BMC Genomics. 2013 Aug 8;14:538. doi: 10.1186/1471-2164-14-538.
Latimeria menadoensis is a coelacanth species first identified in 1997 in Indonesia, at 10,000 Km of distance from its African congener. To date, only six specimens have been caught and just a very limited molecular data is available. In the present work we describe the de novo transcriptome assembly obtained from liver and testis samples collected from the fifth specimen ever caught of this species.
The deep RNA sequencing performed with Illumina technologies generated 145,435,156 paired-end reads, accounting for ~14 GB of sequence data, which were de novo assembled using a Trinity/CLC combined strategy. The assembly output was processed and filtered producing a set of 66,308 contigs, whose quality was thoroughly assessed. The comparison with the recently sequenced genome of the African congener Latimeria chalumnae and with the available genomic resources of other vertebrates revealed a good reconstruction of full length transcripts and a high coverage of the predicted full coelacanth transcriptome.
Given the high genomic affinity between the two coelacanth species, the here described de novo transcriptome assembly can be considered a valuable support tool for the improvement of gene prediction within the genome of L. chalumnae and a valuable resource for investigation of many aspects of tetrapod evolution.
拉蒂迈鱼于 1997 年在印度尼西亚首次被发现，与非洲的同属物种相距 10000 公里。迄今为止，仅捕获了六个标本，并且仅有非常有限的分子数据可用。在本工作中，我们描述了从该物种的第五个标本中收集的肝和睾丸样本的从头转录组组装。
使用 Illumina 技术进行的深度 RNA 测序生成了 145,435,156 对末端读取，占约 14GB 的序列数据，使用 Trinity/CLC 组合策略进行从头组装。对组装结果进行处理和过滤，生成了一组 66,308 个 contigs，对其质量进行了彻底评估。与最近测序的非洲同属物种 Latimeria chalumnae 的基因组以及其他脊椎动物的现有基因组资源进行比较，显示出全长转录本的良好重建和对预测的完整腔棘鱼转录组的高度覆盖。
鉴于两种腔棘鱼物种之间的高基因组亲和力，此处描述的从头转录组组装可以被视为改进 L. chalumnae 基因组中基因预测的有价值的支持工具，并且是研究四足动物进化许多方面的有价值的资源。
