Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina.
Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina.
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深入了解广泛片段化的真核基因组：多核纤毛虫尿拟黄蜂的从头基因组测序
DOI：
10.1093/gbe/evy055
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发表时间：
2018-03-01
影响因子：
3.3
通讯作者：
Song W
中科院分区：
文献类型：
--
作者：
Zheng W;Wang C;Yan Y;Gao F;Doak TG;Song W
纤毛原生生物是一大群单细胞真核生物，每个细胞中都有不同的生殖系和体细胞核。体细胞基因组是从合子核发育而来的，通过一系列的染色体重排，包括碎裂、DNA消除、从头添加端粒和DNA扩增。这一独特的特征使它们成为基因组生物学和进化研究的完美模型。然而，由于DNA污染和培养障碍的问题，纤毛虫的基因组研究仅限于少数几个物种。在这里，我们介绍了一种结合端粒-引物PCR扩增和高通量测序的方法，该方法可以减少DNA污染，有效地获得基因组数据。基于这种方法，我们报道了一种多微核纤毛虫的体细胞基因组草图。1)通过直接钝端克隆，确定柑橘单胞菌的端粒序列为C4A4C4A4C4。2)染色体的基因组分析显示为“一基因一染色体”模式，有少量的多基因染色体。3)分析了氨基酸的用途，确定了终止密码子的重新分配。4)染色体分析显示，在有义链的亚端粒区存在明显的GC不对称偏斜和A与T之间的高度偏倚，在3‘亚端粒区检测到11个碱基的高AT基序区域。5)亚端粒序列也有明显的核苷酸比例的40 nT链振荡。6)在编码链的5‘亚端粒区，显示了潜在的TATA盒区域的分布，这些区域累积在30~50 nT之间。这项工作为基因组研究提供了有价值的参考，并加深了我们对单细胞真核基因组动态性质的理解。
Ciliated protists are a large group of single-celled eukaryotes with separate germline and somatic nuclei in each cell. The somatic genome is developed from the zygotic nucleus through a series of chromosomal rearrangements, including fragmentation, DNA elimination, de novo telomere addition, and DNA amplification. This unique feature makes them perfect models for research in genome biology and evolution. However, genomic research of ciliates has been limited to a few species, owing to problems with DNA contamination and obstacles in cultivation. Here, we introduce a method combining telomere-primer PCR amplification and high-throughput sequencing, which can reduce DNA contamination and obtain genomic data efficiently. Based on this method, we report a draft somatic genome of a multimacronuclear ciliate, Uroleptopsis citrina. 1) The telomeric sequence in U. citrina is confirmed to be C4A4C4A4C4 by directly blunt-end cloning. 2) Genomic analysis of the resulting chromosomes shows a “one-gene one-chromosome” pattern, with a small number of multiple-gene chromosomes. 3) Amino acid usage is analyzed, and reassignment of stop codons is confirmed. 4) Chromosomal analysis shows an obvious asymmetrical GC skew and high bias between A and T in the subtelomeric regions of the sense-strand, with the detection of an 11-bp high AT motif region in the 3′ subtelomeric region. 5) The subtelomeric sequence also has an obvious 40 nt strand oscillation of nucleotide ratio. 6) In the 5′ subtelomeric region of the coding strand, the distribution of potential TATA-box regions is illustrated, which accumulate between 30 and 50 nt. This work provides a valuable reference for genomic research and furthers our understanding of the dynamic nature of unicellular eukaryotic genomes.
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DOI：
10.5635/kjsz.2011.27.3.220
发表时间：
2011-11-01
期刊：
Korean Journal of Systematic Zoology
影响因子：
--
作者：
Baek, Ye-Seul;Jung, Jae-Ho;Min, Gi-Sik
通讯作者：
Min, Gi-Sik
一种新型盐渍土纤毛虫 Lamtostyla salina n 的形态学、形态发生和分子系统发育。
影响因子：
2.9
作者：
Dong, Jingyi;Lu, Xiaoteng;Al-Rasheid, Khaled A. S.
通讯作者：
Al-Rasheid, Khaled A. S.
模因套件：用于发现和搜索的工具。
影响因子：
14.9
作者：
Bailey TL;Boden M;Buske FA;Frith M;Grant CE;Clementi L;Ren J;Li WW;Noble WS
通讯作者：
Noble WS
Parameciumdb：一种将三尿素基因组序列与遗传数据相结合的社区资源。
影响因子：
14.9
作者：
通讯作者：
--
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.