Island ecosystems,serving as natural laboratories,facilitate geographical isolation,ecological specialization,and species divergence.The Sichuan Basin,surrounded by mountain ranges,represents a typical continental island due to its marked environmental spatial heterogeneity.This heterogeneity may contribute to geographical isolation and habitat heterogeneity,resulting in genetic divergence within populations.Therefore,we used the White-browed Laughingthrush(Garrulax sannio)as a model specimen to investigate the genetic divergence in the Sichuan Basin and its surrounding mountain ranges,given its presence in various habitats within and beyond this basin.Employing a RAD-seq dataset of 140 G.sannio individuals from 17 distinct ecological zones in the Sichuan Basin and its surrounding mountain ranges,we conducted PCA,population structure analysis,phylogenetic tree construction,and gene flow analysis to comprehensively analyze G.sannio groups.Additionally,in conjunction with geographical and ecological data,we performed isolation by distance,isolation by environment,PCA,and latent factor mixed model analysis to identify factors influencing the genetic divergence among these G.sannio groups.In summary,the 17 G.sannio groups were categorized into high-elevation,medium-elevation,and low-elevation groups.Genetic divergence in G.sannio may be attributed to both geographical distance and key ecological factors,particularly elevation and key climatic variables.Notably,the high-elevation group exhibited a greater number of SNPs and selected genes associated with the key ecological factors compared to the low-elevation group.The ADCY9 gene and several associated key pathways were identified as crucial elements driving ecological adaptation(elevation and key climatic variables)in the high-elevation group.Furthermore,climate changes during the glacial cycles may have facilitated gene flow among these groups residing in the Sichuan Basin and its surrounding mountain ranges.Our findings provide evidence of genetic divergence in G.sannio influenced by the geographical distance and key ecological factors between the Sichuan Basin and its surrounding mountain ranges.These results lay the groundwork for future research on the molecular systematics of continental islands.

目的 基于单细胞RNA测序(single cell RNA sequencing,scRNA-seq)挖掘阿尔茨海默病(Alzheimer's disease,AD)外周血免疫特征作为生物标志物,系统性探索AD外周血免疫细胞亚型丰度、基因表达特征和细胞通讯异常.方法 从GEO数据库中下载AD外周血免疫细胞scRNA-seq数据集GSE168522,于RAD-Blood网页服务器(http://www.bioinform.cn/RAD-Blood/)中分析AD患者血液细胞组成成分变化,利用CellChat分析AD患者血液中异常的细胞间通讯作用.结果 AD患者和健康人血液中有两种CD8+ T细胞,其中一类高表达颗粒酶K(granzyme K,GZMK)[伪发现率(false discovery rate,FDR)<0.05],另一类高表达GZMA、GZMB和GZMH(FDR<0.05).GZMK+ CD8+ T细胞在AD患者血液中含量升高32.9%(P=5.15E-21),与其他细胞类型的交互作用增加,并可能通过主要组织相容性复合体Ⅰ类(major histocompatibility complex class Ⅰ,MHC-Ⅰ)信号转导异常与AD关联,红细胞为GZMK+ CD8+ T细胞MHC-Ⅰ信号通路异常提供了主要配体,即人类白细胞抗原(human leukocyte antigen,HLA)Ⅰ类分子(HLA-A、HLA-B、HLA-C和HLA-E).血液RESISTIN信号通路仅富集于AD患者血液中,其可能是AD血液特异性信号通路.结论 外周血GZMK+ CD8+ T细胞含量升高、GZMK+ CD8+ T细胞与红细胞的交互作用增加、RESISTIN通路增强是潜在的AD标志物.

