The genome sequence of the colonial chordate, Botryllus schlosseri.
The genome sequence of the colonial chordate, Botryllus schlosseri.
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DOI：
10.7554/elife.00569
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发表时间：
2013-07-02
期刊：
影响因子：
7.7
通讯作者：
Quake SR
中科院分区：
文献类型：
--
作者：
Voskoboynik A;Neff NF;Sahoo D;Newman AM;Pushkarev D;Koh W;Passarelli B;Fan HC;Mantalas GL;Palmeri KJ;Ishizuka KJ;Gissi C;Griggio F;Ben-Shlomo R;Corey DM;Penland L;White RA 3rd;Weissman IL;Quake SR
Botryllus schlosseri 是一种群落尾索动物，遵循有性繁殖后的脊索动物发育计划，但在随后的无性繁殖轮次中调用干细胞介导的出芽程序。由于尾索动物被认为是脊椎动物最接近的现存无脊椎动物亲戚，因此它们是全基因组序列分析的理想对象。使用一种新的真核基因组高通量测序方法，我们对 B. schlosseri 基因组进行了测序并组装了 580 Mbp。基因组组装由近 14,000 个包含内含子的预测基因和 13,500 个无内含子的预测基因组成，其中 40% 可以自信地分为 13 条（16 个单倍体）染色体。对史氏拟杆菌和其他不同分类群之间同源基因的比较揭示了脊椎动物进化和淋巴介导的免疫的基础基因组事件。 B. schlosseri 基因组是研究替代繁殖模式、自然移植反应和干细胞介导的再生的社区资源。 DOI：http://dx.doi.org/10.7554/eLife.00569.001 被囊动物是一个进化类群，包括海鞘和海郁金香等物种。它们的名字来源于一种被称为“外衣”的结构，包裹着它们的囊状身体。作为海洋滤食动物，被囊类动物通过过滤水中的食物颗粒来获取营养，根据物种的不同，它们可以单独生活，也可以群居生活。查尔斯·达尔文认为，被囊类动物可能是了解脊椎动物进化的关键，事实上，今天它们被认为是该类群现存的最近亲。殖民地被囊动物可以有性繁殖，也可以通过出芽进行无性繁殖。相容的菌落能够相互识别并将其血管融合形成一个有机体，而不相容的菌落则相互排斥并保持分离。这种识别过程与哺乳动物对外来器官移植的排斥有些相似。在这里，Voskoboynik 和同事展示了殖民地被囊动物 Botryllus schlosseri 的第一个基因组序列。他们使用了一种新颖的测序方法，显着增加了可通过下一代测序确定的 DNA 分子的长度，并允许轻松解析大的 DNA 重复区域。他们总共对 5.8 亿个 DNA 碱基对进行了测序，估计其中包含大约 27,000 个基因。通过将 B. schlosseri 基因组与许多脊椎动物的基因组进行比较，Voskoboynik 等人。确定了多个 B. schlosseri 基因，这些基因也参与脊椎动物眼睛、心脏和听觉系统的发育和功能，以及可能有助于免疫系统和血细胞进化的其他基因。因此，B. schlosseri 的基因组为研究脊椎动物进化的遗传基础提供了一个重要的新工具。 DOI：http://dx.doi.org/10.7554/eLife.00569.002
Botryllus schlosseri is a colonial urochordate that follows the chordate plan of development following sexual reproduction, but invokes a stem cell-mediated budding program during subsequent rounds of asexual reproduction. As urochordates are considered to be the closest living invertebrate relatives of vertebrates, they are ideal subjects for whole genome sequence analyses. Using a novel method for high-throughput sequencing of eukaryotic genomes, we sequenced and assembled 580 Mbp of the B. schlosseri genome. The genome assembly is comprised of nearly 14,000 intron-containing predicted genes, and 13,500 intron-less predicted genes, 40% of which could be confidently parceled into 13 (of 16 haploid) chromosomes. A comparison of homologous genes between B. schlosseri and other diverse taxonomic groups revealed genomic events underlying the evolution of vertebrates and lymphoid-mediated immunity. The B. schlosseri genome is a community resource for studying alternative modes of reproduction, natural transplantation reactions, and stem cell-mediated regeneration. DOI: http://dx.doi.org/10.7554/eLife.00569.001 The tunicates are an evolutionary group that includes species such as sea squirts and sea tulips. Their name comes from the structure known as a ‘tunic’ that surrounds their sac-like bodies. As marine filter feeders, tunicates obtain nutrients by straining food particles from water, and they can live either alone or in colonies depending on the species. Charles Darwin suggested that tunicates may be the key to understanding the evolution of vertebrates, and indeed today they are regarded as the closest living relatives of this group. Colonial tunicates can reproduce either sexually, or asexually by budding. Compatible colonies have the ability to recognize one another and to fuse their blood vessels to form a single organism, whereas incompatible colonies reject one another and remain separate. This recognition process bears some resemblance to the rejection of foreign organ transplants in mammals. Here, Voskoboynik and co-workers present the first genome sequence of a colonial tunicate, Botryllus schlosseri. They used a novel sequencing approach that significantly increased the length of a DNA molecule that can be determined by next-generation sequencing, and allowed large DNA repeat regions to be easily resolved. In total, they sequenced 580 million base pairs of DNA, which they estimate contains roughly 27,000 genes. By comparing the B. schlosseri genome with those of a number of vertebrates, Voskoboynik et al. identified multiple B. schlosseri genes that also participate in the development and functioning of the vertebrate eye, heart, and auditory system, as well as others that may have contributed to the evolution of the immune system and of blood cells. The genome of B. schlosseri thus provides an important new tool for studying the genetic basis of the evolution of vertebrates. DOI: http://dx.doi.org/10.7554/eLife.00569.002