DataSheet3_Transcriptional Regulation of Pine Male and Female Cone Initiation and Development: Key Players Identified Through Comparative Transcriptomics.ZIP

With long reproductive timescales, large complex genomes, and a lack of reliable reference genomes, understanding gene function in conifers is extremely challenging. Consequently, our understanding of which genetic factors influence the development of reproductive structures (cones) in monoecious conifers remains limited. Genes with inferred roles in conifer reproduction have mostly been identified through homology and phylogenetic reconstruction with their angiosperm counterparts. We used RNA-sequencing to generate transcriptomes of the early morphological stages of cone development in the conifer species Pinus densiflora and used these to gain a deeper insight into the transcriptional changes during male and female cone development. Paired-end Illumina sequencing was used to generate transcriptomes from non-reproductive tissue and male and female cones at four time points with a total of 382.82 Gbp of data generated. After assembly and stringent filtering, a total of 37,164 transcripts were retrieved, of which a third were functionally annotated using the Mercator plant pipeline. Differentially expressed gene (DEG) analysis resulted in the identification of 172,092 DEGs in the nine tissue types. This, alongside GO gene enrichment analyses, pinpointed transcripts putatively involved in conifer reproductive structure development, including co-orthologs of several angiosperm flowering genes and several that have not been previously reported in conifers. This study provides a comprehensive transcriptome resource for male and early female cone development in the gymnosperm species Pinus densiflora. Characterisation of this resource has allowed the identification of potential key players and thus provides valuable insights into the molecular regulation of reproductive structure development in monoecious conifers.

针叶树繁殖周期漫长、基因组庞大复杂且缺乏可靠参考基因组，这使得解析其基因功能极具挑战性。因此，目前学界对雌雄同株针叶树中哪些遗传因子调控繁殖结构（球果）的发育仍认知有限。此前被推测参与针叶树繁殖过程的基因，大多是通过与被子植物同源基因进行同源性分析及系统发育重建得以鉴定的。本研究以针叶树物种赤松（Pinus densiflora）为材料，对其球果发育的早期形态阶段进行RNA测序（RNA-sequencing）以构建转录组，借此深入解析雌雄球果发育过程中的转录调控变化。本研究采用双端Illumina测序（Illumina）技术，对非繁殖组织以及四个发育时间点的雌雄球果进行转录组构建，最终共获得382.82 Gbp的测序数据。经组装与严格过滤后，共得到37164条转录本，其中三分之一通过Mercator植物注释流程（Mercator plant pipeline）完成了功能注释。对9种组织类型开展差异表达基因（Differentially Expressed Gene, DEG）分析，共鉴定得到172092个DEG。结合GO基因富集分析，本研究锁定了一批推测参与针叶树繁殖结构发育的转录本，其中包括多个被子植物开花基因的共直系同源基因，以及若干此前未在针叶树中被报道的基因。本研究为裸子植物赤松（Pinus densiflora）的雄球果及早期雌球果发育提供了一套全面的转录组资源。通过对该转录组资源的解析，本研究鉴定出一批潜在的关键调控因子，从而为解析雌雄同株针叶树繁殖结构发育的分子调控机制提供了宝贵的研究视角。