Genome sequence of the pea aphid Acyrthosiphon pisum.
Genome sequence of the pea aphid Acyrthosiphon pisum.
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DOI：
10.1371/journal.pbio.1000313
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发表时间：
2010-02-23
期刊：
影响因子：
9.8
通讯作者：
International Aphid Genomics Consortium
中科院分区：
文献类型：
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作者：
International Aphid Genomics Consortium
豌豆蚜的基因组显示出显着水平的基因复制和同样显着的基因缺失，这揭示了蚜虫生物学的各个方面，尤其是它与 Buchnera 的共生。蚜虫是重要的农业害虫，也是研究昆虫与植物相互作用、共生、病毒传播和极端表型可塑性发育原因的生物模型。在这里，我们展示了豌豆蚜 Acyrthosiphon pisum 的 464 Mb 基因组组装草案。这是首次发表的基础半变态昆虫的全基因组序列，为多个已发表的全变态昆虫基因组提供了一个外群。豌豆蚜虫是寄主植物专家，它们可以有性和无性繁殖，并且与专性细菌共生体共同进化。在这里，我们重点介绍可能与这些不寻常的生物学特征有关的全基因组分析结果。这些发现包括在 2000 多个基因家族中发现了广泛的基因重复以及进化保守基因的丢失。相对于其他已发表基因组的基因家族扩展包括涉及染色质修饰、miRNA 合成和糖转运的基因。基因损失包括对 IMD 免疫途径、硒蛋白利用、嘌呤回收和整个尿素循环至关重要的基因。豌豆蚜基因组表明，仅从细菌中获得了有限数量的基因；因此，Buchnera 基因数量的减少并不反映基因转移到宿主基因组。豌豆蚜基因组中的代谢基因库存表明，蚜虫和 Buchnera 之间存在广泛的代谢物交换，包括蚜虫和 Buchnera 之间共享氨基酸生物合成。豌豆蚜基因组为基本生物学问题和应用农业问题的后基因组研究提供了基础。蚜虫是农作物和观赏植物的常见害虫。由于它们与合成必需氨基酸的细胞内共生细菌的古老联系，蚜虫以韧皮部（汁液）为食。许多蚜虫物种对多种长寿木本和短命草本寄主的利用是专业化的结果，使蚜虫能够发现和利用合适的寄主植物。这种特化包括由单一基因型产生多种替代表型，包括无性、有性、有翅和无翅形式。我们已经生成了豌豆蚜的基因组序列草案，这种蚜虫是研究共生、发育和寄主植物特化的模型。我们的基因组分析的许多亮点包括扩展的总基因集和显着水平的基因重复，以及蚜虫谱系特异性基因丢失。我们发现豌豆蚜基因组包含甲基化表观遗传调控所需的所有基因，编码许多必需氨基酸合成的基因分布在豌豆蚜及其共生体 Buchnera aphidicola 的基因组之间，并且缺乏许多编码免疫系统成分的基因。这些基因组数据将构成未来蚜虫研究的基础，并且已经支持了理解蚜虫生物学的各种全基因组方法。
The genome of the pea aphid shows remarkable levels of gene duplication and equally remarkable gene absences that shed light on aspects of aphid biology, most especially its symbiosis with Buchnera. Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems. Aphids are common pests of crops and ornamental plants. Facilitated by their ancient association with intracellular symbiotic bacteria that synthesize essential amino acids, aphids feed on phloem (sap). Exploitation of a diversity of long-lived woody and short-lived herbaceous hosts by many aphid species is a result of specializations that allow aphids to discover and exploit suitable host plants. Such specializations include production by a single genotype of multiple alternative phenotypes including asexual, sexual, winged, and unwinged forms. We have generated a draft genome sequence of the pea aphid, an aphid that is a model for the study of symbiosis, development, and host plant specialization. Some of the many highlights of our genome analysis include an expanded total gene set with remarkable levels of gene duplication, as well as aphid-lineage-specific gene losses. We find that the pea aphid genome contains all genes required for epigenetic regulation by methylation, that genes encoding the synthesis of a number of essential amino acids are distributed between the genomes of the pea aphid and its symbiont, Buchnera aphidicola, and that many genes encoding immune system components are absent. These genome data will form the basis for future aphid research and have already underpinned a variety of genome-wide approaches to understanding aphid biology.