基于线粒体细胞色素b基因的中国大沙鼠系统地理格局

通过内蒙、新疆、甘肃的41个大沙鼠样品和1个伊朗撒拉克大沙鼠的mtDNA Cytb基因全序列的遗传分析,对我国大沙鼠(Rhombomys opimus)的分子系统地理学进行了初步探讨。结果表明,我国41个大沙鼠样品的Cytb基因包含了50个核苷酸变异位点(占全序列的4.39%),其中转换48个,颠换2个,共定义23个单倍型。在四个地理种群中,内蒙古中部半荒漠区和阿拉善荒漠区的单倍型多样性最高,甘新荒漠区的单倍型多样性最低;北疆荒漠区的核苷酸多样性最高,内蒙古中部半荒漠区的核苷酸多样性最低。分子变异分析(AMOVA)表明,种群间的遗传变异占51.68%,种群内的遗传变异占48.32%。FST统计结果表明,除内蒙古中部半荒漠区与阿拉善荒漠区地理种群之间差异显著外(P<0.05),其它地理种群间的差异均极显著(P<0.01)。基于单倍型的系统树显示,42只大沙鼠形成三支。其中,伊朗撒拉克地区大沙鼠和中国地区大沙鼠之间的亲缘关系比中国两支大沙鼠之间的亲缘关系远;分析表明,中国分布的大沙鼠两支之间分歧时间估计在0.093Ma前。嵌套支分析表明,大沙鼠历史种群曾发生过异域片段化、受阻碍基因流和持续种群扩张事件。种群扩张分析提示大沙鼠在0.0119Ma前曾经历过一次种群扩张事件,种群可能受到末次冰期波动的影响。     

江西井冈山地区灰胸竹鸡的遗传多样性研究

灰胸竹鸡Bambusicola thoracica是我国特有鸟类.本文采用聚合链式反应和直接测序的方法测定井冈山地区灰胸竹鸡3个种群线粒体DNA(mtDNA)控制区1142 bp的序列,分析其序列变异和种群遗传多样性.30个样本共发现16个变异位点和10种单倍型,其中hapl广泛分布,占所分析样本的23.33%,是其祖先单倍型.3个种群的平均单倍型多样性和核苷酸多样性分别为0.815和0.00243.青原区种群与其它两个种群遗传分化显著,基因交流受限制.受隔离影响,青原区种群遗传多样性最低.在系统发生树上,10种单倍型形成两支,井冈山种群和永新县种群聚在一起,与其地理位置相一致.     

金沙江中下游圆口铜鱼遗传多样性与种群历史动态分析

以线粒体Cytb和CoⅠ基因作为分子标记,对金沙江中下游江段的圆口铜鱼进行遗传多样性和种群历史动态分析.结果显示,393尾圆口铜鱼样本共检测出91个串联基因序列单倍型,呈现较高的单倍型多样性(0.936±0.006)和较低的核苷酸多样性(0.00489±0.00009);基于单倍型构建的分子系统发育树及Median-j...     

大石鸡兰州亚种的mtDNA种群遗传结构、单倍型分布和遗传多样性

大石鸡(Alectorismagna)是中国西北部的特有种。我们测定了大石鸡兰州亚种(A.m.lanzhouensis)8个地理种群106个样本的线粒体DNA控制区5′端458bp序列,研究其种群遗传结构和遗传多样性。27个变异位点共确定25种单倍型,其中单倍型M2广泛分布,而许多单倍型为一些地方种群特有。单倍型分布沿着南北方向变化,存在明显的地理结构。8个种群中核苷酸多样性最高的是定西种群,0.0069,最低的是海原种群,0.0028;单倍型多样性最高的是武山种群,0.86,最低的是北道种群,0.52。北方种群比南方种群具有更高的遗传多样性。系统发生树和单倍型分布表明,大石鸡兰州亚种存在两个明显的分支。溯祖理论、更新世冰期和花粉支持兰州亚种起源于兰州盆地,这个盆地是其遗传多样性的中心。     

POPULATION GENETIC STRUCTURE OF ENDANGERED SPECIES PLATΥPHARODON EXTREMUS ( SCHIZOTHORACINAE, CYPRINIDAE )IN YELLOW RIVER, CHINA

