Taxonomic re-examination of Chlamydomonas strains maintained in the NIES-Collection
Taxonomic re-examination of Chlamydomonas strains maintained in the NIES-Collection
复制标题
DOI：
--
复制
发表时间：
2013-06
期刊：
影响因子：
--
通讯作者：
K. Yumoto;F. Kasai;M. Kawachi
中科院分区：
文献类型：
--
作者：
K. Yumoto;F. Kasai;M. Kawachi
chlamydomonas属（Vo lvoca le s，绿藻科）包含大量物种（超过600种），利用18S rRNA和叶绿体基因进行的分子系统发育分析表明其具有多系性（Buchheim et al., 1997; Hoham et al., 2002; Nozaki et al., 1998; Pröschold et al., 2001）。在以前的研究中，尽管分支之间的关系并不总是很好地解决，但该属内的主要分支是明确的，并且在很大程度上是一致的，（Buchheim等人，1997；Nakada等人，2008；Pröschold等人，2001）。Pröschold et al.（2001）在这些谱系的基础上进行了几次分类修订，并提出了两个新属，但完成该属的分类修订预计需要相当长的时间。在这种情况下，Nakada et al.（2008）基于18S rRNA序列，对包括衣藻在内的卷藻门进行了全面的分子分析，并对其进行了分析，结果表明，该序列是基于18S rRNA序列，而不是基于18S rRNA序列，而不是基于18S rRNA序列，因此，Nakada et al. （Cantino & de Queiroz, 2010）对卷藻门进行了明确定义。在PhyloCode系统中，应用于进化支的名称是根据系统发育关系来定义的（Cantino & de Queiroz, 2010）。因此，我们认为Nakada等人（2008）根据PhyloCode在系统发育上定义的亚群是指示日本筑波国立环境研究所（NIESCollection）微生物培养收集中保存的单个衣藻菌株适当分类位置的最佳方法。衣藻是一种常见的生物，对土壤和水（淡水和海洋）环境中的藻类生物多样性做出了贡献，它们也出现在酸性池塘和雪表面等极端环境中。一些衣藻菌株也被用作基因组学、遗传学、生理学和发育生物学等许多领域基础研究的模型（Harris, 2009）。nises收藏了80多个衣藻菌株，其中大部分是在2007年东京大学IAM收藏关闭时从该收藏转移过来的，有些是作为衣藻物种保存的，没有进行物种水平鉴定。虽然已经发表了大约10株衣单胞菌的18S rDNA序列，但nis收集的大多数衣单胞菌没有分子系统发育数据（Nakada et al., 2010; Nakada & Tomita, 2011）。因此，为了更好地对NIESCollection中的衣藻菌株进行分类表征，我们对其18S rDNA进行了测序，确定了其系统发育位置，并将其分配到Nakada等人（2008）定义的亚群中。同样值得注意的是，已经发表了30株与NIES菌株同源的菌株的18S rDNA序列，并在其他培养物中保存。因此，我们研究了菌株历史和已发表的序列数据，以确认这些菌株的分类身份，并排除了在长期传代培养过程中可能被其他菌株取代的菌株。
INTRODUCTION The genus Ch lamydomonas (Vo lvoca l e s , Chlorophyceae) comprises a large number of species (more than 600), and molecular phylogenetic analyses using 18S rRNA and chloroplast genes have shown it to be polyphyletic (Buchheim et al., 1997; Hoham et al., 2002; Nozaki et al., 1998; Pröschold et al., 2001). In previous studies, the principal clades within the genus were clearly, and for the most part consistently, distinguished, although the relationships among the clades have not always been well resolved (Buchheim et al., 1997; Nakada et al., 2008; Pröschold et al., 2001). On the basis of these lineages, Pröschold et al. (2001) performed several taxonomic revisions and proposed two new genera, but the completion of the taxonomic revision of the genus is expected to take considerable time. Under such circumstances, Nakada et al. (2008) performed comprehensive molecular analyses of Volvocales, including Chlamydomonas species, based on the 18S rRNA g e n e s e q u e n c e , a n d a d o p t e d P h y l o C o d e (International Code of Phylogenetic Nomenclature, Cantino & de Queiroz, 2010) to explicitly define individual clades. In the PhyloCode system, names applied to clades are defined in terms of phylogenetic relationships (Cantino & de Queiroz, 2010) . Accordingly, we consider the subgroups that were phylogenetically defined by Nakada et al. (2008) by following the PhyloCode to be the best way for indicating the appropriate taxonomic positions of individual Chlamydomonas strains maintained in the Microbial Culture Collection at the National Institute for Environmental Studies, Tsukuba, Japan (NIESCollection). Various Chlamydomonas species are familiar organisms that contribute to the algal biodiversity in soil and water (both freshwater and marine) environments, and they also occur in extreme environments such as acidic ponds and snow surfaces. Some Chlamydomonas strains are also used as models in basic research in many fields, such as genomics, genetics, physiology, and developmental biology (Harris, 2009). The NIES-Collection holds more than 80 Chlamydomonas strains, most of which were transferred from the University of Tokyo’s IAM Collection in 2007, when the collection was closed, and some were deposited as Chlamydomonas species without species level identification. No molecular phylogenetic data are available for most of the Chlamydomonas strains in the NIES-Collection, although the 18S rDNA sequences of approximately 10 strains have been published (Nakada et al., 2010; Nakada & Tomita, 2011). Therefore, to better characterize the Chlamydomonas strains in the NIESCollection taxonomically, we sequenced their 18S rDNA, determined their phylogenetic positions, and assigned them to the subgroups defined by Nakada et al. (2008). Also of note, 18S rDNA sequences have been published for 30 strains that originated from the same strains as the NIES strains and have been maintained in other culture collections. Therefore, we investigated the strain histories and the published sequence data to confirm the taxonomic identity of these strains and to exclude the strains that may have been replaced by other strains during long-term subculturing.