科學(xué)家揭秘開花分子時鐘

開花過程受到溫度和日長等環(huán)境因素的調(diào)控，除此之外，冷泉港實驗室研究人員發(fā)現(xiàn)了一種調(diào)節(jié)開花時機的新機制。研究人員使用番茄作為模式生物，發(fā)現(xiàn)如果開花時機缺乏控制，開花程序進行太快，就會導(dǎo)致每個枝條上只開一朵花(通常是7～10朵);相反，如果開花進程減慢，就能開更多花，也就意味著有更多的果實。這一新機制中的關(guān)鍵基因是TMF(TERMINATING FLOWER)，TMF調(diào)控著一條控制開花時機的新通路，TMF功能缺失時會使整個機制紊亂。對番茄開花機制的解析，將有助于提高重要農(nóng)作物的產(chǎn)量。

論文鏈接: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.

艱難梭菌分離菌株基因測序數(shù)據(jù)公布

艱難梭菌是發(fā)達國家中抗生素相關(guān)性腹瀉和衛(wèi)生保健有關(guān)感染的常見致病因素之一。Trevor Lawley等人在全球各地搜集了151種現(xiàn)存的艱難梭菌分離菌株以及英國的145種額外的分離菌株，并對其進行了全基因組測序。通過追蹤有關(guān)艱難梭菌疾病暴發(fā)和傳播的信息，還發(fā)現(xiàn)其中一個菌種027/BI/NAP1包含了兩種不同的細菌世系，其各自都產(chǎn)生了相同的氟喹諾酮耐藥突變。

論文鏈接: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，F(xiàn)QR1 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.

玉米籽粒油分合成關(guān)鍵基因破解

玉米是我國第一大糧食作物，油分是玉米籽粒最重要的營養(yǎng)成分之一，但目前在全基因水平上，高油玉米形成的遺傳基礎(chǔ)尚不明確。中國農(nóng)業(yè)大學(xué)李建生教授及其合作者，利用368份玉米自交系為材料，通過RNA測序獲得了100多萬個單核苷酸多態(tài)性位點，并利用全基因組關(guān)聯(lián)分析方法，對籽粒油分相關(guān)性狀進行了分析，共發(fā)現(xiàn)74個基因與籽粒總油分及組分顯著關(guān)聯(lián)，其中三分之一是編碼油脂代謝的關(guān)鍵酶基因，包括26個與玉米籽?？偤土匡@著相關(guān)的基因。該研究為剖析玉米籽粒油分形成的遺傳結(jié)構(gòu)提供了理論基礎(chǔ)，對進一步改良玉米油分的含量和質(zhì)量有重要指導(dǎo)意義。

論文鏈接: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.

研究揭示結(jié)核分枝桿菌的起源

結(jié)核分枝桿菌是引起結(jié)核病的元兇，是傳播最廣泛、致病能力最強的病菌之一。法國巴斯德研究所領(lǐng)導(dǎo)的研究小組對不同分枝桿菌的基因組進行分析比較后發(fā)現(xiàn)，結(jié)核分枝桿菌與卡式分枝桿菌的基因組總體結(jié)構(gòu)極為相似。此外，研究人員還發(fā)現(xiàn)了結(jié)核分枝桿菌進化出較強傳染性與致病性的若干基因機制。這一成果有助于開發(fā)防治結(jié)核病的新方法。

論文鏈接: 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.

世界首張梅花全基因組圖譜完成

北京林業(yè)大學(xué)張啟翔團隊選取位于梅花起源中心的西藏野生梅花進行基因組測序，從基因組水平，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個成員;推測梅花基因組中6個串聯(lián)重復(fù)的DAM基因和其上游過多的CBF結(jié)合位點是梅花提早解除休眠的關(guān)鍵因子。首張梅花全基因組精細圖譜的構(gòu)建完成，有助于揭示梅花花期早、花香獨特等重要觀賞性狀的遺傳基礎(chǔ)，有助于挖掘與諸多重要性狀相關(guān)的功能基因，為今后進一步揭示梅花花期、抗病調(diào)控機制、梅花及相關(guān)種屬的分子育種奠定基礎(chǔ)。

論文鏈接: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.

科學(xué)家揭示水蛭、海蠕蟲和青貝基因組

冠輪動物是一種種類繁多的動物類群，包括軟體動物(如蝸牛、蛤類和章魚)以及環(huán)節(jié)動物(如水蛭和蚯蚓)。來自萊斯大學(xué)、加州大學(xué)伯克利分校和美國能源部聯(lián)合基因組研究所(JGI)的科學(xué)家們進行了其中三個物種的測序，分別是水蛭(leech)、海蠕蟲(Capitella teleta)和青貝(limpet)，通過比較基因組研究，尋找基因組間可識別的相似性，追蹤發(fā)生在特異基因組中的進化改變。

論文鏈接: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.

科學(xué)家完成首個山羊基因組圖譜

山羊是農(nóng)業(yè)和經(jīng)濟發(fā)展的重要物種之一，還可作為生物醫(yī)學(xué)研究的模型，用于復(fù)雜性狀的遺傳學(xué)基礎(chǔ)研究。中科院昆明動物研究所牽頭解析了山羊的基因組，使其成為首個不依賴于遺傳圖譜而組裝到染色體水平的大型基因組。通過微量核糖核酸(RNA)轉(zhuǎn)錄組技術(shù)，該研究首次全面揭示了山羊絨囊、毛囊在轉(zhuǎn)錄層面的差異，鑒定了50多個與山羊絨形成密切相關(guān)的基因，為提高絨品質(zhì)和我國特有資源絨山羊的選育提供了參考基因資源。山羊基因組測序?qū)τ谶z傳標(biāo)記輔助育種、改善山羊的經(jīng)濟性狀具有重要作用。

論文鏈接: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.

單基因注入可使心臟細胞化身“生物起搏器”

心跳源于竇房結(jié)(SAN)，起搏細胞也聚集于此，起搏細胞產(chǎn)生的電活動，能夠在規(guī)律的模式下蔓延至其他心臟細胞，形成有節(jié)奏的肌肉收縮。通常情況下，接受心臟手術(shù)的患者會將電子起搏器看作自身存活的唯一選擇。美國希達思西奈心臟研究所的科研人員通過注入單個Tbx18基因，對普通心臟細胞進行重新編程，誘導(dǎo)SAN細胞或是iSAN細胞，呈現(xiàn)出所有天然起搏細胞應(yīng)有的關(guān)鍵特征，并保持了與SAN類似的特性，使其成為了高度專業(yè)化的"生物起搏器"，其可成為電子起搏器的替代選擇。

論文鏈接: 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.

我國科學(xué)家破譯世界性害蟲小菜蛾基因組

小菜蛾屬鱗翅目菜蛾科，是危害多種蔬菜的重要寡食性害蟲，被認(rèn)為是分布最廣泛的世界性害蟲，防治工作非常困難，經(jīng)濟損失嚴(yán)重。福建農(nóng)林大學(xué)尤民生團隊在全球首次破譯世界性害蟲小菜蛾基因組，為農(nóng)業(yè)害蟲的可持續(xù)控制提供新的研究思路。該研究是全世界首次公布鱗翅目昆蟲原始類型基因組，對于揭示小菜蛾與十字花科植物協(xié)同進化及其抗藥性的適應(yīng)進化與治理等均具有重要的科學(xué)價值，同時也為鱗翅目昆蟲的進化和比較基因組學(xué)研究提供寶貴的數(shù)據(jù)資源。

論文鏈接: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.