·基因組研究導(dǎo)讀·

高粱全基因組測(cè)序完成

除了作為糧食作物之外，高粱也是一種主要飼料來(lái)源及生物能源作物。中澳兩國(guó)的科學(xué)家對(duì)不同來(lái)源的高粱樣本（包括地方品種、改良品種和野生雜草材料）進(jìn)行了全基因組重測(cè)序，分析發(fā)現(xiàn)高粱與擬高粱都存在豐富的遺傳多樣性，不同的高粱品種間存在著強(qiáng)烈的種群結(jié)構(gòu)差異和復(fù)雜的馴化歷程。此外，還發(fā)現(xiàn)了大量的拷貝數(shù)變異、基因缺失和獲得事件。這些結(jié)果為高粱的遺傳多樣性研究以及育種改良提供了寶貴的遺傳資源。

論文鏈接： Emma S．Mace，et al．．Whole?genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum．

椰棗基因組測(cè)序及功能研究獲進(jìn)展

棗椰是中東和北非地區(qū)廣泛種植的主要農(nóng)作物，具有重要的經(jīng)濟(jì)價(jià)值。研究團(tuán)隊(duì)獲得了椰棗主要栽培品系（Khalas）的高質(zhì)量基因組組裝結(jié)果和另外三個(gè)棗椰品系的高覆蓋度基因組草圖。該研究解析了椰棗從花期到發(fā)育成熟過(guò)程的基因表達(dá)譜，揭示了椰棗多糖成分代謝途徑的幾個(gè)關(guān)鍵轉(zhuǎn)折點(diǎn)，為棗椰基因組學(xué)和各類(lèi)組學(xué)研究奠定了堅(jiān)實(shí)的分子基礎(chǔ)，具有很高的實(shí)用價(jià)值。

論文鏈接： Ibrahim SAl?Mssallem，et al．Genome sequence of the date palm Phoenix dactylifera L．

Nature Communications，doi：10．1038／ncomms3274，Published online：06 August，2013．

Date palm（Phoenix dactylifera L．）is a cultivated woody plant specieswith agricultural and economic importance．Herewe reporta genome assembly for an elite variety（Khalas），which is 605．4 Mb in size and covers＞90%of the genome（～671 Mb）and＞96%of its genes（～41 660 genes）．Genomic sequence analysis demonstrates that P．dactylifera experienced a clear genome?wide duplication after either ancientwhole genome duplications ormassive segmental duplications．Genetic diversity analysis indicates that its stress resistance and sugar metabolism?related genes tend to be enriched in the chromosomal regions where the density of single?nucleotide polymorphisms is relatively low．Using transcriptomic data，we also illustrate the date palm’s unique sugarmetabolism thatunderlies fruit development and ripening．Our large?scale genomic and transcriptomic data pave theway for further genomic studiesnotonly on P．dactylifera butalso other Arecaceae plants．

腔棘魚(yú)基因組測(cè)序完成

腔棘魚(yú)素有“活化石”之稱(chēng)，被認(rèn)為與陸地上行走的四足動(dòng)物及人類(lèi)的遠(yuǎn)祖有親緣關(guān)系。國(guó)際研究小組分別對(duì)生活在非洲東部坦桑尼亞近海和印度尼西亞近海的5條腔棘魚(yú)進(jìn)行了基因組測(cè)序，發(fā)現(xiàn)它們的基因組序列只有0．18%不同，變化速度僅為人類(lèi)和黑猩猩基因組序列四十分之一。還發(fā)現(xiàn)了與形成陸地動(dòng)物四肢和嗅覺(jué)功能有關(guān)的基因群。這對(duì)于研究生物進(jìn)化，尤其是四足動(dòng)物的進(jìn)化具有重要意義。

論文鏈接： Masato Nikaido，et al．．Coelacanth genomes reveal signatures for evolutionary transition from water to land．

Genome Reserch，2013，doi：10．1101／gr．158105．113 2013．Published online：22 July，2013．

