Phylogenomic analysis of transcriptomic sequences of mitochondria and chloroplasts for marine red algae (Rhodophyta) in China

The chloroplast and mitochondrion of red algae （Phylum Rhodophyta） may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their evolutionary lin-eages by using red algal RNA-seq datasets of the 1 000 Plants （1KP） Project and publicly available complete genomes of mitochondria and chloroplasts of Rhodophyta. We have found that red algae were divided into three clades of orders, Florideophyceae, Bangiophyceae and Cyanidiophyceae. Taxonomy resolution for Class Florideophyceae showed that Order Gigartinales was close to Order Halymeniales, while Order Graci-lariales was in a clade of Order Ceramials. We confirmed Prionitis divaricata （Family Halymeniaceae） was closely related to the clade of Order Gracilariales, rather than to genus Grateloupia of Order Halymeniales as reported before. Furthermore, we found both mitochondrial and chloroplastic genes in Rhodophyta under negative selection （Ka/Ks〈1）, suggesting that red algae, as one primitive group of eukaryotic algae, might share joint evolutionary history with these two organelles for a long time, although we identified some dif-ferences in their phylogenetic trees. Our analysis provided the basic phylogenetic relationships of red algae, and demonstrated their potential ability to study endosymbiotic events.     

病毒感染海洋球石藻Emiliania huxleyi的转录组分析

海洋球石藻Emiliania huxleyi及其特异性裂解病毒E. huxleyi virus (EhVs)在调节海洋碳、硫循环及全球气候变化中起着重要作用,也是开展真核生物病毒–宿主相互作用研究的良好模型系统之一。为了探究病毒感染条件下E. huxleyi基因表达水平的变化,以海洋球石藻E. huxley–BOF 92及其专一性裂解病毒EhV-99B1为研究对象,利用Illumina HiSeq 2000高通量测序技术,分别对E. huxleyi病毒感染组(Exp)和非感染对照组(Con)6 h和45 h的藻细胞样品进行转录组测序分析。共得到32 909条平均长度为1 153 bp的基因。病毒感染6 h和45 h分别得到2 617和5 229个差异表达基因,其中共差异表达基因465个。随机选取10条差异表达基因,采用qRT-PCR进行实验验证,结果证实转录组分析可靠。GO功能注释和KEGG通路富集,发现大量基因与氧化应激反应、脂类代谢、碳水化合物代谢及信号转导等代谢过程相关,其中变化最显著的是谷胱甘肽代谢途径。从病毒感染球石藻转录组中筛选出部分与氧化应激反应相关的基因,其中9个基因显著上调,11个基因显著下调,表明宿主能够通过体内的氧化应激反应响应病毒胁迫。     

黄口荔枝螺转录组数据的微卫星标记开发与分析

以黄口荔枝螺转录组测序所得到的拼接序列为基础,利用MISA软件进行微卫星分析,利用Primer5.0设计引物160对。结果显示,83对引物能够成功扩增,引物在黄口荔枝螺渔山列岛群体多态性检测中发现,37个SSR位点能够表现出多态性,一共获得了129个等位基因,各位点等位基因数为2~5个,平均每个位点等位基因数为3.49个,观测杂合度H_o,期望杂合度H_e,多态信息含量PIC范围分别介于0.000~0.800、0.146~0.645、0.139~0.573之间,有9个表现为高度多态,20个表现为中度多态,8个表现为低度多态。实验结果进行Hardy-Weinberg平衡检测后,利用Bonferroni correction法进行校正,有29个位点显著偏离,结果表明渔山列岛黄口荔枝螺群体总体遗传多样性水平较低。     

中国短毛藻属Elachista(褐藻门)的分类学研究I.两个新种

本文对我国沿海岸采集的褐藻门（Phaeopyta）短毛藻科（Elachistaceae）短毛藻属（Elachista Duby）海藻进行了分类学研究。发现2个新种,即长海短毛藻E.changhaiensis Luan et Ding sp.nov.和暗色短毛藻E.fusca Luan et Ding sp.nov.。文中对此2个种的形态特征进行了较详细的特征描述,并对新种提供了相应的英语特征描述,以及较完整的其他分类学信息,与相似种进行了比较。长海短毛藻藻体黄褐色,长同化丝直径7~22 μm,多室囊长95~150 μm,由23~38个小室组成;短同化丝长200~350 μm,由11~24个细胞组成。暗色短毛藻藻体暗褐色,长同化丝直径8~14 μm,多室囊分枝,长75~150 μm,由27~39个小室组成;短同化丝着生于长同化丝的基部,长0.13~0.33 mm,由5~13个细胞组成。模式标本保存在中国科学院海洋研究所海洋生物标本馆（AST）。     