极边扁咽齿鱼Platypharodon extremus是黄河上游的特有鱼类,近年来由于过度捕捞、环境变迁等因素,其资源量剧减,种群处于濒危状态.研究中采集了分布于黄河上游的3个种群(n= 107),基于线粒体DNA控制区695bp 序列,共检测到101个可变位点,占总分析位点的14.5％,其中58个为简约信息位点.3种群共界定了87个单倍型,种群平均单倍型多样性h= 0.995,核苷酸多样性π=0.0129.结果表明,极边扁咽齿鱼的种群遗传多样性水平较高.分子方差分析(AMOVA)表明,3群体间总遗传分化系数Fst= 0.0528,群体间尚未有显著的遗传分化.系统发生树显示3种群的单倍型混合分布,各进化枝之间分歧度很低,没有形成明显的单倍型组,也没有显示出单倍型与地理位置的对应关系.3个群体共享1个单倍型(Hap_ 31),推测它们来自于共同的祖先.歧点分布和Fu’Fs中性检测显示极边扁咽齿鱼并未经历种群扩张.     

基于线粒体D-loop区和Cyt b基因分析广西禾花鲤三个群体遗传结构

研究基于线粒体D-loop区和Cyt b基因部分序列, 分析了广西全州、融水、环江三地禾花鲤(Cyprinus carpio)的遗传结构。在3个群体中共鉴定到19种D-loop与Cyt b序列的组合单倍型, 总的单倍型多样性(H_d)和核苷酸多样性(π)分别为0.916±0.010和0.008±0.004, 禾花鲤线粒体DNA具有单倍型多样性高和核苷酸多样性低的特点。环江群体单倍型多样性最低, 但是核苷酸多样性却最高, 反映了环江群体存在最明显的谱系混杂。分子方差分析(AMOVA)显示遗传变异主要来源于群体内部(71.54%), 禾花鲤三个群体间有显著的遗传分化(F_st=0.285; P<0.01)。系统发育分析表明, 多数样本的线粒体单倍型属于华南鲤(C. carpio rubrefusus)类型, 同时三地禾花鲤中均检测到一定频率的西鲤(C. carpio carpio)或远东鲤(C. carpio haematopterus)类型的线粒体单倍型, 提示禾花鲤可能受到鲤养殖品种的杂交渐渗。研究初步揭示了广西禾花鲤的种质资源现状, 为禾花鲤这一地方特色“稻鱼共作”品种的选育和苗种管理提供了必要的依据。     

大石鸡边缘种群的遗传结构

大石鸡（Alectoris magna）分布于青海西部、东部,甘肃中部和宁夏西部的干部和半干旱区,由于环境变化,其种群向甘肃南部森林被砍伐的地区扩散,形成涟缘种群。本研究采用聚合酶链式反应（PCR）和直接测序的方法获得了采自甘肃的大石鸡一个边缘种群和两个中心地理种群共39个个体的线粒体DNA（mtDNA）控制区基因（D－loop）456－457个核苷酸的基因序列,16个变异位点（占整个序列的3.5%）有15个单倍型。边缘扩散种群有3种单倍型,M6与另两个种群共有,单倍型频率为0.108,而M4和M5为其特有,单倍型频率分别为0.081和0.027。边缘种群的单倍型比率和遗传多样性分别为37.5%和0.549。中心地理种群1和种群2各有7个单倍型,除M6炳种群共有,其余为自所特有,单倍型比率分别为46.7%和50.0%,遗传多样性分别是0.729和0.786。边缘种群的单倍型比率和遗传多样性均低于中心地理种群。     

假眼小绿叶蝉地理种群的线粒体DNA 16S rRNA基因序列分析及遗传分化研究

测定了12个不同地理种群的茶树害虫假眼小绿叶蝉Empoasca vitis(Gothe)和1个外群共103个个体的线粒体DNA 16S rRNA基因部分序列,比较其同源性,计算核苷酸组成,并构建单倍型进化关系图。结果表明:在获得的假眼小绿叶蝉536 bp的序列中A+T含量占76.8%,其中56个核苷酸位点存在变异;100个个体共检测出56种单倍型,单倍型多样性指数(H)为0.971,核苷酸多样性指数(Pi)0.006;12个种群间的平均基因流(Nm)为1.64。总群体的固定系数Fst为0.026;AMOVA分子方差分析结果表明假眼小绿叶蝉的遗传分化主要来自于种群内部(97.4%)。各地理种群的遗传距离与地理分布不具有直接对应的关系。根据构建的单倍型进化关系网,各地理种群的单倍型呈现一种混杂的分布格局,未显示出与地理分布的一致性。     