Abstract：Coelacanths are known as“l(fā)iving fossils”，as they show remarkablemorphological resemblance to the fossil record，and belong to themost primitive lineage of living Sarcopterygii（lobe?finned fishes and tetrapods）．Coelacanthsmay be key to elucidating the tempo and mode of evolution from fish to tetrapods．Here，we report the genome sequences of five coelacanths，including four Latimeria chalumnae individuals（three specimens from Tanzania and one from Comoros）and one L．menadoensis individual from Indonesia．These sequences cover two African breeding populations and two known extant coelacanth species．The genome is～2．74 Gbp and contains a high proportion（～60%）of repetitive elements．The genetic diversity among the individualswas extremely low，suggesting a small population size and／or a slow rate of evolution．We found a substantial number of genes that encode olfactory and pheromone receptors with features characteristic of tetrapod receptors for the detection of airborne ligands．We also found that limb enhancers of bmp7 and gli3，both of which are essential for limb formation，are conserved between coelacanth and tetrapods but not ray?finned fishes．We expect that some tetrapod?like genesmay have existed early in the evolution of primitive Sarcopterygii and were later co?opted to adapt to terrestrial environments．These coelacanth genomes will provide a cornerstone for studies to elucidate how ancestral aquatic vertebrates evolved into terrestrial animals．

青海蒙古族人全基因組序列圖譜繪制完成

蒙古人是一個(gè)中亞族群，全世界約有2 000多萬(wàn)，一支遷移到青藏高原并逐漸適應(yīng)了這里高海拔低氧的環(huán)境?？蒲袌F(tuán)隊(duì)成功繪制出了世界首部青海蒙古族人的全基因組序列圖譜，并發(fā)現(xiàn)了青海蒙古族人具有高原適應(yīng)的特殊遺傳基因。這對(duì)進(jìn)一步了解亞洲人群的多樣性，以及研究和低氧環(huán)境適應(yīng)性有關(guān)的遺傳因素提供了重要的指導(dǎo)，也對(duì)研究人類(lèi)在特殊環(huán)境條件下的適應(yīng)性有重要意義。

論文鏈接： Jinchuan Xing，et al．．Genomic analysis of natural selection and phenotypic variation in high?altitude Mongolians．

PLoSGenetics，2013，9（7）：e1003634．doi：10．1371／journal．pgen．1003634．Published online：18 July，2013．

Abstract：Deedu（DU）Mongolians，whomigrated from the Mongolian steppes to the Qinghai?Tibetan Plateau approximately 500 years ago，are challenged by environmental conditions similar to native Tibetan highlanders．Identification of adaptive genetic factors in this population could provide insight into coordinated physiological responses to this environment．Here we examine genomic and phenotypic variation in this unique population and present the first complete analysis of a Mongolian whole?genome sequence．High?density SNP array data demonstrate that DU Mongolians share genetic ancestry with other Mongolian as well as Tibetan populations，specifically in genomic regions related with adaptation to high altitude．Several selection candidate genes identified in DUMongolians are shared with other Asian groups（e．g．，EDAR），neighboring Tibetan populations（including high?altitude candidates EPAS1，PKLR，and CYP2E1），as well as genes previously hypothesized to be associated with metabolic adaptation（e．g．，PPARG）．Hemoglobin concentration，a trait associated with high?altitude adaptation in Tibetans，is at an intermediate level in DU Mongolians compared to Tibetans and Han Chinese at comparable altitude．Whole?genome sequence from a DU Mongolian（Tianjiao1）shows that about 2%of the genomic variants，includingmore than 300 protein?coding changes，are specific to this individual．Our analyses of DU Mongolians and the first Mongolian genome provide valuable insight into genetic adaptation to extreme environments．

