Satjarak Anchittha, Graham Linda E
Department of Botany, Chulalongkorn University, Bangkok, Thailand.
Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin, USA.
J Phycol. 2017 Oct;53(5):1072-1086. doi: 10.1111/jpy.12566. Epub 2017 Aug 21.
The wall-less green flagellate Pyramimonas parkeae is classified in clade I of the prasinophytes, a paraphyletic assemblage representing the last common ancestor of Viridiplantae, a monophyletic group composed of the green algae and land plants. Consequently, P. parkeae and other prasinophytes illuminate early-evolved Viridiplantae traits likely fundamental in the systems biology of green algae and land plants. Cellular structure and organellar genomes of P. parkeae are now well understood, and transcriptomic sequence data are also publically available for one strain of this species, but corresponding nuclear genomic sequence data are lacking. For this reason, we obtained shotgun genomic sequence and assembled a draft nuclear genome for P. parkeaeNIES254 to use along with existing transcriptomic sequence to focus on carbohydrate-active enzymes. We found that the P. parkeae nuclear genome encodes carbohydrate-active protein families similar to those previously observed for other prasinophytes, green algae, and early-diverging embryophytes for which full nuclear genomic sequence is publically available. Sequences homologous to genes related to biosynthesis of starch and cell wall carbohydrates were identified in the P. parkeae genome, indicating molecular traits common to Viridiplantae. For example, the P. parkeae genome includes sequences clustering with bacterial genes that encode cellulose synthases (Bcs), including regions coding for domains common to bacterial and plant cellulose synthases; these new sequences were incorporated into phylogenies aimed at illuminating the evolutionary history of cellulose production by Viridiplantae. Genomic sequences related to biosynthesis of xyloglucans, pectin, and starch likewise shed light on the origin of key Viridiplantae traits.
无壁绿藻帕克氏扁藻被归类于绿藻门的第一进化枝，绿藻门是一个并系类群，代表了绿色植物（一个由绿藻和陆地植物组成的单系类群）的最后一个共同祖先。因此，帕克氏扁藻和其他绿藻门植物阐明了绿色植物早期进化的特征，这些特征可能是绿藻和陆地植物系统生物学中的基础特征。帕克氏扁藻的细胞结构和细胞器基因组现在已经得到了很好的理解，并且该物种一个菌株的转录组序列数据也已公开，但相应的核基因组序列数据却缺失。出于这个原因，我们获得了鸟枪法基因组序列，并为帕克氏扁藻NIES254组装了一个核基因组草图，以便与现有的转录组序列一起用于聚焦碳水化合物活性酶。我们发现，帕克氏扁藻的核基因组编码的碳水化合物活性蛋白家族与之前在其他绿藻门植物、绿藻以及全核基因组序列已公开的早期分化的有胚植物中观察到的相似。在帕克氏扁藻基因组中鉴定出了与淀粉和细胞壁碳水化合物生物合成相关基因的同源序列，这表明了绿色植物共有的分子特征。例如，帕克氏扁藻基因组包含与编码纤维素合酶（Bcs）的细菌基因聚类的序列，包括编码细菌和植物纤维素合酶共有的结构域的区域；这些新序列被纳入系统发育树中，旨在阐明绿色植物纤维素产生的进化历史。与木葡聚糖、果胶和淀粉生物合成相关的基因组序列同样揭示了绿色植物关键特征的起源。
