Tomasello Salvatore, Manzo Eleonora, Karbstein Kevin
Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Göttingen, Göttingen, Germany.
Department of Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Jena, Germany.
Front Plant Sci. 2024 Sep 12;15:1429494. doi: 10.3389/fpls.2024.1429494. eCollection 2024.
Chloroplast genomes (plastomes) represent a very important source of valuable information for phylogenetic and biogeographic reconstructions. The use of short reads (as those produced from Illumina sequencing), along with read assembly, has been considered the "gold standard" for plastome reconstruction. However, short reads often cannot reconstruct long repetitive regions in chloroplast genomes. Long Nanopore (ONT) reads can help bridging long repetitive regions but are by far more error-prone than those produced by Illumina sequencing. is the largest genus of tribe Heliantheae (Asteraceae) and includes species of economic importance as ornamental or as invasive weeds. However, no complete chloroplast genomes have been published yet for the genus. We utilized Illumina and Nanopore sequencing data and different assembly strategies to reconstruct the plastome of and evaluated the usefulness of the Nanopore assemblies. The two plastome sequence assemblages, one obtained with the Nanopore sequencing and the other inferred with Illumina reads, were identical, except for missing bases in homonucleotide regions. The best-assembled plastome of was 152,050 bp in length and contained 80, 29, and four unique protein-coding genes, tRNAs, and rRNAs, respectively. When used as reference for mapping Illumina reads, all plastomes performed similarly. In a phylogenetic analysis including 28 other plastomes from closely related taxa (from the ), the two chloroplast genomes grouped together and were nested among the other members of the tribe Heliantheae s.str. Our study highlights the usefulness of the Nanopore technology for assembling rapidly and cost-effectively chloroplast genomes, especially in taxonomic groups with paucity of publicly available plastomes.
叶绿体基因组（质体基因组）是系统发育和生物地理重建中非常重要的有价值信息来源。使用短读长（如Illumina测序产生的读长）以及读长组装，被认为是质体基因组重建的“金标准”。然而，短读长往往无法重建叶绿体基因组中的长重复区域。长的纳米孔（ONT）读长有助于跨越长重复区域，但到目前为止，其错误率远高于Illumina测序产生的读长。向日葵属是向日葵族（菊科）中最大的属，包括具有经济重要性的观赏植物或入侵杂草物种。然而，该属尚未有完整的叶绿体基因组发表。我们利用Illumina和纳米孔测序数据以及不同的组装策略来重建向日葵属的质体基因组，并评估纳米孔组装的实用性。两种质体基因组序列组装，一种通过纳米孔测序获得，另一种由Illumina读长推断得出，除了同核苷酸区域的缺失碱基外，二者是相同的。组装效果最佳的向日葵属质体基因组长度为152,050 bp，分别包含80个、29个和4个独特的蛋白质编码基因、tRNA和rRNA。当用作Illumina读长映射的参考时，所有质体基因组表现相似。在一项包括来自近缘类群（来自向日葵族）的其他28个质体基因组的系统发育分析中，两个向日葵属叶绿体基因组聚在一起，并嵌套在向日葵族狭义成员之中。我们的研究突出了纳米孔技术在快速且经济高效地组装叶绿体基因组方面的实用性，尤其是在公开可用质体基因组匮乏的分类群中。
