INRA, UMR CBGP (INRA/IRD/CIRAD/Montpellier Supagro), Campus International de Baillarguet, CS30016, F-34988 Montferrier-sur-Lez Cedex, France.
Max Planck Institute for Chemical Ecology, Department of Entomology, 07745 Jena, Germany.
Insect Biochem Mol Biol. 2014 Mar;46:31-42. doi: 10.1016/j.ibmb.2014.01.005. Epub 2014 Jan 24.
The pine processionary moth Thaumetopoea pityocampa is a Mediterranean lepidopteran defoliator that experiences a rapid range expansion towards higher latitudes and altitudes due to the current climate warming. Its phenology - the time of sexual reproduction - is certainly a key trait for the local adaptation of the processionary moth to climatic conditions. Moreover, an exceptional case of allochronic differentiation was discovered ca. 15 years ago in this species. A population with a shifted phenology (the summer population, SP) co-exists near Leiria, Portugal, with a population following the classical cycle (the winter population, WP). The existence of this population is an outstanding opportunity to decipher the genetic bases of phenology. No genomic resources were so far available for T. pityocampa. We developed a high-throughput sequencing approach to build a first reference transcriptome, and to proceed with comparative analyses of the sympatric SP and WP. We pooled RNA extracted from whole individuals of various developmental stages, and performed a transcriptome characterisation for both populations combining Roche 454-FLX and traditional Sanger data. The obtained sequences were clustered into ca. 12,000 transcripts corresponding to 9265 unigenes. The mean transcript coverage was 21.9 reads per bp. Almost 70% of the de novo assembled transcripts displayed significant similarity to previously published proteins and around 50% of the transcripts contained a full-length coding region. Comparative analyses of the population transcriptomes allowed to investigate genes specifically expressed in one of the studied populations only, and to identify the most divergent homologous SP/WP transcripts. The most divergent pairs of transcripts did not correspond to obvious phenology-related candidate genes, and 43% could not be functionally annotated. This study provides the first comprehensive genome-wide resource for the target species T. pityocampa. Many of the assembled genes are orthologs of published Lepidoptera genes, which allows carrying out gene-specific re-sequencing. Data mining has allowed the identification of SNP loci that will be useful for population genomic approaches and genome-wide scans of population differentiation to identify signatures of selection.
松毛虫 Thau metopoea pityocampa 是一种地中海鳞翅目食叶动物，由于当前气候变暖，其分布范围迅速向高纬度和高海拔地区扩展。其物候学——即有性繁殖的时间——无疑是毛毛虫适应气候条件的关键特征。此外，大约 15 年前，在这个物种中发现了一个异常的异时性分化案例。一个物候期发生变化的种群（夏季种群，SP）与一个遵循经典周期的种群（冬季种群，WP）共存于葡萄牙莱里亚附近。这种种群的存在为破译毛毛虫的物候学遗传基础提供了一个绝佳的机会。到目前为止，T. pityocampa 还没有基因组资源。我们开发了一种高通量测序方法来构建第一个参考转录组，并对共存的 SP 和 WP 进行比较分析。我们从不同发育阶段的个体中提取 RNA 并进行混合，结合 Roche 454-FLX 和传统 Sanger 数据，对两个种群进行转录组特征分析。获得的序列聚类为大约 12000 个转录本，对应于 9265 个 unigenes。平均转录本覆盖率为 21.9 个读长/碱基对。近 70%的从头组装转录本与先前发表的蛋白质具有显著相似性，约 50%的转录本包含完整的编码区。对种群转录组的比较分析允许研究仅在一个研究种群中特异性表达的基因，并鉴定出最具差异的同源 SP/WP 转录本。最具差异的转录本对并不对应于明显的物候相关候选基因，且 43%的转录本无法进行功能注释。这项研究为目标物种 T. pityocampa 提供了第一个全面的全基因组资源。许多组装的基因是已发表的鳞翅目基因的直系同源基因，这使得进行基因特异性重测序成为可能。数据挖掘允许鉴定 SNP 位点，这些位点将有助于群体基因组学方法和种群分化的全基因组扫描，以鉴定选择的特征。
