Repeat structure of the catfish genome:: a genomic and transcriptomic assessment of Tc1-like transposon elements in channel catfish (Ictalurus punctatus)
Repeat structure of the catfish genome:: a genomic and transcriptomic assessment of Tc1-like transposon elements in channel catfish (Ictalurus punctatus)
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DOI：
10.1007/s10709-006-9115-4
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发表时间：
2007-09-01
期刊：
影响因子：
1.5
通讯作者：
Liu, Zhanjiang
中科院分区：
文献类型：
--
作者：
Nandi, Samiran;Peatman, Eric;Liu, Zhanjiang
我们已经评估了Tcllmariner转座因子超家族成员在癍点叉尾鮰（Ictalurus punctatus）基因组中的分布和多样性，以及评估Tcl转座酶在该物种中的转录程度。通过使用PCR扩增和测序，评估随机BAC末端序列（BES）相当于1.2%的基因组覆盖率，并筛选超过45,000鲶鱼EST，一个显着比例的Tcl样元件及其相关的转录本被捕获。高达4.2%的鲶鱼基因组中的碱基对似乎是由Tcl样转座子相关序列和鲶鱼细胞mRNA的显着部分，约0.6%，从转座子相关序列的正义和反义方向转录。基于重复掩蔽的结果，来自鲶鱼的多达10%的BAC末端序列（这是对基因组的随机调查）含有Tcl元件的一些残余，表明这些元件作为转座子的大量小残余存在于鲶鱼基因组中。系统发育分析允许鲶鱼Tcl转座酶类型与其他脊椎动物和无脊椎动物物种中发现的比较。尽管存在许多类型的Tcl-样序列，还不能被放置在分支与强有力的统计支持，很明显，多个家庭的Tcl-样元素存在于癍点叉尾鮰。
We have assessed the distribution and diversity of members of the Tcllmariner superfamily of transposable elements in the channel catfish (Ictalurus punctatus) genome as well as evaluating the extent of transcription of Tcl transposases in the species. Through use of PCR amplification and sequencing, assessment of random BAC end sequences (BES) equivalent to 1.2% genome coverage, and screening of over 45,000 catfish ESTs, a significant proportion of Tcl-like elements and their associated transcripts were captured. Up to 4.2% of the catfish genome in base pairs appears to be composed of Tcl-like transposon-related sequences and a significant fraction of the catfish cellular mRNA, approximately 0.6%, was transcribed from transposon-related sequences in both sense and antisense orientations. Based on results of repeat-masking, as much as 10% of BAC end sequences from catfish, which is a random survey of the genome, contain some remnant of Tcl elements, suggesting that these elements are present in the catfish genome as numerous, small remnants of the transposons. Phylogenetic analysis allowed comparison of catfish Tcl transposase types with those found in other vertebrate and invertebrate species. In spite of the existence of many types of Tcl-like sequences that are not yet able to be placed in clades with strong statistical support, it is clear that multiple families of Tcl-like elements exist in channel catfish.