科学家揭秘开花分子时钟

开花过程受到温度和日长等环境因素的调控，除此之外，冷泉港实验室研究人员发现了一种调节开花时机的新机制。研究人员使用番茄作为模式生物，发现如果开花时机缺乏控制，开花程序进行太快，就会导致每个枝条上只开一朵花(通常是7～10朵);相反，如果开花进程减慢，就能开更多花，也就意味着有更多的果实。这一新机制中的关键基因是TMF(TERMINATING FLOWER)，TMF调控着一条控制开花时机的新通路，TMF功能缺失时会使整个机制紊乱。对番茄开花机制的解析，将有助于提高重要农作物的产量。

论文链接:Cora A MacAlister，et al..Synchronization of the flowering transition by the tomato TERMINATING FLOWER gene.

The transition to flowering is a major determinant of plant architecture，and variation in the timing of flowering can have profound effects on inflorescence architecture，flower production and yield.Here，we show that the tomato mutant terminating flower(tmf)flowers early and converts the multiflowered inflorescence into a solitary flower as a result of precocious activation of a conserved floral specification complex encoded by ANANTHA(AN)and FALSIFLORA(FA).Without TMF，the coordinated flowering process is disrupted，causing floral identity genes，such as AN and members of the SEPALLATA(SEP)family，to activate precociously，while the expression of flowering transition genes，such as FRUITFULL(FUL)，is delayed.Indeed，driving AN expression precociously is sufficient to cause early flowering，and this expression transforms multiflowered inflorescences into normal solitary flowers resembling those of the Solanaceae species petunia and tobacco.Thus，by timing AN activation，TMF synchronizes flower formation with the gradual reproductive transition，which，in turn，has a key role in determining simple versus complex inflorescences.

艰难梭菌分离菌株基因测序数据公布

艰难梭菌是发达国家中抗生素相关性腹泻和卫生保健有关感染的常见致病因素之一。Trevor Lawley等人在全球各地搜集了151种现存的艰难梭菌分离菌株以及英国的145种额外的分离菌株，并对其进行了全基因组测序。通过追踪有关艰难梭菌疾病暴发和传播的信息，还发现其中一个菌种027/BI/NAP1包含了两种不同的细菌世系，其各自都产生了相同的氟喹诺酮耐药突变。

论文链接:Miao He，et al..Emergence and global spread of epidemic healthcare-associated Clostridium difficile.

Nature Genetics，2013，45:109 －113.doi:10.1038/ng.2478.Published online:09 December，2012.

Abstract:Epidemic C.difficile(027/BI/NAP1)has rapidly emerged in the past decade as the leading cause of antibiotic-associated diarrhea worldwide.However，the key events in evolutionary history leading to its emergence and the subsequent patterns of global spread remain unknown.Here，we define the global population structure of C.difficile 027/BI/NAP1 using whole-genome sequencing and phylogenetic analysis.We show that two distinct epidemic lineages，FQR1 and FQR2，not one as previously thought，emerged in North America within a relatively short period after acquiring the same fluoroquinolone resistance-conferring mutation and a highly related conjugative transposon.The two epidemic lineages showed distinct patterns of global spread，and the FQR2 lineage spread more widely，leading to healthcare-associated outbreaks in the UK，continental Europe and Australia.Our analysis identifies key genetic changes linked to the rapid transcontinental dissemination of epidemic C.difficile 027/BI/NAP1 and highlights the routes by which it spreads through the global healthcare system.

玉米籽粒油分合成关键基因破解

玉米是我国第一大粮食作物，油分是玉米籽粒最重要的营养成分之一，但目前在全基因水平上，高油玉米形成的遗传基础尚不明确。中国农业大学李建生教授及其合作者，利用368份玉米自交系为材料，通过RNA测序获得了100多万个单核苷酸多态性位点，并利用全基因组关联分析方法，对籽粒油分相关性状进行了分析，共发现74个基因与籽粒总油分及组分显著关联，其中三分之一是编码油脂代谢的关键酶基因，包括26个与玉米籽粒总含油量显著相关的基因。该研究为剖析玉米籽粒油分形成的遗传结构提供了理论基础，对进一步改良玉米油分的含量和质量有重要指导意义。

论文链接:Hui Li，et al..Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels.

Nature Genetics，2013，45:43 －50.doi:10.1038/ng.2484.Published online:16 December，2012.

Abstract:Maize kernel oil is a valuable source of nutrition.Here we extensively examine the genetic architecture of maize oil biosynthesis in a genome-wide association study using 1.03 million SNPs characterized in 368 maize inbred lines，including‘high-oil’lines.We identified 74 loci significantly associated with kernel oil concentration and fatty acid composition(P ＜1.8×10－6)，which we subsequently examined using expression quantitative trait loci(QTL)mapping，linkage mapping and coexpression analysis.More than half of the identified loci localized in mapped QTL intervals，and one-third of the candidate genes were annotated as enzymes in the oil metabolic pathway.The 26 loci associated with oil concentration could explain up to 83%of the phenotypic variation using a simple additive model.Our results provide insights into the genetic basis of oil biosynthesis in maize kernels and may facilitate marker-based breeding for oil quantity and quality.

