Fang Jingping, Xu Xiuming, Chen Qinchang, Lin Aiting, Lin Shaoqing, Lei Wen, Zhong Cairong, Huang Yongji, He Yongjin
College of Life Science, Fujian Normal University, Fuzhou, China.
Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, China.
Front Microbiol. 2022 Sep 27;13:966219. doi: 10.3389/fmicb.2022.966219. eCollection 2022.
The haptophyte is considered as a promising source for food supplements due to its rich fucoxanthin and polyunsaturated fatty acids content. Here, the mitochondrial genome (mitogenome) was sequenced using a combination of Illumina and PacBio sequencing platforms. This 39,258 bp circular mitogenome has a total of 46 genes, including 20 protein-coding genes, 24 tRNA genes and two rRNA genes. A large block of repeats (~12.7 kb) was segregated in one region of the mitogenome, accounting for almost one third of the total size. A -spliced gene was first identified in mitogenome and was verified by RNA-seq and DNA-seq data. The massive expansion of tandem repeat size and - to -splicing shift could be explained by the high mitogenome rearrangement rates in haptophytes. Strict SNP calling based on deep transcriptome sequencing data suggested the lack of RNA editing in both organelles in this species, consistent with previous studies in other algal lineages. To gain insight into haptophyte mitogenome evolution, a comparative analysis of mitogenomes within haptophytes and among eight main algal lineages was performed. A core gene set of 15 energy and metabolism genes is present in haptophyte mitogenomes, consisting of 1 , 3 , 7 , 2 and 2 ribosomal genes. Gene content and order was poorly conserved in this lineage. Haptophyte mitogenomes have lost many functional genes found in many other eukaryotes including /, , , genes, which make it contain the smallest gene set among all algal taxa. All these implied the rapid-evolving and more recently evolved mitogenomes of haptophytes compared to other algal lineages. The phylogenetic tree constructed by genes of 204 algal mitogenomes yielded well-resolved internal relationships, providing new evidence for red-lineages that contained plastids of red algal secondary endosymbiotic origin. This newly assembled mitogenome will add to our knowledge of general trends in algal mitogenome evolution within haptophytes and among different algal taxa.
由于其富含岩藻黄质和多不饱和脂肪酸，定鞭藻被认为是一种很有前景的食品补充剂来源。在此，利用Illumina和PacBio测序平台相结合的方法对线粒体基因组（线粒体基因组）进行了测序。这个39258 bp的环状线粒体基因组共有46个基因，包括20个蛋白质编码基因、24个tRNA基因和2个rRNA基因。一大块重复序列（约12.7 kb）在线粒体基因组的一个区域中分离出来，几乎占总大小的三分之一。在该线粒体基因组中首次鉴定出一个A - 剪接基因，并通过RNA测序和DNA测序数据进行了验证。串联重复序列大小的大量扩展和 - 到 - 剪接的转变可以通过定鞭藻中较高的线粒体基因组重排率来解释。基于深度转录组测序数据的严格单核苷酸多态性（SNP）检测表明，该物种的两个细胞器中均不存在RNA编辑，这与之前在其他藻类谱系中的研究结果一致。为了深入了解定鞭藻线粒体基因组的进化，对定鞭藻内以及八个主要藻类谱系之间的线粒体基因组进行了比较分析。定鞭藻线粒体基因组中存在一个由15个能量和代谢基因组成的核心基因集，包括1个、3个、7个、2个和2个核糖体基因。该谱系中的基因含量和顺序保守性较差。定鞭藻线粒体基因组已经丢失了许多在许多其他真核生物中发现的功能基因，包括/、、、基因，这使得它在所有藻类分类群中拥有最小的基因集。所有这些都表明，与其他藻类谱系相比，定鞭藻的线粒体基因组进化迅速且较为新近。由204个藻类线粒体基因组的基因构建的系统发育树产生了分辨率良好的内部关系，为包含红藻次生内共生起源质体的红系谱系提供了新的证据。这个新组装的线粒体基因组将增加我们对定鞭藻内以及不同藻类分类群之间藻类线粒体基因组进化总体趋势的认识。
