Although most of the tens of thousands of diatom species are obligate photoautotrophs, many mixotrophic species can also use extracellular organic carbon for growth, and a small number of obligate heterotrophs have lost photosynthesis entirely. We sequenced the genome of a nonphotosynthetic diatom, Nitzschia sp. strain Nitz4, to determine how carbon metabolism was altered in the wake of this rare and radical trophic shift in diatoms. Like other groups that have lost photosynthesis, the genomic consequences were most evident in the plastid genome, which is exceptionally AT-rich and missing photosynthesis-related genes. The relatively small (27 Mb) nuclear genome did not differ dramatically from photosynthetic diatoms in gene or intron density. Genome-based models suggest that central carbon metabolism, including a central role for the plastid, remains relatively intact in the absence of photosynthesis. All diatom plastids lack an oxidative pentose phosphate pathway (PPP), leaving photosynthesis as the main source of plastid NADPH. Consequently, nonphotosynthetic diatoms lack the primary source of NADPH required for essential biosynthetic pathways that remain in the plastid. Genomic models highlighted similarities between nonphotosynthetic diatoms and apicomplexan parasites for provisioning NADPH in their plastids. The ancestral absence of a plastid PPP might constrain loss of photosynthesis in diatoms compared to Archaeplastida, whose plastid PPP continues to produce reducing cofactors following loss of photosynthesis. Finally, Nitzschia possesses a complete β-ketoadipate pathway. Previously known only from fungi and bacteria, this pathway may allow mixotrophic and heterotrophic diatoms to obtain energy through the degradation of abundant plant-derived aromatic compounds.

中文翻译：

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非光合作用硅藻的基因组提供了对异养性代谢转变和光合作用丧失限制的见解

尽管成千上万的硅藻物种大部分是专性光合自养生物，但许多混合营养型物种也可以利用细胞外有机碳来生长，少数专性异养生物完全丧失了光合作用。我们对非光合硅藻Nitzschia sp。的基因组进行了测序。菌株Nitz4，以确定硅藻这种罕见而根本的营养转变后碳代谢如何发生改变。像其他失去光合作用的群体一样，基因组后果在质体基因组中最为明显，该基因组富含AT且缺少与光合作用相关的基因。相对较小的（27 Mb）核基因组在基因或内含子密度方面与光合硅藻没有显着差异。基于基因组的模型表明中心碳代谢，包括质体的中心作用，在没有光合作用的情况下仍保持相对完整。所有的硅藻质体都缺乏氧化戊糖磷酸途径（PPP），而光合作用是质体NADPH的主要来源。因此，非光合硅藻缺乏质体中必需的生物合成途径所需的NADPH的主要来源。基因组模型突出了非光合硅藻和apicomplexan寄生虫之间的相似性，以在其质体中供应NADPH。与原始质体相比，质体PPP的祖先缺乏可能会限制硅藻的光合作用，而后者的质体PPP在光合作用丧失后会继续产生还原性辅因子。最后，Nitzschia具有完整的β-酮己二酸途径。以前仅以真菌和细菌为人所知，