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Abstract：
The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily \"short\" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.
摘要：
这里介绍了罕见的非洲窄特有苔藓PhyscomitrellopsisAfricana的第一个染色体尺度参考基因组。从73x纳米孔长读数和163xBGI-seq短读数组装，414Mb参考包含26条染色体和22,925个蛋白质编码基因(BUSCO:C:94.8%[D:13.9%])。这个基因组包含两个基因，它们经受住了微生物污染物的严格过滤，在其他陆地植物中没有同源物，因此被解释为来自微生物的两个独特的水平基因转移。Further,在Physcomitriumpatens中确定的273种已发布的HGT候选人中，PhyscomitrellopsisAfricana共享176种，但是缺少98个，强调，在过去的4000万年中，在P.patens与非洲P.furicana的共同祖先不同之后，可能获得了多达91个基因。这些观察结果表明，通过HGT获得相当连续的基因，然后是潜在的损失，在真菌科的多样化过程中。我们的发现展示了植物HGTs在进化“短”时间尺度上的动态通量，除了成功整合的持久影响，就像那些仍然在现存的非洲物理中保持功能的人一样。此外，这项研究描述了用于区分污染物和候选HGT事件的信息过程。