中外科研人員繪出老虎基因組圖譜

老虎是地球上最大的貓科動(dòng)物物種，也是世界上最瀕臨滅絕的物種。研究人員報(bào)告從頭組裝了東北虎的全基因組序列，以及孟加拉虎、非洲獅、白非洲獅和雪豹的基因組序列。通過(guò)對(duì)這些基因組進(jìn)行比較遺傳分析，研究人員發(fā)現(xiàn)了一系列能夠闡明這些近緣但又不同的物種共享一些特征的基因，其中包括了一些與極強(qiáng)肌肉力量和高度適合食肉（hypercarnivorous）相關(guān)的遺傳標(biāo)記。本研究為東北虎及其它大型貓科動(dòng)物的種質(zhì)資源保護(hù)奠定了重要的遺傳學(xué)基礎(chǔ)。

論文鏈接： Yun Sung Cho，et al．The tiger genome and comparative analysiswith lion and snow leopard genomes．

Nature Communications，doi：10．1038／ncomms3433．Published online：17 September，2013．

Abstract：Tigers and their close relatives（Panthera）are some of theworld’smostendangered species．Herewe report the de novo assembly of an Amur tiger whole?genome sequence as well as the genomic sequences of a white Bengal tiger，African lion，white African lion and snow leopard．Through comparative genetic analyses of these genomes，we find genetic signatures thatmay reflectmolecular adaptations consistent with the big cats’hypercarnivorous diet and muscle strength．We report a snow leopard?specific genetic determinant in EGLN1（Met39＞Lys39），which is likely to be associated with adaptation to high altitude．We also detect a TYR260G＞A mutation likely responsible for the white lion coat colour．Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny．Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close，but distinct，species．

中國(guó)科學(xué)家發(fā)布細(xì)粒棘球絳蟲(chóng)基因組草圖

細(xì)粒棘球絳蟲(chóng)是一種重要的動(dòng)物源性寄生蟲(chóng)，全球至少有5千萬(wàn)人感染。我國(guó)科學(xué)家成功繪制出了細(xì)粒棘球絳蟲(chóng)基因組序列草圖，并提供了其與宿主的相互作用、養(yǎng)分吸收、節(jié)裂、生殖、免疫逃避和成熟機(jī)制的一些新認(rèn)識(shí)，這一研究工作為包蟲(chóng)病的診斷試劑、治療藥物和預(yù)防疫苗的研制提供了一個(gè)基本的全基因組信息平臺(tái)，對(duì)提高包蟲(chóng)病的診斷和治療水平，加速包蟲(chóng)病的控制有積極意義。

論文鏈接： Huajun Zheng，et al．The genome of the hydatid tapeworm Echinococcus granulosus．

Nature Genetics，2013，doi：10．1038／ng．2757．Published online：08 September，2013．

Abstract：Cystic echinococcosis（hydatid disease），caused by the tapeworm E．granulosus，is responsible for considerable human morbidity and mortality．This cosmopolitan disease is difficult to diagnose，treat and control．We present a draft genomic sequence for the worm comprising 151．6 Mb encoding11 325 genes．Comparisonswith the genome sequences from other taxa show that E．granulosus has acquired a spectrum of genes，including the EgAgB family，whose products are secreted by the parasite to interact and redirect host immune responses．We also find that genes in bile salt pathwaysmay control the bidirectional development of E．granulosus，and sequence differences in the calcium channel subunit EgCavβ1 may be associated with praziquantel sensitivity．Our study offers insights into host interaction，nutrient acquisition，strobilization，reproduction，immune evasion and maturation in the parasite and provides a platform to facilitate the development of new，effective treatments and interventions for echinococcosis control．

Communications，

10．1038／ncomms3320．Published online：27 August，2013．Abstract：Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world’s poorest people．Its small diploid genome and phenotypic diversitymake it an ideal C4 grassmodel as a complement to C3 rice．Here we present high coverage（16～45×）resequenced genomesof44 sorghum lines representing the primary gene pooland spanning dimensionsof geographic origin，end?use and taxonomic group．We also report the first resequenced genome of S．propinquum，identifying 8M high?quality SNPs，1．9M indels and specific gene loss and gain events in S．bicolor．We observe strong racial structure and a complex domestication history involving at least two distinct domestication events．These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum，providing an unmatched resource for the genetic improvement of sorghum and other grass species．