物种的遗传多样性是决定物种适应性和生存能力的关键因素.生境片段化是造成生物多样性丧失的重要因素之一,对植物种群的遗传多样性有着重要影响.水角(Hydrocera triflora)作为一种濒危植物,其遗传多样性状况和濒危机制尚未有报道.该文收集了水角 7 个种群共计 34 个样本,利用简化基因组测序技术(RAD-seq)获得了单核苷酸变异位点(SNP).通过种群遗传多样性和遗传结构的分析,并结合种群历史动态分析和不同气候情景下物种潜在分布区预测,探讨了水角的濒危机制.结果表明:(1)水角遗传多样性较低(Ho=0.1569、He=0.1654、π=0.1865),遗传分化系数较高;AMOVA分析表明,遗传变异主要发生在种群内.(2)Mantel检测表明环境距离与遗传距离、地理距离均呈显著正相关,分别为P=0.0412 和P= 0.0082.(3)水角的有效种群大小从全新世中期开始持续下降,与琼北火山群的喷发时间一致.(4)与当代气候相比,虽然在未来气候变化下水角的潜在分布区总面积变动不大,但在高CO2排放的情景下,大量的高适生区将会丧失并转化为低适生区,特别是位于马来群岛的适生区几乎完全消失.该研究结果表明,生境片段化导致了水角较低的遗传多样性和有效种群大小的持续下降.因此,自身更新能力低以及人为活动干扰、城市化等不利的环境条件是导致其濒危的主要原因.建议加强对水角的就地保护,采用人工授粉等方法提高其基因流以增加其种群的遗传多样性,同时,要着重保护湿地免遭破坏.

Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere.Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses.Here,we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus in-dividuals and two outgroups.Both nuclear and plastome data recovered a well-resolved phylogeny.The species were divided into three main clades corresponding to their inflorescence types,-the racemose group,the solitary-flower group and the corymbose group-with the latter two sister to one another.Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago.The diversification of the three major clades began between the Paleocene and Miocene,suggesting that paleoclimatic events were an important driving force for Prunus diversification.Ancestral state re-constructions revealed that the most recent common ancestor of Prunus had racemose inflorescences,and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis,respectively.We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies.Prunus has undergone extensive hybridization events,although it is difficult to identify conclusively specific instances of hybridization when using SNP data,especially deep in the phylogeny.Our study provides well-resolved nuclear and plastid phylogenies of Prunus,reveals substantial cytonuclear discord at shallow scales,and sheds new light on inflorescence evolution in this economically important lineage.

Background:The Emei Shan Liocichla (Liocichla omeiensis) is an endemic bird species to southwestern China with a small geographic range.However,little was known about the genetic status of this threatened species.Methods:We applied restriction-site-associated DNA sequencing (RAD-Seq) for rapid mass identification of microsatellite markers of the Emei Shan Liocichla.Results:A total of 11,564 microsatellite sequences were obtained,600 random loci were designed for screening and 24 polymorphic microsatellite loci were selected for further validation.The average allele number,average observed heterozygosity and average expected heterozygosity were relatively low in our samples,which were 6.08,0.6618 and 0.7048,respectively,indicating that the Emei Shan Liocichla might have lost some genetic diversity.Further analyses suggested that the populations distributed on two mountains (Daxiangling and Xiaoliangshan) showed a modest degree of genetic differentiation.Conclusions:These novel microsatellite markers provided valuable preliminary knowledge regarding the genetic status of the Emei Shan Liocichla and can be useful in further studies,as well as in the management and conservation of this species.

Microsatellites are highly polymorphic markers which have been used in a wide range of genetic studies.In recent years,various sources of next-generation sequencing data have been used to develop new microsatellite loci,but compared with the more common shotgun genomic sequencing or transcriptome data,the potential utility of RAD-seq data for microsatellite ascertainment is comparatively under-used.In this study,we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii.Of 8,823,053 clean reads generated for ten individuals of a population,94,851 (～1％) contained microsatellite motifs.These corresponded to 2993 unique loci,of which 526 (～18％) exhibited polymorphism.Of which,237 were suitable for designing microsatellite primer pairs,and 128 loci were randomly selected for PCR validation and microsatellite screening.Out of the 128 primer pairs,16 loci gave dear,reproducible patterns,and were then screened and characterized in 24 individuals from two populations.The total number of alleles per locus ranged from two to ten (mean =4.875),and within-population expected heterozygosity from zero to 0.789 (mean =0.530),indicating that these microsatellite loci will be useful for population genetics and speciation studies of T.florinii.This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.

