Santos Vanessa, Silva Edson Ferreira da, Almeida Cícero
Universidade Federal Rural de Pernambuco, Recife, PE, Brazil.
Universidade Federal de Alagoas, Laboratório de Recursos Genéticos, Arapiraca, AL, Brazil.
Genet Mol Biol. 2020 Nov 9;43(4):e20190175. doi: 10.1590/1678-4685-GMB-2019-0175. eCollection 2020.
Repetitive DNA is an important component of eukaryotic genomes, accounting for more than 90% of the genome size of some species, including mobile elements and satellite DNA sequences. The aim of study was to characterize the genome of Hancornia speciosa Gomes using C-value genome size estimate and repetitive DNA sequences analysis. The genome size estimate was obtained by flow cytometry and the repetitive DNA sequences were accessed using graph-based clustering. Evolutionary relationships among species of Apocynaceae was obtained using reads of Catharanthus roseus L., Rhayza stricta Decne, and Asclepias syriaca L. from the NCBI and analyzed by graph-based clustering. The genome size estimates in two botanical varieties showed 2C-values ranging from 0.88 to 1.08 pg, indicating small genome size. Clusters representing repeats making up at least 0.01% of the genome revealed the proportion of repetitive DNA ranging from 19.87% (H. speciosa) to 51.674% (A. syriaca), of which the mobile elements were more abundant. Satellite DNA sequences were not found in H. speciosa and R. stricta, while at least one satellite was detected in C. roseus and A. syriaca, suggesting that the LTR retrotransposon Ty3/Gypsy/Chromovirus may have replaced the satellite DNA in H. speciosa and R. stricta.
重复DNA是真核生物基因组的重要组成部分，在某些物种的基因组大小中占比超过90%，包括可移动元件和卫星DNA序列。本研究的目的是通过C值基因组大小估计和重复DNA序列分析来表征汉科尼亚美丽木棉（Hancornia speciosa Gomes）的基因组。通过流式细胞术获得基因组大小估计值，并使用基于图谱的聚类方法获取重复DNA序列。利用来自NCBI的长春花（Catharanthus roseus L.）、硬毛瑞香（Rhayza stricta Decne）和叙利亚马利筋（Asclepias syriaca L.）的reads获得夹竹桃科物种之间的进化关系，并通过基于图谱的聚类进行分析。两个植物变种的基因组大小估计显示2C值范围为0.88至1.08 pg，表明基因组较小。代表占基因组至少0.01%的重复序列的聚类揭示了重复DNA的比例范围为19.87%（美丽木棉）至51.674%（叙利亚马利筋），其中可移动元件更为丰富。在美丽木棉和硬毛瑞香中未发现卫星DNA序列，而在长春花和叙利亚马利筋中至少检测到一个卫星，这表明LTR反转录转座子Ty3/Gypsy/Chromovirus可能已取代了美丽木棉和硬毛瑞香中的卫星DNA。
