DataSheet1_Organelle genome assembly, annotation, and comparative analyses of Typha latifolia and T. domingensis: two keystone species for wetlands worldwide.pdf

Typha is a cosmopolitan aquatic plant genus that includes species with widespread global distributions. In previous studies, a revised molecular phylogeny was inferred using seven plastid loci from nine Typha species across different geographic regions. By utilizing complete organellar genomes, we aim to provide a more comprehensive dataset that offers a robust phylogenetic signal for resolving Typha species evolutionary relationships. Here, we assembled T. latifolia and T. domingensis mitochondrial genomes (mitogenomes) using a combination of short-read and long-read data (PacBio, ONT). The mitogenomes of both species are assembled into single circular molecules of 395,136 bp and 395,140 bp in length, respectively, with a similar GC content of 46.7%. A total of 39 protein-coding genes, 17 tRNA genes, and 3 rRNA genes were annotated in both mitogenomes. The plastid genomes (plastomes) of both species possess typical quadripartite structures observed across most plants, with sizes of 161,545 bp and 161,230 bp. The overall average GC content of the plastomes of both species was 36.6%. The comparative analysis of the plastome and mitogenome revealed that 12 mitogenome DNA fragments share similar sequences with in the repeat regions of the corresponding plastomes, suggesting a past transfer of repeat regions into the mitogenome. Additionally, the mitogenomes of the two Typha species exhibited high sequence conservation with several syntenic blocks. Phylogenetic analysis of the organellar genomes of the two Typha species and 10 related species produced congruent phylogenetic trees. The availability of these organellar genomes from two Typha species provide valuable genetic resources for studying the evolution of Typhaceae and will improve taxonomic classifications within the family.

香蒲属（Typha）是一类广布全球的水生植物属，包含多个在全球范围内广泛分布的物种。既往研究基于不同地理区域的9种香蒲属植物的7个质体基因座（plastid loci），构建了修订后的分子系统发育树。本研究借助完整的细胞器基因组（organellar genomes），旨在构建更为全面的数据集，以提供可靠的系统发育信号，用于解析香蒲属物种的演化关系。
本研究结合短读长与长读长测序数据（PacBio、ONT），组装得到宽叶香蒲（T. latifolia）与多米尼加香蒲（T. domingensis）的线粒体基因组（mitogenomes）。两种香蒲的线粒体基因组均组装为单环状分子，长度分别为395136 bp与395140 bp，GC含量均约为46.7%，二者较为接近。两个线粒体基因组中共注释得到39个蛋白质编码基因、17个转运RNA（tRNA）基因与3个核糖体RNA（rRNA）基因。
两种香蒲的质体基因组（plastomes）均具有多数植物共有的典型四分体结构，基因组大小分别为161545 bp与161230 bp，二者质体基因组的整体平均GC含量为36.6%。
对质体基因组与线粒体基因组的比较分析显示，12个线粒体基因组DNA片段与对应质体基因组的重复区域序列高度相似，这表明过往曾发生重复区域向线粒体基因组的转移事件。此外，两种香蒲的线粒体基因组在多个共线性区域（syntenic blocks）表现出高度的序列保守性。
对两种香蒲的细胞器基因组以及10个近缘物种的细胞器基因组进行系统发育分析，得到了一致的系统发育树。这两种香蒲的细胞器基因组的公开，为香蒲科（Typhaceae）的演化研究提供了宝贵的遗传资源，同时将有助于完善该科内的分类学界定。