我国部分黄牛品种线粒体D-loop区遗传多样性与起源分化

为了解我国地方黄牛品种线粒体DNA的遗传变异情况, 文章测定了16个地方黄牛品种206个个体线粒体D-loop区的全序列, 共检测到101个变异位点; 99种单倍型, 其中73种是普通牛单倍型, 26种是瘤牛单倍型; 平均核苷酸差异为22.6920, 单倍型多样度为0.9320, 核苷酸多样度为0.0227, 表明我国黄牛品种遗传多样性非常丰富。构建的NJ进化树显示16个品种来源于两大母系: 普通牛和瘤牛; 构建的Network图表明73种普通牛单倍型可以分为3大单倍型群; 26种瘤牛单倍型分为5种单倍型群, 推测我国瘤牛在迁移过程中, 至少经历了4次群体扩张事件。通过分析比较地方黄牛品种与内罗门牛共有的 H3单倍型, 发现其中只有16%的序列与内罗门牛的H3单倍型非常相似, 其余84%的序列均发生了鸟嘌呤变异, 推测这些变异很可能是我国瘤牛固有的变异。     

黄河上游极边扁咽齿鱼种群遗传结构

极边扁咽齿鱼Platypharodon extremus是黄河上游的特有鱼类,近年来由于过度捕捞、环境变迁等因素,其资源量剧减,种群处于濒危状态。研究中采集了分布于黄河上游的3个种群（n=107）,基于线粒体DNA控制区695bp序列,共检测到101个可变位点,占总分析位点的14.5%,其中58个为简约信息位点。3种群共界定了87个单倍型,种群平均单倍型多样性h=0.995,核苷酸多样性π=0.0129。结果表明,极边扁咽齿鱼的种群遗传多样性水平较高。分子方差分析（AMOVA）表明,3群体间总遗传分化系数Fst=0.0528,群体间尚未有显著的遗传分化。系统发生树显示3种群的单倍型混合分布,各进化枝之间分歧度很低,没有形成明显的单倍型组,也没有显示出单倍型与地理位置的对应关系。3个群体共享1个单倍型（Hap₃1）,推测它们来自于共同的祖先。歧点分布和Fu’Fs中性检测显示极边扁咽齿鱼并未经历种群扩张。     

辽东湾斑海豹MHC-DQB基因的遗传多样性分析

本文从25份斑海豹样本中获得141 bp片段,发现21个变异位点,定义了12个MHC-DQB等位基因,氨基酸变异率为25.5%.等位基因之间的遗传距离范围是0.0071～0.1064,平均值为0.0577,不同等位基因之间的碱基差异是1～15 bp,平均差异数为8 bp.与其他鳍足类动物对比后发现,斑海豹MHC-DQB...     

Single nucleotide polymorphisms and linkage disequilibrium in sunflower

Genetic diversity in modern sunflower (Helianthus annuus L.) cultivars (elite oilseed inbred lines) has been shaped by domestication and breeding bottlenecks and wild and exotic allele introgression⁻the former narrowing and the latter broadening genetic diversity. To assess single nucleotide polymorphism (SNP) frequencies, nucleotide diversity, and linkage disequilibrium (LD) in modern cultivars, alleles were resequenced from 81 genic loci distributed throughout the sunflower genome. DNA polymorphisms were abundant; 1078 SNPs (1/45.7 bp) and 178 insertions-deletions (INDELs) (1/277.0 bp) were identified in 49.4 kbp of DNA/genotype. SNPs were twofold more frequent in noncoding (1/32.1 bp) than coding (1/62.8 bp) sequences. Nucleotide diversity was only slightly lower in inbred lines (θ = 0.0094) than wild populations (θ = 0.0128). Mean haplotype diversity was 0.74. When extraploted across the genome (~3500 Mbp), sunflower was predicted to harbor at least 76.4 million common SNPs among modern cultivar alleles. LD decayed more slowly in inbred lines than wild populations (mean LD declined to 0.32 by 5.5 kbp in the former, the maximum physical distance surveyed), a difference attributed to domestication and breeding bottlenecks. SNP frequencies and LD decay are sufficient in modern sunflower cultivars for very high-density genetic mapping and high-resolution association mapping.     

