Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes:: analysis of a pilot genome project
Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes:: analysis of a pilot genome project
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DOI：
10.1007/s00412-004-0295-3
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发表时间：
2004-09-01
期刊：
影响因子：
1.6
通讯作者：
Landweber, LF
中科院分区：
文献类型：
--
作者：
Cavalcanti, ARO;Stover, NA;Landweber, LF
螺毛纤毛虫的大分子基因组几乎完全是多倍体、单基因染色体（“纳米染色体”）。我们最近为该群体的成员 Oxytricha trifallax (Sterkiella histriomuscorum) 进行了一项试点基因组计划，其中随机克隆了 2000 条纳米染色体并进行了末端测序。在这里，我们描述了为这些分子预测的编码区的全局特性，包括核苷酸组成、密码子使用和内含子特性。在识别剪接供体、受体和分支位点时，我们发现尖毛虫中较长的内含子在供体位点比较小的内含子具有更强的信号，正如在秀丽隐杆线虫和果蝇中发现的那样，尽管内含子总体尺寸较小。对多基因染色体的系统搜索确定了 11 种候选纳米染色体。我们将这个大型数据集的结果与早期研究获得的结果以及纤毛虫和其他真核生物记录的统计数据进行比较。
The macromiclear genomes of spirotrichous ciliates are almost entirely polyploid, single-gene chromosomes ("nanochromosomes"). We recently performed a pilot genome project for a member of this group, Oxytricha trifallax (Sterkiella histriomuscorum), in which similar to2000 nanochromosomes were cloned at random and end-sequenced. Here we describe the global properties of the coding regions predicted for these molecules, including nucleotide composition, codon usage, and intron properties. In identifying splice donor, acceptor and branch sites, we found that longer introns in Oxytricha have a stronger signal at the donor site than do smaller introns, as has been found for Caenorhabditis elegans and Drosophila, despite the overall small size of the introns. A systematic search for multi-gene chromosomes identified 11 candidate nanochromosomes. We compare the results from this large dataset with those obtained from earlier studies and with statistics recorded from ciliates and other eukaryotes.