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拟南芥(Arabidopsis thaliana (L.) Heynh)全基因组的公布开创了植物基因组学研究的新时代[1-2],其基因组的成功测序使植物学家开始关注其他植物基因组。由于多数植物具有较大的基因组或较为复杂的倍性,使其基因组的解析面临巨大的挑战。下一代测序技术(NGS)的兴起改变了基因组学的研究规则[3],越来越多的植物基因组已成功测序,例如近年来已经测序完成的多倍体小麦[4]、藜麦[5]、巨桉[6]和胡杨[7]等。虽然,越来越多物种的基因组已成功测序公布,但对植物大多数基因的功能仍然知之甚少,例如在拟南芥和水稻中分别只有40%和1%左右的基因是基于实验研究的证据而进行的注释[8-9],其他植物实验注释的基因数量相对更少,这阻碍了进一步了解生物学过程中植物是如何发生及演化的问题。
NGS也可用于研究植物不同品种和家系的重测序,可通过全基因组关联分析来鉴定性状关联的基因组位点,例如水稻[10]、玉米[11-12]和大豆[13]。虽然遗传学和基因组学得到了很大发展,但是鉴定复杂性状相关基因和鉴定这些性状潜在的通路仍然较困难,已有的实验方法也只是提供少量的功能和表型注释。系统生物学方法已被用来进行基因-表型的关联研究,关联推定原则[14-15]已在很多物种中被用来基于基因网络以系统鉴定与特定功能或表型相关的基因,例如拟南芥和水稻等[16-17],而这种方式有效性的前提是该物种具备准确完善的功能基因网络,因此,构建一个高质量的功能基因网络是进行关联推定的重要前提。
功能基因网络是指网络中的2个基因相互关联以行使相同的功能,即如果2个基因处于同一生物学过程或者通路,代表这2个基因网路中的2个节点在网络中是相互连接的[18]。功能基因网络中的连接并不一定表示基因产物的直接物理相互作用,但基因产物具有直接物理作用的2个基因一定在网络中形成连接,因此,功能基因网络比直接物理相互作用(如蛋白-蛋白相互作用网络和蛋白-DNA相互作用网络)能更抽象也更广泛地描述生物系统。功能基因网络可以整合不同类型的数据形成一个单独网络,而不是将代表不同分子作用关系的网络简单地叠合在一起;此外,其准确度和覆盖度是通过统一标准去衡量不同类型的数据获得的功能关联是否参与同一过程或者通路来表示的,可对不同类型的数据直接进行比较。功能基因网络的一个重要用途是进行基因功能预测[19-20],如基因A在功能基因网络中与基因B相互连接,已知基因B参与功能X,则通过关联推导,基因A也参与功能X。如果基因A在网络中与参与功能X的基因C、D和E相互连接,则更能说明基因A参与功能X。
林木大多为多年生木本植物,为人们提供了大量的生物质材料,并由此带来巨大的商业价值;然而,这些植物通常具有很长的生长周期且携带的基因组相对较大,对其直接进行分子生物学实验相对困难,这就更需要通过一些模式树种的深入研究来解析其共有机制,如木材形成与发育机制等[21]。杨树、云杉等不仅是研究林木的模式植物[22-24],而且还具有重要的经济价值,如杨树在我国3/4的国土面积上均能种植,是现有人工林中适生范围最大,用途最广的林木,已成为我国人造板工业材和纸浆材的主要原料[25],研究这些木本植物的生长发育和木材的形成等生理过程也有助于了解其它林木植物,对其表型的机理研究也能更加有效地促进优良品种的培育与发掘[26-28]。虽然杨树、云杉等木本植物的基因组已成功测序[29],一些与杨树特征相关的基因也被鉴定,但仍然有大量的基因以及与重要特性相关的基因有待进一步研究和注释。随着高通量测序的不断发展,基于RNA-seq的转录组研究以及基于重测序的标记关联分析,产生了大量的功能基因组数据[30-32],这些数据对了解林木基因型及表型提供了重要信息,在功能基因网络水平上极大地促进了对林木特征进行的系统研究。
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目前,已通过不同方法或者方法组合构建出多个植物物种的功能基因网络,同时基于构建的功能基因网络进行构建数据库平台。功能基因网络的数据库平台主要分为两种类型,一种是物种特异性的数据库,包括通过同源映射、共表达、基因组上下文等方法的拟南芥功能基因网络数据库AraNet[33]、水稻功能基因网络及其数据库RiceNet[34]以及大豆功能基因网络SoyNet[86]、通过共表达方法构建的大豆功能网络数据库SFGD[100]、葡萄功能基因网络数据库VTCdb[102]和棉花共表达网络数据库ccNET[97],其中,在SFGD、VTCdb和ccNET中,不仅包含通过共表达构建的功能基因网络,同时也对基因进行了深入注释;另一种是植物的功能基因网络数据库,包括多个物种,如通过共表达方法构建的PlaNet数据库[113]包含拟南芥、大麦、二尾短柄草和苜蓿等多种物种的共表达网络,ATTED-Ⅱ[103]含有拟南芥、玉米和葡萄等物种的共表达网络数据,STRING数据库[111]中含有多种方法获得的拟南芥和水稻等几种植物的基因功能关联信息。
表 1 植物功能基因网络数据库
Table 1. Databases for plant functional gene networks
网络数据库名称
Name of network database包含物种①
Organisms功能关联推断方法②
Link inference method参考文献
References单物种功能基因网络数据库
