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何燕, 尹家奇, 生欣. 艾美游仆虫大核基因组与转录组测序及结构特征[J]. 水生生物学报, 2021, 45(5): 1014-1023. DOI: 10.7541/2021.2020.212
引用本文: 何燕, 尹家奇, 生欣. 艾美游仆虫大核基因组与转录组测序及结构特征[J]. 水生生物学报, 2021, 45(5): 1014-1023. DOI: 10.7541/2021.2020.212
HE Yan, YIN Jia-Qi, SHENG Xin. MACRONUCLEUS GENOME AND TRANSCRIPTOME SEQUENCING AND STRUCTURE ANALYSIS OF EUPLOTES AMIETI[J]. ACTA HYDROBIOLOGICA SINICA, 2021, 45(5): 1014-1023. DOI: 10.7541/2021.2020.212
Citation: HE Yan, YIN Jia-Qi, SHENG Xin. MACRONUCLEUS GENOME AND TRANSCRIPTOME SEQUENCING AND STRUCTURE ANALYSIS OF EUPLOTES AMIETI[J]. ACTA HYDROBIOLOGICA SINICA, 2021, 45(5): 1014-1023. DOI: 10.7541/2021.2020.212

艾美游仆虫大核基因组与转录组测序及结构特征

MACRONUCLEUS GENOME AND TRANSCRIPTOME SEQUENCING AND STRUCTURE ANALYSIS OF EUPLOTES AMIETI

  • 摘要: 为获得艾美游仆虫(Euplotes amieti)大核基因组结构特征、分析基因功能及其表达调控方式, 研究采用高通量测序技术对艾美游仆虫进行了大核基因组与转录组测序, 结果显示基因组测序最终得到原始reads数据为10.92 Gb, 过滤后得到50287条Contigs。GC含量较低, 为31%; 其中两端同时具有端粒的微染色体数量为27542条, 占54.76%, 只含有一端端粒的基因数量为6118条。Contigs进行基因结构分析, 96.5%的基因能够被预测出功能, 最终得到27650条基因, 平均外显子长度为311.69 bp; 内含子较短, 平均长度为150 bp。转录组测序结果为76219898条, 拼接后获得38588条转录组Unigenes, 其平均长度为1189 bp。将转录组的38588条Unigenes比对发现有2%—3%基因发生了编程性移码, 其中, 绝大多数为+1PRF; 除此之外, 艾美游仆虫的终止密码子还存在重配现象, 其终止密码子为UAA和UAG, 而UGA编码半胱氨酸或硒代半胱氨酸。这与游仆虫属的编程性移码及终止密码子重配的特点一致。将27650条基因组Contigs与38588条转录组Unigenes成功获得注释。基因功能分析显示转录本显著富集于细胞生长与死亡、膜转运、运输与细胞学过程等。将基因组与转录组随机各抽取50个基因进行PCR验证。95%的基因均验证成功。结果表明艾美游仆虫除了具有游仆虫特有的微染色体、密码子重新分配和程序性移码等基因组特征外, 还具有大量“联合微染色体”, 编码大量与感受外界环境变化、细胞周期与蛋白表达调控等相关的特殊蛋白质, 并通过一定量的miRNA与锌指类转录因子对基因进行表达调控。

     

    Abstract: To explore genome structure characteristics, gene function and expression regulation of Euplotes amieti, high-throughput sequencing technique was used to sequence the macronucleus genome and transcriptome of Euplotes amieti. A total of 10.92 Gb data and 50287 Contigs were obtained after filtration. The GC content was 31% and the average length of exons and introns were 311.69 bp and 150 bp, respectively. The number of microchromosomes with telomeres at both ends was 27542, accounting for 54.76%, and the number of genes containing only one telomere was 6118. 38588 Unigenes were split, and the average length was 1189 bp. There were 2%—3% PRF in the total Unigenes, and most of which were +1PRF. Besides, the stop codon of Euplotes amieti also has a reconfiguration phenomenon. The stop codons are UAA and UAG, while UGA codes cysteine and selenocysteine. This was consistent with the characteristics of programmed ribosomal frameshifting and stop codon reassignments in Euplotes. 27650 genomic contigs and 38588 transcriptome Unigenes were successfully annotated. Gene function analysis showed that transcripts were significantly enriched in multiple biological processes, mainly involved cell growth and death, membrane transport, transport, and cytology. Moreover, 50 genes were randomly selected from the genome and transcriptome for PCR verification, and 95% of them were successfully verified. The results indicated that in addition to the characteristic microchromosomes and programmed frameshift, the Euplotes amieti had a large number of “combined microchromosomes” and encoded a large number of special proteins related to the perception of changes in the external environment, cell cycle, and protein expression regulation. In addition,, the gene expression may be regulated by some miRNA and zinc finger transcription factors.

     

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