基于RAD-seq简化基因组测序技术获得椭圆叶花锚(Halenia ellipiticaD.Don)简化基因组水平上的序列信息并开发SSR分子标记.利用SR search软件检测而得到双端各有至少100 bp的五种类型的SSR(二、三、四、五、六核苷酸)位点共6 201个,并成功设计其中3 865个SSR引物.在能成功设计引物的SSR位点中,三核苷酸SSR位点最多;重复序列长度包括17种(12～ 36 bp);重复序列的基序共达316种,其中五核苷酸基序种类最多(91种).从中挑选65对可对应五种SSR类型的引物,经梯度PCR检验后,利用椭圆叶花锚的4个居群32个个对可扩增的引物进行PCR和聚丙烯酰氨凝胶电泳检测,其中14对引物能在绝大多数个体中扩增,且13对具多态性.13个多态性位点的等位基因数量均值为5.462,多态性较高且不连锁(P＜0.05);其中10个位点在多数居群中偏离哈迪温伯格平衡(P＜0.01)且存在较高的纯合子数量(观测杂合度H.均值0.226);近交系数在-0.443～1,均值为0.656;基因流Nm为0.474.

该研究利用基于全基因组限制性酶切位点简化基因组测序技术(RAD-seq技术),开发濒危植物羊踯躅(Rhododendron molleG.Don)全基因组SSR标记,并对3个群体共63份羊踯躅材料进行验证鉴定,为进一步研究羊踯躅的遗传多样性和群体遗传结构以及保护利用提供技术支持.结果显示:(1)羊踯躅基因组测序获得原始数据7.653G bp,过滤后为7.513G bp;经组装发现,羊踯躅171.534Mbp的基因组分布在498 252 contigs中.(2)通过SSR检测,在11 961SSR位点中获得了11 687对SSR分子标记,并且二核苷酸为基序的重复类型最丰富,达51.76％.(3)随机选取128对SSR标记在6个羊踯躅株系中进行PCR扩增,获得20对高多态性的SSR标记.(4)用所选的20对多态性SSR标记对3个群体共63份羊踯躅材料进行验证分析发现,这些多态性SSR标记位点的等位基因数为4～16个,期望杂合度(He)为0.489～0.908.研究表明,羊踯躅的SSR丰度适中,且二核苷酸为羊踯躅中最丰富的重复序列,该实验进一步证明RAD-seq技术是一种经济有效的基因测序方法,实验中开发的SSR引物将有助于进一步研究羊踯躅和其他近缘种的群体结构和多样性.

土沉香(Aquilaria sinensis)是生产中药沉香的重要树种,现被列为国家二级重点保护野生植物.该研究通过采集该地区83株土沉香样品,利用限制性酶切位点相关DNA测序(restriction site-associated DNA sequencing,RAD-seq)方法获得的18个微卫星体作为分子标记,计算了五桂山土沉香种群的整体观测杂合度(observed-heterozygosity) 、期望杂合度(expected-heterozygosity) 、种群整体近交系数及其个体间的亲缘关系,并对种群可能经历的种群缩小或种群扩张状况进行了分析.结果表明:与同属其它物种以及同一生活史物种相比,五桂山地区土沉香遗传多样性略低(观测杂合度和期望杂合度分别为0.523和0.522),但种群整体处于随机交配状态(近交系数为-0.002).瓶颈效应分析表明该种群没有经历瓶颈效应,且81.810%的个体间无亲缘关系,说明这一地区土沉香并非少数个体发育起来;种群扩张分析表明其种群大小有增长情形.综合这些结果可以看出,中山市五桂山土沉香种群整体遗传健康状况良好,较好地保存了该区域种质资源遗传多样性,为今后的保护和合理开发提供了优质资源储备.

The rapid expansion of next-generation sequencing (NGS) has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome-partitioning approaches in plant phylogenomics: genome skimming, transcriptome sequencing (RNA-seq), restriction site associated DNA sequencing (RAD-Seq), and targeted capture (Hyb-seq). Of these four genome-partitioning approaches, targeted capture (especially Hyb-seq) shows the greatest promise for plant phylogenetics over the next few years. This review will aid researchers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion of whole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.