Improved Spirodela polyrhiza genome and proteomic analyses reveal a conserved chromosomal structure with high abundance of chloroplastic proteins favoring energy production
Improved Spirodela polyrhiza genome and proteomic analyses reveal a conserved chromosomal structure with high abundance of chloroplastic proteins favoring energy production
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DOI：
10.1093/jxb/erab006
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发表时间：
2021-01-17
影响因子：
6.9
通讯作者：
Michael, Todd P.
中科院分区：
文献类型：
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作者：
Harkess, Alex;McLoughlin, Fionn;Michael, Todd P.
浮萍是扁豆科水生单子叶植物中快速繁殖的单系植物。考虑到它们的克隆，指数级快速繁殖，一个关键问题是，在没有减数分裂重组的情况下，整个物种的基因组结构是否保守。在这里，我们研究了螺旋藻（Spirodela polyrhiza）或大浮萍（greater ducducweed）的基因组和蛋白质组学，它在该家族中具有最大的身体计划但最小的基因组大小（1C=150 Mb）。利用Oxford Nanopore测序结合Hi-C脚手架，我们生成了一个高度连续的，染色体尺度的S. polyrhiza系Sp7498 （sp7498_hc）组装。sp7498_hc和Sp9509基因组组装都显示出与最近的Sp7498 PacBio组装相比存在较大的染色体取向偏差，这突出了对正交远程支架技术（如Hi-C和BioNano光学定位）的需求。Sp7498的鸟枪蛋白组学证实了与2250相似的蛋白表达，并揭示了高丰度的参与光合作用和碳水化合物代谢等功能的蛋白。此外，叶绿体蛋白质的增加与叶绿体密度有关。该Sp7498_HiC基因组是在一个牛津纳米孔MinION流动细胞和一个Hi-C文库在教室环境中廉价和快速生成的。将这些数据与质谱生成的蛋白质组相结合，说明了浮萍作为基因组学和蛋白质组学基础教育模型的实用性。
Duckweeds are a monophyletic group of rapidly reproducing aquatic monocots in the Lemnaceae family. Given their clonal, exponentially fast reproduction, a key question is whether genome structure is conserved across the species in the absence of meiotic recombination. Here, we studied the genome and proteome of Spirodela polyrhiza, or greater duckweed, which has the largest body plan yet the smallest genome size in the family (1C=150 Mb). Using Oxford Nanopore sequencing combined with Hi-C scaffolding, we generated a highly contiguous, chromosome-scale assembly of S. polyrhiza line Sp7498 (Sp7498_HiC). Both the Sp7498_HiC and Sp9509 genome assemblies reveal large chromosomal misorientations relative to a recent PacBio assembly of Sp7498, highlighting the need for orthogonal long-range scaffolding techniques such as Hi-C and BioNano optical mapping. Shotgun proteomics of Sp7498 verified the expression of similar to 2250 proteins and revealed a high abundance of proteins involved in photosynthesis and carbohydrate metabolism among other functions. In addition, a strong increase in chloroplast proteins was observed that correlated to chloroplast density. This Sp7498_HiC genome was generated cheaply and quickly with a single Oxford Nanopore MinION flow cell and one Hi-C library in a classroom setting. Combining these data with a mass spectrometry-generated proteome illustrates the utility of duckweed as a model for genomics- and proteomics-based education.