Miniature genome in the marine chordate Oikopleura dioica
Miniature genome in the marine chordate Oikopleura dioica
复制标题
DOI：
10.1126/science.294.5551.2506
复制
发表时间：
2001-12-21
期刊：
影响因子：
56.9
通讯作者：
Chourrout, D
中科院分区：
文献类型：
--
作者：
Seo, HC;Kube, M;Chourrout, D
Oikopleura dioica是一种小型浮游脊索动物，属于幼虫纲（图1A）。脊索动物包括脊椎动物、头索动物和尾索动物，尾索动物又分为海鞘动物、海樽动物和幼虫动物。幼虫可能来自尾索动物的最基底分支，因此，它们一直是脊索动物创新研究的目标，例如尾巴、脊索或背神经系统（1，2）。Oikopleura dioica在所有海洋中都有发现，可以在实验室中永久培养。其非常短的生命周期（20 ℃下4天，29 ℃下2天）和高雌性生殖力（平均300个卵母细胞）为非脊椎脊索动物的遗传分析提供了无与伦比的前景。在这里，我们表明，Oikopleura dioica也是有吸引力的基因组为基础的研究，因为异常高的基因密度和基因压实。Oikopleura和海鞘玻璃海鞘之间的精子DNA含量的流式细胞仪比较产生的值为72 - 13 Mb的Oikopleura基因组。在大规模鸟枪测序中，128，386个短读段组装在43，990个非冗余重叠群中，代表总共32.6 Mb。用现有模型处理的这些数据（3）表明最小基因组大小为51 Mb。鸟枪数据集也准确地匹配，平均，50%的113个表达序列标签（EST）的长度，导致第三次估计为65 Mb。然后，我们通过BLASTX分析了407个来自Oikopleura的1-kb长的基因组片段和4个来自Ciona的粘粒序列，比较了Oikopleura和Ciona的基因密度。BLASTX比对在10 09 E值截止值的两倍，频繁与Oikopleura片段（25%相比，12%）和两倍长的Oikopleura（平均45个氨基酸相比，26个氨基酸每个酶，分别）。对113个EST序列的BLASTX分析表明，该程序未能检测到一半的Oikopleura编码序列。所有BLASTX结果表明，Oikopleura的平均基因密度为每5 kb一个基因，约15，000个基因（4）。
Oikopleura dioica is a small pelagic chordate belonging to the class of larvaceans (Fig. 1A). Chordates include vertebrates, cephalochordates, and urochordates, and urochordates are divided into ascidians, thaliaceans, and larvaceans. Larvaceans may be derived from the most basal branch of urochordates, and for this reason, they have been targeted for studies of chordate innovations, such as the tail, the notochord, or the dorsal nervous system (1, 2). Found in all oceans, Oikopleura dioica can be permanently cultured in the laboratory. Its very short life cycle (4 days at 20 C, 2 days at 29 C) and high female fecundity (300 oocytes on average) offer incomparable perspectives for genetic analysis among nonvertebrate chordates. Here, we show that Oikopleura dioica is also attractive for genome-based studies, because of unusually high gene density and gene compaction. Flow cytometry comparison of sperm DNA content between Oikopleura and the ascidian Ciona intestinalis yielded a value of 72 13 Mb for the Oikopleura genome. In a large-scale shotgun sequencing, 128,386 short reads were assembled in 43,990 nonredundant contigs representing a total of 32.6 Mb. These data, treated with an existing model (3), suggest a minimal genome size of 51 Mb. The shotgun data set also accurately matched, on average, 50% of the length of 113 expressed sequence tags (ESTs), leading to a third estimation of 65 Mb. All these results concur to indicate that Oikopleura has the smallest genome ever found in a chordate.We then compared the density of genes in Oikopleura and in Ciona through a BLASTX analysis of 407 1-kb-long genomic fragments from Oikopleura and four cosmid sequences from Ciona (4) divided into 1-kb fragments. The BLASTX alignments at a 10 09 e-value cutoff were twice as frequent with Oikopleura fragments (25% compared with 12%) and twice as long for Oikopleura (average 45 amino acids compared with 26 amino acids per kilobase, respectively). BLASTX analysis of 113 ESTs showed that this program failed to detect half of Oikopleura coding sequences. All BLASTX results suggest for Oikopleura an average gene density of one gene every 5 kb and about 15,000 genes (4).