Department of Evolutionary Ecology, Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Isla de la Cartuja, 41092 Sevilla, Spain.
Departamento de Genética, Universidad de Granada, 18071 Granada, Spain.
Genes (Basel). 2023 Jan 7;14(1):166. doi: 10.3390/genes14010166.
Genomic resources are essential to understanding the evolution and functional biology of organisms. Nevertheless, generating genomic resources from endangered species may be challenging due to the scarcity of available specimens and sampling difficulties. In this study, we compare the transcriptomes of the sporophyte and the gametophyte of the endangered fern . After Illumina sequencing and transcriptome assembly of the gametophyte, annotation proved the existence of cross-species contamination in the gametophyte sample. Thus, we developed an decontamination step for the gametophyte sequences. Once the quality check of the decontaminated reads passed, we produced a de novo assembly with the decontaminated gametophyte reads (with 43,139 contigs) and another combining the sporophyte and decontaminated gametophyte reads (with 42,918 contigs). A comparison of the enriched GO terms from the top 1000 most expressed transcripts from both tissues showed that the gametophyte GO term set was enriched in sequences involved in development, response to stress, and plastid organization, while the sporophyte GO term set had a larger representation of more general metabolic functions. This study complements the available genomic resources on the life cycle of the endangered fern .
基因组资源对于理解生物的进化和功能生物学至关重要。然而，由于濒危物种的可用样本稀缺且采样困难，从这些物种中生成基因组资源可能具有挑战性。在这项研究中，我们比较了濒危蕨类植物的孢子体和配子体的转录组。在对配子体进行 Illumina 测序和转录组组装后，注释证实了配子体样本中存在跨物种污染。因此，我们为配子体序列开发了一个去污染步骤。一旦去污染后读取的质量检查通过，我们就使用去污染的配子体读取（包含 43,139 个 contigs）进行从头组装，并使用孢子体和去污染的配子体读取进行另一个组装（包含 42,918 个 contigs）。比较两个组织中表达最丰富的前 1000 个转录本的富集 GO 术语表明，配子体 GO 术语集在涉及发育、应激反应和质体组织的序列中富集，而孢子体 GO 术语集则有更多更一般的代谢功能的代表性。这项研究补充了濒危蕨类植物生命周期的可用基因组资源。