Molecular variability in the Celleporella hyalina (Bryozoa; Cheilostomata) species complex: evidence for cryptic speciation from complete mitochondrial genomes

The bryozoan Celleporella has been shown to be composed of multiple, often cryptic, lineages. We sequenced two complete mitochondrial (mt) genomes of the Celleporella hyalina species complex from Wales, UK and Norway (i) to determine genetic divergence at the complete mt genome level, and (ii) to design new molecular markers for examining the interrelationships amongst the major lineages. In addressing (i), we estimated genetic divergence at three levels: (a) nucleotide diversity (π), (b) genome size, and (c) gene order. Genes nad4L, nad6, and atp8 showed the highest levels of divergence, and rrnL, rrnS, and cox1 showed the lowest levels. Inter-genome nucleotide divergence of protein-coding and ribosomal RNA genes, measured as π, was 0.21. The two genomes differed substantially in size, with the Norwegian genome being 2,573 base pairs (bp) longer than the Welsh genome, 17,265 and 14,692 bp, respectively. This difference in size is attributable to long non-coding regions present in the Norwegian genome. Both genomes exhibit similar gene orders, except for the translocation of one transfer RNA (trnA). Considering the high nucleotide diversity, genome size difference and change in gene order, these mt genomes are considered sufficiently divergent to have originated from two distinct species. In addressing (ii) we designed PCR primers that flank the most conserved regions of the genome: 1,300 bp of cox1 and a contiguous 2,000 bp fragment of rrnL + rrnS. The primers have yielded products for tissue from Wales, Norway, New Zealand, Alaska and Chile and should provide useful tools in establishing species- and population-level diversity within the Celleporella complex.     

松江鲈鱼野生群体遗传多样性的RAPD分析和SCAR标记的转化

首先,从294条10个碱基随机引物中,筛选出32条多态性引物,对富春江、黄河、滦河和鸭绿江等4个松江鲈鱼(Trachidermusfasciatus)野生群体共120尾个体进行RAPD分析。结果表明,松江鲈鱼野生群体的遗传多样性较丰富,其主要表现在:①在扩增得到的591个位点中,有515个(87.14%)位点呈现多态性,群体间多态位点比率(P)的大小顺序为:富春江群体89.17%>黄河群体87.99%>鸭绿江群体86.63%>滦河群体83.25%。②松江鲈鱼群体间的Shannon信息指数(IT)和Nei’s遗传多样性指数(HT)分别在0.3393~0.3566和0.2157~0.2279间,滦河群体的值较其他3群体稍低;若作为一个整体,则总的Shannon信息指数(IT)和Nei’s遗传多样性指数(HT)分别为0.3710±0.2153和0.2336±0.1643。③虽然群体间基因流值(Nm)在5.76103～19.84497间,显示各地理群体间存在程度不同的基因交流,但分子方差分析(AMOVA)结果却表明,各群体间存在显著(P<0.05)或极显著(P<0.01)的遗传分化。④聚类分析表明,鸭绿江群体首先与黄河群体聚为一支,再与富春江群体相聚,最后与单独一支的滦河群体聚类,表明鸭绿江、黄河、富春江等3群体间的遗传距离与彼此间的地理距离远近密切相关,而滦河群体与它们的遗传距离较远。其次,从获得的S1225525bp、S1225605bp、S1225841bp、S1345695bp、S1345825bp等5个特异RAPD条带中,成功地由S1225605bp、S1225841bp条带分别转化出SCAR01560bp、SCAR02443bp的SCAR标记。这两个标记的出现频率,在鸭绿江群体最高(96.67%和93.33%)、富春江群体其次(83.33%和90%)、黄河群体再其次(56.67%和66.67%)、滦河群体最低(13.33%和20%)。因此,SCAR01560bp、SCAR02443bp可作为鉴别松江鲈鱼滦河群体与其他3群体的分子标记。     

The complete mitochondrial genome of Calicogorgia granulosa (Anthozoa: Octocorallia): potential gene novelty in unidentified ORFs formed by repeat expansion and segmental duplication

