·基因组研究导读·

·基因组研究导读·

高粱全基因组测序完成

除了作为粮食作物之外，高粱也是一种主要饲料来源及生物能源作物。中澳两国的科学家对不同来源的高粱样本（包括地方品种、改良品种和野生杂草材料）进行了全基因组重测序，分析发现高粱与拟高粱都存在丰富的遗传多样性，不同的高粱品种间存在着强烈的种群结构差异和复杂的驯化历程。此外，还发现了大量的拷贝数变异、基因缺失和获得事件。这些结果为高粱的遗传多样性研究以及育种改良提供了宝贵的遗传资源。

论文链接： Emma S．Mace，et al．．Whole⁃genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum．

椰枣基因组测序及功能研究获进展

枣椰是中东和北非地区广泛种植的主要农作物，具有重要的经济价值。研究团队获得了椰枣主要栽培品系（Khalas）的高质量基因组组装结果和另外三个枣椰品系的高覆盖度基因组草图。该研究解析了椰枣从花期到发育成熟过程的基因表达谱，揭示了椰枣多糖成分代谢途径的几个关键转折点，为枣椰基因组学和各类组学研究奠定了坚实的分子基础，具有很高的实用价值。

论文链接： 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．

腔棘鱼基因组测序完成

腔棘鱼素有“活化石”之称，被认为与陆地上行走的四足动物及人类的远祖有亲缘关系。国际研究小组分别对生活在非洲东部坦桑尼亚近海和印度尼西亚近海的5条腔棘鱼进行了基因组测序，发现它们的基因组序列只有0．18%不同，变化速度仅为人类和黑猩猩基因组序列四十分之一。还发现了与形成陆地动物四肢和嗅觉功能有关的基因群。这对于研究生物进化，尤其是四足动物的进化具有重要意义。

论文链接： 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“living 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组序列图谱绘制完成

蒙古人是一个中亚族群，全世界约有2 000多万，一支迁移到青藏高原并逐渐适应了这里高海拔低氧的环境。科研团队成功绘制出了世界首部青海蒙古族人的全基因组序列图谱，并发现了青海蒙古族人具有高原适应的特殊遗传基因。这对进一步了解亚洲人群的多样性，以及研究和低氧环境适应性有关的遗传因素提供了重要的指导，也对研究人类在特殊环境条件下的适应性有重要意义。

论文链接： 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．

中外科研人员绘出老虎基因组图谱

老虎是地球上最大的猫科动物物种，也是世界上最濒临灭绝的物种。研究人员报告从头组装了东北虎的全基因组序列，以及孟加拉虎、非洲狮、白非洲狮和雪豹的基因组序列。通过对这些基因组进行比较遗传分析，研究人员发现了一系列能够阐明这些近缘但又不同的物种共享一些特征的基因，其中包括了一些与极强肌肉力量和高度适合食肉（hypercarnivorous）相关的遗传标记。本研究为东北虎及其它大型猫科动物的种质资源保护奠定了重要的遗传学基础。

论文链接： 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．

中国科学家发布细粒棘球绦虫基因组草图

细粒棘球绦虫是一种重要的动物源性寄生虫，全球至少有5千万人感染。我国科学家成功绘制出了细粒棘球绦虫基因组序列草图，并提供了其与宿主的相互作用、养分吸收、节裂、生殖、免疫逃避和成熟机制的一些新认识，这一研究工作为包虫病的诊断试剂、治疗药物和预防疫苗的研制提供了一个基本的全基因组信息平台，对提高包虫病的诊断和治疗水平，加速包虫病的控制有积极意义。

论文链接： 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．