Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri are agronomically important weed species. Here, we present the most contiguous draft assemblies of these three species to date. We utilized a combination of Pacific Biosciences long-read sequencing and chromatin contact mapping information to assemble and order sequences of A. palmeri to near-chromosome-level resolution, with scaffold N50 of 20.1 Mb. To resolve the issues of heterozygosity and co-assembly of alleles in diploid species, we adapted the trio binning approach to produce haplotype assemblies of A. tuberculatus and A. hybridus. This approach resulted in an improved assembly of A. tuberculatus, and the first genome assembly for A. hybridus, with contig N50s of 2.58 and 2.26 Mb, respectively. Species-specific transcriptomes and information from related species were used to predict transcripts within each assembly. Syntenic comparisons of these species and Amaranthus hypochondriacus identified sites of genomic rearrangement, including duplication and translocation, while genetic map construction within A. tuberculatus highlighted the need for further ordering of the A. hybridus and A. tuberculatus contigs. These multiple reference genomes will accelerate genomic studies in these species to further our understanding of weedy evolution within Amaranthus.

中文翻译：

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瘤苋、杂苋和掌苋的基因组草图。

瘤苋、杂苋和棕榈苋是农艺学上重要的杂草物种。在这里，我们展示了迄今为止这三个物种最连续的草案集会。我们结合了 Pacific Biosciences 的长读长测序和染色质接触图谱信息，以接近染色体水平的分辨率组装和排序帕尔梅里氏菌的序列，支架 N50 为 20.1 Mb。为了解决二倍体物种中等位基因的杂合性和共组装问题，我们采用了三重分箱方法来产生结核菌和杂交菌的单倍型组装。这种方法改进了A. tuberculatus的组装，并首次组装了A.hybridus的基因组，重叠群 N50 分别为 2.58 和 2.26 Mb。物种特异性转录组和来自相关物种的信息用于预测每个组装内的转录本。这些物种和苋菜的同线比较确定了基因组重排的位点，包括重复和易位，而结核菌内的遗传图谱构建则强调了对杂交菌和结核菌重叠群进行进一步排序的需要。这些多个参考基因组将加速这些物种的基因组研究，以进一步了解苋属植物的杂草进化。