Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA.
Institute at Brown for Environment and Society, Brown University, Providence, RI 02912, USA.
G3 (Bethesda). 2021 Feb 9;11(2). doi: 10.1093/g3journal/jkab010.
The lack of genomic resources for tropical canopy trees is impeding several research avenues in tropical forest biology. We present genome assemblies for two Neotropical hardwood species, Jacaranda copaia and Handroanthus (formerly Tabebuia) guayacan, that are model systems for research on tropical tree demography and flowering phenology. For each species, we combined Illumina short-read data with in vitro proximity-ligation (Chicago) libraries to generate an assembly. For Jacaranda copaia, we obtained 104X physical coverage and produced an assembly with N50/N90 scaffold lengths of 1.020/0.277 Mbp. For H. guayacan, we obtained 129X coverage and produced an assembly with N50/N90 scaffold lengths of 0.795/0.165 Mbp. J. copaia and H. guayacan assemblies contained 95.8% and 87.9% of benchmarking orthologs, although they constituted only 77.1% and 66.7% of the estimated genome sizes of 799 and 512 Mbp, respectively. These differences were potentially due to high repetitive sequence content (>59.31% and 45.59%) and high heterozygosity (0.5% and 0.8%) in each species. Finally, we compared each new assembly to a previously sequenced genome for Handroanthus impetiginosus using whole-genome alignment. This analysis indicated extensive gene duplication in H. impetiginosus since its divergence from H. guayacan.
热带树冠层树木缺乏基因组资源，这阻碍了热带森林生物学的几个研究领域。我们为两种新热带硬木物种 Jacaranda copaia 和 Handroanthus（以前称为 Tabebuia）guayacan 提供了基因组组装，它们是研究热带树木动态和开花物候的模式系统。对于每个物种，我们将 Illumina 短读数据与体外邻近连接（芝加哥）文库相结合，以生成组装。对于 Jacaranda copaia，我们获得了 104X 的物理覆盖率，并产生了 N50/N90 支架长度为 1.020/0.277 Mbp 的组装。对于 H. guayacan，我们获得了 129X 的覆盖率，并产生了 N50/N90 支架长度为 0.795/0.165 Mbp 的组装。J. copaia 和 H. guayacan 组装体包含 95.8%和 87.9%的基准同源物，尽管它们仅占 799 和 512 Mbp 估计基因组大小的 77.1%和 66.7%。这些差异可能是由于每个物种的高重复序列含量（>59.31%和 45.59%）和高杂合性（0.5%和 0.8%）所致。最后，我们使用全基因组比对将每个新组装与之前为 Handroanthus impetiginosus 测序的基因组进行了比较。该分析表明，自 H. guayacan 分化以来，H. impetiginosus 中发生了广泛的基因复制。