Databases containing the gene network of single speciesAraNet At AA, CE, GC [33] CCNet Cc CE [97] PPIM Zm CE, GC, TM [35] PRIN Os AA [98] RED Os CE [99] RiceNet Os AA, CE, GC [34] SFGD Gm CE [100] TomatoNet Le AA, CE, GC [101] PoplarNet Pt AA, CE, GC [20] VTCdb Vv CE [102] 多物种功能基因网络数据库
Databases containing the gene networks of mutiple speciesATTED-Ⅱ At, Vv, Zm, Me, Pt, Os, Gm CE [103] BMRF At, Me, Pt, Os, Gm, Le AA, CE [104] CoP At, Ba, Vv, Zm, Pt, Os, Gm, Ta CE [105] CORNET At, Zm AA, CE [106] PlaNet At, Ba, Br, Me, Pt, Os, Gm, Tc, Ta CE [107] PlantExpress At, Os CE [108] PlantGenIE At, Pa, Pt CE [109] PLANEX At, Br, Vv, Zm, Os, Gm, Le, Ta CE [110] STRING At, Br, Vv, Pt, Os, Sg AA, CE, GC [111] VirtualPlant At, Mc, Zm, Os, Gm AA, CE [112] 注:①At:拟南芥;Ba:大麦;Br:二尾短柄草;Mc:木薯;Cc:棉花;Vv:葡萄;Zm:玉米;Me:苜蓿;Pa:云杉;Pt:杨树;Os:水稻;Gm:大豆;Sg:高粱;Le:番茄;Tc:烟草;Ta:小麦;②AA:同源映射;CE:共表达;GC:基因组上下文;TM:文献挖掘
Note: ①At: Arabidopsis, Ba: Barley, Br: Brachypodium, Mc:Cassava, Cc: Gossypium, Vv: Grapevine, Zm: Maize, Me: Medicago, Pa: Conifer, Pt: Poplar, Os: Rice, Gm: Soybean, Sg: Sorghum, Le: Tomato, Tc: Tobacco, Ta:Wheat. -
Lorenz W等[114]使用cDNA芯片研究云杉12个基因型与环境组合的基因表达模式,使用共表达方式构建功能基因网络,通过网络的拓扑分析获得了根组织耐旱相关的候选基因。Grnlund等[115]基于杨树表达谱芯片数据通过多层网络模型构建共表达网络,分析发现,该网络表现出明显的模块化构成;Cai等[116]利用公共数据库的杨树表达芯片数据构建杨树的共表达基因网络,通过网络聚类分析,发现6个模块与植物细胞壁生物合成相关,进一步通过顺式作用元件分析发现,在其中两个模块中鉴定到10个潜在的重要顺式作用元件。Kavka等[117]研究杨树在磷缺乏条件下营养相关的共表达功能基因网络,通过聚类分析在差异表达基因的子网络中获得11个模块,发现其中1个模块与磷缺乏响应具有较大的相关性。Dash等[118]研究杨树根部在响应低氮条件下,根部发育的共表达基因网络并鉴定与促进根部发育以响应低氮密切相关的网络模块。
Lamara等[119]结合关联分析和共表达网络分析,从1 694株白杉群体所携带的2 652个基因中,鉴定到其含有的SNPs与木材密度、硬度、微纤维角度和木材胸径等性状显著关联,在木质部的共表达功能网络中发现了200多个显著关联的基因。拟南芥虽然是草本植物,但被证明它可作为研究木材形成发育的优良模式植物[120]。众多研究表明,在草本植物和林木植物中微管及木材形成的分子机制是非常保守的,大量的转录因子、植物激素以及其他因子在拟南芥和木本植物中都参与了调控木质部的发育[120]。Taylor-Teeples等[121]在拟南芥中采用酵母单杂交技术构建转录因子与次生细胞壁代谢基因之间的蛋白-DNA调控网络,发现了大量新的基因功能关联。Davin等[122]使用拟南芥soc1ful突变体研究木质部形成中差异表达基因的功能关联网络,发现功能基因网络中的hub节点在草本组织和木本组织中具有明显地差异表达。Jokipii-Lukkari等[123]以云杉形成层和木质部的多个部位的组织为样本通过RNA-Seq测序构建基因表达谱,进而构建共表达功能基因网络,通过与拟南芥和杨树木材发育共表达网络的比较,发现了云杉的某些特有次生细胞壁发育的功能基因关系,同时还构建了NorWood网络服务平台可供研究者查询云杉木材形成基因共表达网络信息。Raherison等[124]通过Piceaglauca的芯片表达数据构建共表达网络,以研究Piceaglauca功能网络的模块化构成以及模块功能和进化特征,并重点鉴定了木材形成发育基因子网络,进而研究了微管组织发育相关基因的表达和功能分化。
植物功能基因网络及其应用
Functional Gene Network and Its Application in Forestry