研究揭示结核分枝杆菌的起源

结核分枝杆菌是引起结核病的元凶，是传播最广泛、致病能力最强的病菌之一。法国巴斯德研究所领导的研究小组对不同分枝杆菌的基因组进行分析比较后发现，结核分枝杆菌与卡式分枝杆菌的基因组总体结构极为相似。此外，研究人员还发现了结核分枝杆菌进化出较强传染性与致病性的若干基因机制。这一成果有助于开发防治结核病的新方法。

论文链接: Philip Supply，et al..Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis.

Nature Genetics，doi:10.1038/ng.2517.Published online:06 January，2013.

Abstract:Global spread and limited genetic variation are hallmarks of M.tuberculosis，the agent of human tuberculosis.In contrast，Mycobacterium canettii and related tubercle bacilli that also cause human tuberculosis and exhibit unusual smooth colony morphology are restricted to East Africa.Here，we sequenced and analyzed the whole genomes of five representative strains of smooth tubercle bacilli(STB)using Sanger(4～5× coverage)，454/Roche(13～18× coverage)and/or Illumina DNA sequencing(45～105× coverage).We show that STB isolates are highly recombinogenic and evolutionarily early branching，with larger genome sizes，higher rates of genetic variation，fewer molecular scars and distinct CRISPR-Cas systems relative to M.tuberculosis.Despite the differences，all tuberculosis-causing mycobacteria share a highly conserved core genome.Mouse infection experiments showed that STB strains are less persistent and virulent than M.tuberculosis.We conclude that M.tuberculosis emerged from an ancestral STB-like pool of mycobacteria by gain of persistence and virulence mechanisms，and we provide insights into the molecular eve nts involved.

世界首张梅花全基因组图谱完成

北京林业大学张启翔团队选取位于梅花起源中心的西藏野生梅花进行基因组测序，从基因组水平，揭示了合成梅花花香中重要成分乙酸苯甲酯的BEAT基因家族34个成员;推测梅花基因组中6个串联重复的DAM基因和其上游过多的CBF结合位点是梅花提早解除休眠的关键因子。首张梅花全基因组精细图谱的构建完成，有助于揭示梅花花期早、花香独特等重要观赏性状的遗传基础，有助于挖掘与诸多重要性状相关的功能基因，为今后进一步揭示梅花花期、抗病调控机制、梅花及相关种属的分子育种奠定基础。

论文链接:Qixiang Zhang，et al..The genome of Prunus mume.

Nature Communications，2012，3:1318.doi:10.1038/ncomms2290.Published:27 December，2012.

Abstract:Prunus mume(mei)，which was domesticated in China more than 3 000 years ago as ornamental plant and fruit，is one of the first genomes among Prunus subfamilies of Rosaceae been sequenced.Here，we assemble a 280 M genome by combining 101-fold next-generation sequencing and optical mapping data.We further anchor 83.9%of scaffolds to eight chromosomes with genetic map constructed by restrictionsite-associated DNA sequencing.Combining P.mume genome with available data，we succeed in reconstructing nine ancestral chromosomes of Rosaceae family，as well as depicting chromosome fusion，fission and duplication history in three major subfamilies.We sequence the transcriptome of various tissues and perform genome-wide analysis to reveal the characteristics of P.mume，including its regulation of early blooming in endodormancy，immune response against bacterial infection and biosynthesis of flower scent.The P.mume genome sequence adds to our understanding of Rosaceae evolution and provides important data for improvement of f ruit trees.

科学家揭示水蛭、海蠕虫和青贝基因组

冠轮动物是一种种类繁多的动物类群，包括软体动物(如蜗牛、蛤类和章鱼)以及环节动物(如水蛭和蚯蚓)。来自莱斯大学、加州大学伯克利分校和美国能源部联合基因组研究所(JGI)的科学家们进行了其中三个物种的测序，分别是水蛭(leech)、海蠕虫(Capitella teleta)和青贝(limpet)，通过比较基因组研究，寻找基因组间可识别的相似性，追踪发生在特异基因组中的进化改变。

论文链接:Oleg Simakov，et al..Insights into bilaterian evolution from three spiralian genomes.

Nature，doi:10.1038/nature11696.Published online:19 December，2012.

Abstract:Current genomic perspectives on animal diversity neglect two prominent phyla，the molluscs and annelids，that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology.Here we describe the draft genomes of the owl limpet(Lottia gigantea)，a marine polychaete(Capitella teleta)and a freshwater leech(Helobdella robusta)，and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective.We find that the genome organization，gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes(for example，amphioxus and sea urchin)than those of other protostomes that have been sequenced to date(flies，nematodes and flatworms).The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor，establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long-and short-range genetic linkages across metazoans.Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution，including varying rates of rearrangement，intron gain and loss，expansions and contractions of gene families，and the evolution of clade-specific genes that produce the unique content of each genome.