Mitochondrial genomes of many nonbilaterian animals show high diversity of genome size and gene content, revealing many intergenic regions (IGRs), diverse repeats and additional genes. Here we present a new complete mitogenome of the cnidarian sea fan species, Calicogorgia granulosa (Anthozoa: Octocorallia) and its novel genomic features. The 20,246 bp of the complete mitogenome, which is the largest among the nine octocorals sequenced to date, contains 13 protein coding genes, 2 rRNAs and a tRNA within its circular form of mitochondrial DNA. We found an identical segmental duplication (S1 and S2, 913 bp) composed of an ORF (672 bp) coding for a hypothetical protein within which Direct Variant Repeat (DVR) expansions reside in-frame to the coding sequence. Additionally, the duplicated segmental DNA showed no variation in nucleotide sequences both between S1 and S2 and across multiple individual samples. Upon these observations, we discuss plausible causes for the intramitochondrial segmental duplication and the absence of sequence variation, and a need for further investigation of the novel ORF as well. In conclusion the present mitogenome of C. granulosa adds more information to our understanding of the diversity and evolution of mitogenomes of nonbilaterian animals.     

A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification

Phylogenetic analyses of Mycena sect. Calodontes using ITS previously suggested ten cryptic monophyletic ITS lineages within the Mycena pura morphospecies. Here, we compare ITS data (645 bp incl. gaps) from 46 different fruit bodies that represent the previously described ITS diversity with partial tEF-1-α (423 bp) and RNA polymerase II (RPB1) (492 bp) sequence data to test the genealogical concordance.While neither of the markers were in complete topological agreement, the branches differing between the tEF and RPB1 trees had a low bootstrap (<50) support, and the partition homogeneity incongruence length difference (ILD) tests were not significant. ILD tests revealed significant discordances between ITS and the tEF and RPB1 markers in several lineages. And our analyses suggested recombination between ITS1 and ITS2, most pronounced in one phylospecies that was identical in tEF and RPB1. Based on the agreement between tEF and RPB1, we defined 11 mutually concordant terminal clades as phylospecies inside the M. pura morphospecies; most of them cryptic. While neither of the markers showed an unequivocal barcoding gap between inter- and intraspecific diversity, the overlap was most pronounced for ITS (intraspecific diversity 0-3.5 %, interspecific diversity 0.4 %-8.8 %). A clustering analysis on tEF separated at a 1.5 % level returned all phylogenetic species as Operational Taxonomic Units (OTUs), while ITS at both a 1.5 % level and at a 3 % threshold level not only underestimated diversity as found by the tEF and RPB1, but also identified an OTU which was not a phylogenetic species. Thus, our investigation does not support the universal suitability of ITS for species recognition in particular, and emphasises the general limitation of single gene analyses combined with single percentage separation values.     

Pattern of soil methanotrophs on the natural vertical zones of the North Tianshan Mountain