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摘要: 功能基因网络既能够衡量基因之间的功能关联关系,也可以预测基因间的直接相互作用,可为未知功能基因的功能注释提供重要信息,本文简要介绍功能基因网络的概念、功能基因关联挖掘的计算方法和实验方法、功能基因网络的分析方法以及在植物和林木中的应用研究进展。随着林木生物信息学大数据的不断增长,功能基因网络将得到更深入的应用。Abstract: Functional gene network measures the functional association among genes, also predicts the direct interaction among genes, which can provide important information for the functional annotation of unknown functional genes. This review briefly introduces the concept and function of functional gene network, computational method and experimental method for exploring gene association relation, the method for functional gene network analysis, as well as the research and application progress in plant science and forest science. With the increasing of forest bioinformatics data, it is expected that functional gene network will be in-depth applied in research.
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Key words:
- Function gene network
- / Co-expression
- / Phylogenetic profile
- / Forestry tree
- / Poplar
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表 1 植物功能基因网络数据库
Table 1. Databases for plant functional gene networks
网络数据库名称
Name of network database包含物种①
Organisms功能关联推断方法②
Link inference method参考文献
References单物种功能基因网络数据库
Databases containing the gene network of single speciesAraNet At AA, CE, GC [33] CCNet Cc CE [97] PPIM Zm CE, GC, TM [35] PRIN Os AA [98] RED Os CE [99] RiceNet Os AA, CE, GC [34] SFGD Gm CE [100] TomatoNet Le AA, CE, GC [101] PoplarNet Pt AA, CE, GC [20] VTCdb Vv CE [102] 多物种功能基因网络数据库
Databases containing the gene networks of mutiple speciesATTED-Ⅱ At, Vv, Zm, Me, Pt, Os, Gm CE [103] BMRF At, Me, Pt, Os, Gm, Le AA, CE [104] CoP At, Ba, Vv, Zm, Pt, Os, Gm, Ta CE [105] CORNET At, Zm AA, CE [106] PlaNet At, Ba, Br, Me, Pt, Os, Gm, Tc, Ta CE [107] PlantExpress At, Os CE [108] PlantGenIE At, Pa, Pt CE [109] PLANEX At, Br, Vv, Zm, Os, Gm, Le, Ta CE [110] STRING At, Br, Vv, Pt, Os, Sg AA, CE, GC [111] VirtualPlant At, Mc, Zm, Os, Gm AA, CE [112] 注:①At:拟南芥;Ba:大麦;Br:二尾短柄草;Mc:木薯;Cc:棉花;Vv:葡萄;Zm:玉米;Me:苜蓿;Pa:云杉;Pt:杨树;Os:水稻;Gm:大豆;Sg:高粱;Le:番茄;Tc:烟草;Ta:小麦;②AA:同源映射;CE:共表达;GC:基因组上下文;TM:文献挖掘
Note: ①At: Arabidopsis, Ba: Barley, Br: Brachypodium, Mc:Cassava, Cc: Gossypium, Vv: Grapevine, Zm: Maize, Me: Medicago, Pa: Conifer, Pt: Poplar, Os: Rice, Gm: Soybean, Sg: Sorghum, Le: Tomato, Tc: Tobacco, Ta:Wheat. -
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