科学家完成首个山羊基因组图谱

山羊是农业和经济发展的重要物种之一，还可作为生物医学研究的模型，用于复杂性状的遗传学基础研究。中科院昆明动物研究所牵头解析了山羊的基因组，使其成为首个不依赖于遗传图谱而组装到染色体水平的大型基因组。通过微量核糖核酸(RNA)转录组技术，该研究首次全面揭示了山羊绒囊、毛囊在转录层面的差异，鉴定了50多个与山羊绒形成密切相关的基因，为提高绒品质和我国特有资源绒山羊的选育提供了参考基因资源。山羊基因组测序对于遗传标记辅助育种、改善山羊的经济性状具有重要作用。

论文链接:Yang Dong，et al..Sequencing and automated whole-genome optical mapping of the genome of a domestic goat(Capra hircus).

Nature Biotechnology，doi:10.1038/nbt.2478.Published online:23 December，2012.

Abstract:We report the ～2.66-Gb genome sequence of a female Yunnan black goat.The sequence was obtained by combining short-read sequencing data and optical mapping data from a high-throughput whole-genome mapping instrument.The whole-genome mapping data facilitated the assembly of super-scaffolds＞5× longer by the N50 metric than scaffolds augmented by fosmid end sequencing(scaffold N50=3.06 Mb，super-scaffold N50=16.3 Mb).Super-scaffolds are anchored on chromosomes based on conserved synteny with cattle，and the assembly is well supported by two radiation hybrid maps of chromosome 1.We annotate 22 175 protein-coding genes，most of which were recovered in the RNA-seq data of ten tissues.Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat reveal 51 genes that are differentially expressed between the two types of hair follicles.This study，whose results will facilitate goat genomics，shows that whole-genome mapping technology can be used for the de novo assembly of large genomes.

单基因注入可使心脏细胞化身“生物起搏器”

心跳源于窦房结(SAN)，起搏细胞也聚集于此，起搏细胞产生的电活动，能够在规律的模式下蔓延至其他心脏细胞，形成有节奏的肌肉收缩。通常情况下，接受心脏手术的患者会将电子起搏器看作自身存活的唯一选择。美国希达思西奈心脏研究所的科研人员通过注入单个Tbx18基因，对普通心脏细胞进行重新编程，诱导SAN细胞或是iSAN细胞，呈现出所有天然起搏细胞应有的关键特征，并保持了与SAN类似的特性，使其成为了高度专业化的"生物起搏器"，其可成为电子起搏器的替代选择。

论文链接: Nidhi Kapoor，et al..Direct conversion of quiescent cardiomyocytes to pacemaker cells by expression of Tbx18.

Nature Biotechnology，2013，31:54 －62.doi:10.1038/nbt.2465.Published online:16 December，2012.

Abstract:The heartbeat originates within the sinoatrial node(SAN)，a small structure containing ＜10 000 genuine pacemaker cells.If the SAN fails，the ～ 5 billion working cardiomyocytes downstream of it become quiescent，leading to circulatory collapse in the absence of electronic pacemaker therapy.Here we demonstrate conversion of rodent cardiomyocytes to SAN cells in vitro and in vivo by expression of Tbx18，a gene critical for early SAN specification.Within days of in vivo Tbx18 transduction，9.2% of transduced，ventricular cardiomyocytes develop spontaneous electrical firing physiologically indistinguishable from that of SAN cells，along with morphological and epigenetic features characteristic of SAN cells.In vivo，focal Tbx18 gene transfer in the guinea-pig ventricle yields ectopic pacemaker activity，correcting a bradycardic disease phenotype.Myocytes transduced in vivo acquire the cardinal tapering morphology and physiological automaticity of native SAN pacemaker cells.The creation of induced SAN pacemaker(iSAN)cells opens new prospects for bioengineered pacemakers.

我国科学家破译世界性害虫小菜蛾基因组

小菜蛾属鳞翅目菜蛾科，是危害多种蔬菜的重要寡食性害虫，被认为是分布最广泛的世界性害虫，防治工作非常困难，经济损失严重。福建农林大学尤民生团队在全球首次破译世界性害虫小菜蛾基因组，为农业害虫的可持续控制提供新的研究思路。该研究是全世界首次公布鳞翅目昆虫原始类型基因组，对于揭示小菜蛾与十字花科植物协同进化及其抗药性的适应进化与治理等均具有重要的科学价值，同时也为鳞翅目昆虫的进化和比较基因组学研究提供宝贵的数据资源。

论文链接:Minsheng You，et al..A heterozygous moth genome provides insights into herbivory and detoxification.

Nature Genetics，doi:10.1038/ng.2524.Published online:13 January 2013.

Abstract:How an insect evolves to become a successful herbivore is of profound biological and practical importance.Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants，but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood.We report the first whole-genome sequence of a basal lepidopteran species，Plutella xylostella，which contains 18 071 protein-coding and 1 412 unique genes with an expansion of gene families associated with perception and the detoxification of plant defense compounds.A recent expansion of retrotransposons near detoxification-related genes and a wider system used in the metabolism of plant defense compounds are shown to also be involved in the development of insecticide resistance.This work shows the genetic and molecular bases for the evolutionary success of this worldwide herbivore and offers wider insights into insect adaptation to plant feeding，as well as opening avenues for more sustainable pest management.