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首页> 外文期刊>BMC Genomics >Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals
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Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals

机译：转录组深层测序和法维亚珊瑚表达亚型的聚类

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Background Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the northern Red Sea. Results We obtained 80 million 75 bp paired-end cDNA reads from two Favia adult samples collected at 65 m (Fav1, Fav2) on the Illumina GA platform, and generated two de novo assemblies using ABySS and CAP3. After removing redundancy and filtering out low quality reads, our transcriptome datasets contained 58,268 (Fav1) and 62,469 (Fav2) contigs longer than 100 bp, with N50 values of 1,665 bp and 1,439 bp, respectively. Using the proteome of the sea anemone Nematostella vectensis as a reference, we were able to annotate almost 20% of each dataset using reciprocal homology searches. Homologous clustering of these annotated transcripts allowed us to divide them into 7,186 (Fav1) and 6,862 (Fav2) homologous transcript clusters (E-value ≤ 2e-30). Functional annotation categories were assigned to homologous clusters using the functional annotation of Nematostella vectensis. General annotation of the assembled transcripts was improved 1-3% using the Acropora digitifera proteome. In addition, we screened these transcript isoform clusters for fluorescent proteins (FPs) homologs and identified seven potential FP homologs in Fav1, and four in Fav2. These transcripts were validated as bona fide FP transcripts via robust fluorescence heterologous expression. Annotation of the assembled contigs revealed that 1.34% and 1.61% (in Fav1 and Fav2, respectively) of the total assembled contigs likely originated from the corals’ algal symbiont, Symbiodinium spp. Conclusions Here we present a study to identify the homologous transcript isoform clusters from the transcriptome of Favia corals using a far-related reference proteome. Furthermore, the symbiont-derived transcripts were isolated from the datasets and their contribution quantified. This is the first annotated transcriptome of the genus Favia, a major increase in genomics resources available in this important family of corals.
机译：背景基因组和转录组序列数据是解决生态问题的重要工具。使用结合下一代测序，从头转录组组装，基因注释和合成基因构建的方法，我们鉴定和聚类了来自北红海北部法维亚珊瑚的蛋白质家族。结果我们从Illumina GA平台上以65 m（Fav1，Fav2）收集的两个Favia成年样品中获得了8000万个75 bp配对末端cDNA读数，并使用ABySS和CAP3产生了两个从头组装。删除冗余并过滤掉低质量的读段后，我们的转录组数据集包含58,268（Fav1）和62,469（Fav2）个重叠群，长度超过100 bp，N50值分别为1,665 bp和1,439 bp。使用海葵Nematostella vectensis的蛋白质组作为参考，我们能够使用相互同源性搜索注释几乎每个数据集的20％。这些带注释的转录本的同源聚类使我们可以将它们分为7,186（Fav1）和6,862（Fav2）个同源转录本簇（E值≤2e -30 ）。使用线虫线虫的功能注释将功能注释类别分配给同源簇。装配的笔录的一般注释使用刺槐蛋白质组提高了1-3％。此外，我们筛选了这些转录异构体簇中的荧光蛋白（FPs）同源物，并在Fav1中鉴定了七个潜在的FP同源物，在Fav2中鉴定了四个潜在的FP同源物。通过强大的荧光异源表达，这些转录物被证实为真正的FP转录物。对已组装重叠群的注释表明，在已组装重叠群的总数中，分别有1.34％和1.61％（分别在Fav1和Fav2中）源自珊瑚的藻类共生菌Symbiodinium spp。结论在此，我们进行了一项研究，使用远相关的参考蛋白质组从Favia珊瑚的转录组中鉴定出同源转录亚型簇。此外，从数据集中分离了共生体转录本，并定量了其贡献。这是Favia属的第一个带注释的转录组，是这个重要珊瑚家族中可用的基因组资源的重大增加。

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