De novo transcriptome assembly of the plant Helianthemum marifolium for the study of adaptive mechanisms

The genus Helianthemum, commonly known as rockroses, encompasses 140 species primarily distributed in the Palearctic region, with notable diversification driven by climatic and geological changes. These plants are valuable for studying speciation processes and ecological divergence. The chemical properties of the leaves have also been investigated for containing valuable bioactive compounds with several therapeutic properties. However, the availability of genomic resources for species in this genus are almost entirely lacking. Here, we assembled and annotated the first reference transcriptome of Helianthemum marifolium, a species with wide morphological variability and infraspecific diversity. Illumina paired-end RNA sequences were generated using leaves from 16 individuals, representing the four recognized subspecies, all cultivated in a greenhouse. RNA reads were assembled with Trinity and Oases, and EvidentialGene produced a transcriptome with 122,002 transcripts. The transcriptome showed 59524 hits on the UniProtBK database through BLASTx. This transcriptome will be an invaluable resource for transcriptome-level population studies, conservation genetics of the many endangered species within the genus, and for deepen into the metabolic pathways of leaf-derived compounds. RNA-seq profiling of the four subspecies (andalusicum, marifolium, molle and origanifolium) of the species Helianthemum marifolium (Cistaceae).

半日花属（Helianthemum），俗称岩蔷薇（rockroses），包含140个物种，主要分布于古北界（Palearctic region），其类群的显著分化由气候与地质变迁驱动。该类群是研究物种形成过程与生态分化的理想材料。其叶片的化学特性亦得到广泛研究，因含有多种具备治疗活性的珍贵生物活性化合物（bioactive compounds）。然而，该属物种的基因组资源（genomic resources）几乎完全缺失。
本研究组装并注释了细叶半日花（Helianthemum marifolium）的首个参考转录组（reference transcriptome），该物种具有广泛的形态变异与种内多样性（infraspecific diversity）。研究采集了栽培于温室中的16个个体的叶片，这些个体涵盖了该物种已被正式认定的4个亚种，由此生成了Illumina双端RNA测序序列（Illumina paired-end RNA sequences）。使用Trinity与Oases软件对RNA测序读段进行组装，再经EvidentialGene流程筛选，最终得到包含122002条转录本的转录组数据集。通过BLASTx比对，该转录组在通用蛋白质知识库（UniProtBK）中获得了59524条匹配序列。
该转录组将成为开展转录组水平群体研究、该属诸多濒危物种的保护遗传学（conservation genetics）研究，以及深入解析叶片来源化合物代谢通路（metabolic pathways）的宝贵资源。本研究同时提供了隶属于半日花科（Cistaceae）的细叶半日花4个亚种（andalusicum、marifolium、molle与origanifolium）的RNA测序转录谱（RNA-seq profiling）数据。