Methane is one of the most important greenhouse gases and plays an essential role in atmospheric chemistry. Knowledge about methanotrophs and their diversity is important to understand the microbial mediation of the greenhouse gas CH₄ under climate change. The methanotrophs is one of main functional microbial groups in soil mediating methane cycles of terrestrial ecosystem. The purpose of this study was to explore spatial distribution pattern of methanotrophs diversity and the major factors affecting soil methanotrophs diversity along an elevation gradient on vertical natural belt of the North Tianshan Mountains, soil samples were collected at six sites in 2010, which were desert grassland belt (H1), Mountain grassland belt (H2), Mountain forest belt (H3), sub-alpine cushion belt (H4), alpine cushion belt (H5), alpine tundra vegetation (H6). Methanotrophs diversity in six sites from the North Tianshan Mountain were assessed with terminal restriction fragment length polymorphism (T-RFLP).The carbon–nitrogen ratio was significant difference under different vertical natural belt, ranged from 10.34 to 20.10, soil organic carbon were lowest in alpine tundra vegetation and highest in Mountain forest belt, those numbers of belts ranging from H1 to H3 were increased, with increasing elevation, then H3 to H6 were decreased. The total number of Terminal Restriction Fragments (T-RFs) derived from all those soil samples was 233, indicating high genetic diversity of methanotrophs on vertical natural belt of the North Tianshan Mountains. Microbial communities of T-RFs 55 bp, 242 bp, 376 bp represented the dominant species in sampling sites. However, some of the T-RFs were more sensitive to environment, such as 79 bp, 176 bp and 250 bp. Methanotrophs diversity index and T-RFs numbers were lowest in mountain forest belt and highest in subalpine cushion belt. Along the elevation gradient, the trendency of those numbers are as follows, H1>H2>H3<H4>H5>H6. Cluster analysis revealed that the samples could be separated into two groups, H4, H5 and H6 clustered into one group, while H2 and H3 clustered into other group.The community shifts were further investigated by Principle component analysis (PCA). The first PCA axis, which is related to the main compositional variation, separated the communities of the different sites. The main variation was mainly caused by changes in the relative abundance of the 58 bp, 87 bp, 137 bp, 243 bp and 248 bp T-RFs.Based on canonical correspondence analysis (CCA), Shannon index(H) of methanotrophs was positively correlated with soil pH and C/N ratio and negatively correlated with elevation, content of total nitrogen and total phosphorus; and Simpson index (D) and Evenness (E) were positively correlated with soils’ C/N ratio, soil surface temperature, pH and organic carbon, and negatively with elevation, total nitrogen and total phosphorus; indicating that plant communities and soil nutrients influence the soil microbial structure.Our research showed that soil methanotrophs was high genetic diversity along the elevation gradient on vertical natural belt in the North Tianshan Mountain. Soil microorganisms were positively correlated with vegetation, soils pH, C/N ratio, and soil moisture, total nitrogen, these parameters might be the main factors controlling soil methanotrophs diversity.     

Assessing the use of the mitochondrial cox1 marker for use in DNA barcoding of red algae (Rhodophyta)

The red algae, a remarkably diverse group of organisms, are difficult to identify using morphology alone. Following the proposal to use the mitochondrial cytochrome c oxidase subunit I (cox1) for DNA barcoding animals, we assessed the use of this gene in the identification of red algae using 48 samples plus 31 sequences obtained from GenBank. The data set spanned six orders of red algae: the Bangiales, Ceramiales, Corallinales, Gigartinales, Gracilariales and Rhodymeniales. The results indicated that species could be discriminated. Intraspecific variation was between 0 and 4 bp over 539 bp analyzed except in Mastocarpus stellatus (0-14 bp) and Gracilaria gracilis (0-11 bp). Cryptic diversity was found in Bangia fuscopurpurea, Corallina officinalis, G. gracilis, M. stellatus, Porphyra leucosticta and P. umbilicalis. Interspecific variation across all taxa was between 28 and 148 bp, except for G. gracilis and M. stellatus. A comparison of cox1 with the plastid Rubisco spacer for Porphyra species revealed that it was a more sensitive marker in revealing incipient speciation and cryptic diversity. The cox1 gene has the potential to be used for DNA barcoding of red algae, although a good taxonomic foundation coupled with extensive sampling of taxa is essential for the development of an effective identification system.     

A first insight into peach [Prunus persica (L.) Batsch] SNP variability

Three factors may have reduced the diversity at both individual gene and whole genome levels in cultivated peach: its self-compatible mating system, the narrow genetic basis of most commercial cultivars, and the recent strong selection towards agronomically interesting traits. Previous diversity analyses with markers such as simple sequence repeats (SSRs) have revealed low levels of genetic variability. Here, we sequenced 23 genome-wide distributed DNA fragments in 47 occidental peach varieties, also observing reduced variability levels. On average, there was one single nucleotide polymorphism (SNP) every 598 bp and one indel every 4,189 bp. As expected, variability was higher in non-coding than in coding regions (one SNP every 390 non-coding bp versus one in 1,850 bp in coding DNA). In general, SNPs were observed at relatively high frequency, mean minor allele frequency?=?0.225, meaning that a large proportion of the SNPs discovered by sequencing similar germplasm will be useful for other purposes, such as association mapping. The average heterozygosity of the varieties was 0.28, with a low correlation between SSR and SNP heterozygosity. The whole sequence of two candidate genes, a pectate lyase 1 candidate for fruit firmness (CGPAA2668) and a sucrose synthase 1 candidate for sugar content (CGPPB6189), in the 47 varieties revealed that they both may have suffered a process of balancing selection.