Boyce Thompson Institute, Ithaca, New York, USA.
School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom.
Genome Biol Evol. 2021 Nov 5;13(11). doi: 10.1093/gbe/evab233.
Members of eustigmatophyte algae, especially Nannochloropsis and Microchloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. Although extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis and Microchloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis strains C73 and C141 (60 Mb) and Vischeria strain C74 (106 Mb), which are the sister groups to Nannochloropsis and Microchloropsis in the order Eustigmatales. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis and Microchloropsis, long interspersed nuclear element repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and nonmevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis and Microchloropsis that have only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis and Microchloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.
真眼点藻门的藻类成员，特别是拟球藻属和微拟球藻属，由于其极高的脂类含量，已被用于生物燃料生产。尽管已经为拟球藻属和微拟球藻属提供了广泛的基因组、转录组和合成生物学工具包，但对其他真眼点藻属知之甚少。在这里，我们呈现了 Monodopsis 菌株 C73 和 C141（60Mb）和 Vischeria 菌株 C74（106Mb）的三个近染色体和无间隙基因组组装，它们在真眼点藻目中与拟球藻属和微拟球藻属是姐妹群。这些基因组包含异常高比例的简单重复序列，范围从总组装大小的 12%到 21%。与拟球藻属和微拟球藻属不同，Monodopsis 和 Vischeria 中富含长散布核元件重复序列，这些重复序列可能构成着丝粒区域。我们发现，Monodopsis 和 Vischeria 中都存在萜类生物合成的甲羟戊酸途径和非甲羟戊酸途径，而拟球藻属和微拟球藻属只有后者。我们的分析进一步表明，Monodopsis 和 Vischeria 中有广泛的剪接前导 trans-splicing，占基因的 36-61%。总的来说，Monodopsis 和 Vischeria 的高质量基因组不仅为推进拟球藻属和微拟球藻属的研究提供了急需的外群，而且为真眼点藻属藻类的生物学和进化提供了新的视角。
