Characterization of genome-wide microsatellites of <Emphasis Type="Italic">Saccharina japonica</Emphasis> based on a preliminary assembly of Illumina sequencing reads

Microsatellites or simple sequence repeats (SSR) function widely and locate dependently in genome. However, their characteristics are often ignored due to the lack of genomic sequences of most species. Kelp (Saccharina japonica), a brown macroalga, is extensively cultured in China. In this study, the genome of S. japonica was surveyed using an Illumina sequencing platform, and its microsatellites were characterized. The preliminarily assembled genome was 469.4 Mb in size, with a scaffold N₅₀ of 20529 bp. Among the 128370 identified microsatellites, 90671, 25726 and 11973 were found in intergenic regions, introns and exons, averaging 339.3, 178.8 and 205.4 microsatellites per Mb, respectively. These microsatellites distributed unevenly in S. japonica genome. Mononucleotide motifs were the most abundant in the genome, while trinucleotide ones were the most prevalent in exons. The microsatellite abundance decreased significantly with the increase of motif repeat numbers, and the microsatellites with a small number of repeats accounted for a higher proportion of the exons than those of the intergenic regions and introns. C/G-rich motifs were more common in exons than in intergenic regions and introns. These characteristics of microsatellites in S. japonica genome may associate with their functions, and ultimately their adaptation and evolution. Among the 120140 pairs of designed microsatellite primers, approximately 75% were predicted to be able to amplify S. japonica DNA. These microsatellite markers will be extremely useful for the genetic breeding and population evolution studies of kelp.     

Cloning and characterization of a delta-6 desaturase encoding gene from Nannochloropsis oculata

A gene(NANOC-D6D) encoding a desaturase that removes two hydrogen atoms from fatty acids at delta 6 position was isolated from a cDNA library of Nannochloropsis oculata(Droop) D.J.Hibberd(Eustigmatophyceae).The unicellular marine microalga N.oculata synthesizes rich long chain polyunsaturated fatty acids(LCPUFAs),including eicosapentaenoic acid(20:5n-3,EPA).The deduced protein contains 474 amino acids that fold into 4 trans-membrane domains.The neighbor-joining phylogenetic tree indicates that NANOC-D6D is ...     

Molecular Grouping of Grateloupia Tissues Collected Along Chinese Coast and Microsatellite Diversity Analysis of G. asiatica

Genus Grateloupia is one of the most speciose genera in family Halymeniales. It is also one of the sources for natural materials, food and medicine. With different environments, Grateloupia change their morphological characteristics, making their morphological identification very difficult. In addition, few of the species diversity in this genus has been described before. In this study, phylogenetic analysis based on rbc L gene sequence was employed to group Grateloupia collected from three locations along Chinese coast. The microsatellites were also used to evaluate their genetic diversity. In total, the tissue parts of 6 putative species were collected from G. asiatica, G. livida, G. lanceolate, G. catenata, G. turuturu and G. filicina. In order to evaluate their genetic diversity and then conserve them better, 40 microsatellites available for Grateloupia were used to evaluate their genetic diversity, and 11 microsatellites were found to be applicable to determine the genetic diversity of G. asiatica. It was found that the genetic diversity of G. asiatica around Qingdao was very rich. We suggested that the species of genus Grateloupia should be identified based on rbc L phylogenetic analysis before the diversity evaluation with microsatellites. The microsatellites should be developed for each species of Grateloupia so that their genetic diversity can be evaluated appropriately.     

我国引种海带(Laminaria japonica)和长海带(L.longissima)配子体克隆的随机扩增多态性DNA分析

运用RAPD技术,对引种我国的海带(Laminaria japonica)和长海带(L.longissima)的22个配子体克隆进行分析。筛选的19条随机引物共获得252个位点.扩增片段大小在200～2000bp之间,多态性位点228个,占90.5%。配子体克隆遗传变异分析表明,长海带和海带的遗传多样性都比较高,两者之间的遗传分化较为明显,且种间变异大于种内变异。长海带和海带雄配子体克隆的遗传变异程度均低于雌配子体克隆。另外,两个种的雌、雄配子体之间均存在一定程度的分化,且长海带雌、雄配子体之间的遗传分化大于海带配子体。     

Identification of Microplankton in South China Sea with Image-Matching Individual PCR

In this study, marine microplankton were identified by combining standard light microscopy with Sanger 18S rRNA gene sequencing. The image-matching individual PCR technique was applied to identify the image collectable unicellular microplankton to genera. Instead of pure strain culture and morphological identification, microplankton individual cells were isolated and fixed with glutaraldehyde, frozen and stored for months. Finally, they were imaged under a microscope and molecularly identified via phylogenetic analysis of their 18S ribosomal RNA gene(18S rDNA). Microplankton cells were collected at 30 locations in South China Sea, and were assigned to 21 known and 4 unidentified genera(2 uncultured fungi and 2 uncultured stramenopiles) with phylogenetic analysis in parallel to the morphological identification.     

长菱形藻(Nitzschia longissima)和新月细柱藻(Cylindrotheca closterium)分子分类研究

本研究自胶州湾分离了两种底栖硅藻,形态学初步鉴定为长菱形藻和新月细柱藻。对其18S rDNA和rbcL基因进行了测序并用邻接法构建了系统树。结果表明,两藻在18S rD-NA和rbcL基因序列上均存在较大的差异,基于DNA序列的分类结果与形态学分类结果一致。在依据形态指标难以确定藻类分类地位的情况下,18S rDNA和rbcL基因序列是有用的鉴定工具。     

Cryopreservation of Gametophytes of Laminaria japonica （Phaeophyta） Using Encapsulation-Dehydration with Two-Step Cooling Method

Gametophytes of Laminaria japonica were cryopreserved in liquid nitrogen using encapsulation-dehydration with two-step cooling method. Gametophytes cultured at 10℃ and under continuous irradiance of 30 μmol m-2 s-1 for 3 weeks were encapsulated in calcium alginate beads. The beads were dehydrated in 0.4 molL-1 sucrose prepared with seawater for 6 h, desiccated in an incubator set at 10℃ and 70% relative humidity for 4 h, pre-frozen at either -40℃ or -60℃ for 30 min, and stored in liquid nitrogen for ＞24 h. As high as 43% of survival rate was observed when gametophytes were thawed by placing the beads in 40℃seawater and re-hydrated in 0.05 molL-1 citrate sodium prepared using 30‰ NaC1 7 d later. More cells of male gametophytes survived the whole procedure in comparison with female gametophytes. The cells of gametophytes surviving the preservation were able to grow asexually and produce morphologically normal sporophytes.