方差分析显示,鲤科肉食性鱼类的肋骨数与脊椎骨数的比值显著少于植食性鱼类(P＜0.05),而脊椎骨数、尾椎数则显著多于植食性鱼类(P＜0.05)。中上层鱼类的脊椎骨数、尾椎数显著多于下层鱼类(P＜0.05)。极小型鱼类的脊椎骨数、肋骨数,以及肋骨数与脊椎骨数之比显著少于大型鱼类(P＜0.05)。表明鲤科鱼类的中轴骨骼数与其系统发育和生态习性及体型具有明显的相关性。     

肝外胆管解剖变异和先天发育异常MRCP研究

目的:归纳肝外胆管解剖变异和先天发育异常的MRCP(magnetic resonance cholangiopancreatography,MRCP)表现。方法:回顾分析2010年1月到2015年6月间PACS存储的6817例图像资料,首先判定图像质量,然后记录肝门区胆管分支汇入方式、胆囊管插入位置、胆管先天发育异常及其表现。结果:1590例存在肝外胆管解剖变异和先天发育异常。其中胆囊管汇入位置异常发生率14.72%(787/5347),肝门区胆管分支汇入状态异常发生率17.97%(961/5347)。包括肝门区胆管分支汇入状态正常,胆囊管汇入位置异常575例,发生率10.75%(575/5347)。胆囊管汇入位置正常,肝门区胆管分支汇入状态异常749例,发生率14.01%(749/5347)。胆囊管汇入位置和肝门区胆管分支汇入状态异常并存212例,发生率3.96%(212/5347)。先天性发育异常即先天胆管扩张症54例,发生率1.01%(54/5347)。结论:肝外胆管解剖变异和先天发育异常复杂多样,MRCP能够准确显示大部分解剖变异种类及其毗邻关系,但是受图像质量及所罹患病种制约。     

Clinical,Molecular, and Computational Analysis in two cases with mitochondrial encephalomyopathy associated with SUCLG1 mutation in a consanguineous family

Deficiency of the mitochondrial enzyme succinyl COA ligase (SUCL) is associated with encephalomyopathic mtDNA depletion syndrome and methylmalonic aciduria. This disorder is caused by mutations in both SUCL subunits genes: SUCLG1 (α subnit) and SUCLA2 (β subnit). We report here, two Tunisian patients belonging to a consanguineous family with mitochondrial encephalomyopathy, hearing loss, lactic acidosis, hypotonia, psychomotor retardation and methylmalonic aciduria. Mutational analysis of SUCLG1 gene showed, for the first time, the presence of c.41T > C in the exon 1 at homozygous state. In-silico analysis revealed that this mutation substitutes a conserved methionine residue to a threonine at position 14 (p.M14T) located at the SUCLG1 protein mitochondrial targeting sequence. Moreover, these analysis predicted that this mutation alter stability structure and mitochondrial translocation of the protein. In Addition, a decrease in mtDNA copy number was revealed by real time PCR in the peripheral blood leukocytes in the two patients compared with controls.     

中国东北产6种藓类植物的染色体观察

苔藓植物细胞学研究始于 2 0世纪 [1 ] 。我国有关这方面的研究自 1 988年开始 ,据 1 998年周云龙统计 ,国内学者共报道了 94种苔藓植物的染色体数目 ,其中苔类有 1 6科、1 9属、2 3种 ,5种为首次报道 ;藓类有 2 1科、37属、71种 ,2 7种为首次报道[2 ] 。这些研究为苔藓植物的系统学、生态学、遗传学等提供了直接或间接的资料和证据。1 　材料和方法将采集的苔藓植物培养在室内北窗台上。取生长旺盛的茎尖用对二氯苯饱和水溶液预处理 5～ 7h,卡诺固定液 (纯酒精∶冰醋酸 =3∶ 1 )固定 ,95%酒精∶盐酸 ( 1∶ 1 )离析1 0～ 2 0 min后剥离茎尖…     

中国南部亚热带森林地表植被动态变化

系统研究了南方5个亚热带森林生态系统地表植被的动态变化情况.研究方法是:在每个研究区域内,按照地形梯度分别布设50个1m2 的样方,记录样方内所有物种的频度及相关的环境变量,5个研究区域共设250个样方,每个样方分别调查两次.通过单元及多元统计方法分析表明:维管植物物种频度在一个区域明显下降,另二个区域显著增加;苔藓物种频度在一个区域有明显下降,另一个区域明显增加;苔藓物种数量在3个区域显著增加,另二个区域显著下降;维管植物物种数量显著增加在二个区域;物种组成沿着第一个植被梯度轴DCA 1没有显著变化,沿着第二个植被梯度轴DCA 2在二个区域有显著变化.综合分析表明,苔藓对气候变化及其波动反映敏感,是较好的气候变化及气候波动生物指示因子,而管植物数量及频度的变化没有明显证据显示与土壤酸化和大气污染有紧密关系.     

新疆猪毛菜属植物染色体数及核型分析

以5种新疆猪毛菜属植物为材料,常规压片法制片后观察记录染色体数,并进行核型分析。实验结果表明:钠猪毛菜体细胞染色体数2n=18;浆果猪毛菜2n=2x=18=12m 6sm,属2A核型;木本猪毛菜2n=2x=18=16m 2sm,属2A核型;东方猪毛菜2n=4x=36=26m 10sm,属2B核型;长刺猪毛菜2n=4x=36=24m 4sm 8st,属2B核型。猪毛菜属植物的染色体基数为9,东方猪毛菜、长刺猪毛菜为四倍体,其它3种均为二倍体。与Бочанцев基于形态学特征建立的分组系统及各组的演化地位相比,东方猪毛菜属于原始的硬叶猪毛菜组,而本研究表明该种在核型上相对较为进化;其余3种核型地位与所属组的演化地位相符。     

国产蕺菜的染色体数目变异及核穿壁现象

蕺菜 Houttuynia cordata Thunb.属三白草科蕺菜属,俗称鱼腥草、侧耳根等,主要分 布于 亚洲东部和东南部,我国以长江流域及其以南各省区常见。蕺菜药蔬兼用,为极具开发前景 的植物资源。部分学者曾对蕺菜染色体数目进行过报道,但报道的染色体数目不尽一致（梁汉兴,1991,1995; Hsu,1968; Nilsamranchit et al, 1999）,并且对此 现象未作较为详细而深入的解释。本文对国内部分省区收集的蕺菜种质资源进行染色体数目分析,旨在从细胞学角度探讨蕺菜的遗传多样性,为