Distribution of green algal mats throughout shallow soft bottoms of the Swedish Skagerrak archipelago in relation to nutrient sources and wave exposure

Distribution and biomass of green algal mats were studied in marine shallow (0–1 m) soft-bottom areas on the Swedish west coast from 1994 to 1996, by combining aerial photography surveys with ground truth sampling. Filamentous green algae, dominated by species of the genera Cladophora and Enteromorpha, were generally present throughout the study area during July and August, and largely absent in late April and early May. These algae occurred at 60 to 90% of the locations investigated during the summer, and were estimated to cover between 30 and 50% of the total area of shallow soft bottoms of the Swedish Skagerrak archipelago. The distributional patterns were similar during the three years of the investigation and appeared unrelated to annual local nutrient inputs from point sources and river discharge. We postulate that the apparent lack of such a relationship is due to an altered state of nutrient dynamics throughout the archipelago. Mechanisms are likely to involve long-term, diffuse elevations in nutrient levels in coastal waters of the Skagerrak and the Kattegat over several decades leading to current eutrophic conditions, exceeding nutrient requirements for abundant filamentous algal growth. Patterns of algal abundance in our study were largely related to physical factors such as exposure to wind, waves and water exchange under conditions where nutrient loads among embayments seemed to be unlimited. Further, our results show that sediments covered by algal mats had higher carbon and nitrogen contents than unvegetated sediments. We hypothesise that sustained high nutrient loads, manifested in extensive biomass of filamentous algae during summer months, are re-mineralised via decay and sedimentation in the benthic realm. Hence, accumulated carbon and nutrients in the sediment could, in turn, constitute the basic pool for future algal mat production overlying soft bottoms in areas where tidal exchange is limited.     

中国南麂列岛产海洋底栖硅藻新种-南麂侧链藻(Pleurosira nanjiensis sp. nov.)的形态与分子系统学研究

本文描述了采自南麂列岛小柴屿岩相潮间带的一海洋底栖硅藻新种,南麂侧链藻（Pleurosira nanjiensis sp.nov.）。本研究使用光学显微镜和扫描电子显微镜对该种进行了形态学观察,并基于SSU rRNA和rbcL基因重建了其系统发育关系。南麂侧链藻具有壳面橄榄形、椭圆形或圆形,壳面隆起,单眼突出于壳表面,2–3个唇状突（rimportulae）,放射排列的线纹等特征,区别于其他侧链藻。     

广西北海金海湾红树林保护区自由生活海洋线虫联体线虫属（Comesoma）两个新记录种

在2021年春季对广西北海金海湾红树林保护区的自由生活海洋线虫进行分类和多样性研究中发现联体线虫属（Comesoma）国内2个新记录种,分别为百慕大联体线虫（Comesoma bermudense）和赫尔曼联体线虫（Comesoma hermani）,并对其特征进行了描述与图示。百慕大联体线虫主要特征为：4根头刚毛,长度为21~31 μm,4根亚头刚毛,长度为5~7 μm;虫体表皮具横排的侧分化点纹,颈部有不规则排列的颈刚毛;口腔前部膨大,底部角质化;螺旋状化感器,2.5圈;两条细长的交接器,弧长189~200 μm,引带没有突起,肛前附器乳突状;金海湾标本交接器弦长与尾长之比为0.7~0.9,大于其模式种的0.4~0.6。赫尔曼联体线虫主要特征为：口腔前部呈杯状,基部加厚,后部狭窄;螺旋状化感器,2.5圈;两条细长的交接器,弧长187~192 μm,引带没有突起;金海湾标本雄性体长约为2.2~2.4 mm,大于模式种的1.7~2.1 mm。该属物种在红树林湿地为首次报道。     

中国福建省红树林湿地中自由生活海洋线虫(联体线虫科)的2个新种

本文描述了中国福建省红树林湿地中自由生活海洋线虫的2个新种。Sabatieria conicoseta sp.nov.的主要特征是：具有短的锥形体刚毛、12-15个管状的肛前附器以及长度为12-15 μm的直的引带突起。Dorylaimopsis papilla sp.nov.的主要特征是：交接器中部具有角质化带状隔膜,近端头状具一小钩,其长度为肛门所在位置体直径的1.5–1.8倍,具有长度为37-40μm的背尾指向的引带突起。泄殖孔前具16-18个微型乳突状的肛前附器。     

基于转录组数据的青蛤微卫星标记开发与验证

本研究利用青蛤(Cyclina sinensis)的转录组信息开发微卫星标记,共获得12418个微卫星位点。其中单核苷酸重复次数最多,共8422个,占比67.08%;其次是三核苷酸重复,共1501个,占比12.09%;双核苷酸的重复有1419个,占比11.43%。在所有重复单元类型中,A/T重复出现频率最高,占单核苷酸重复的48.75%。随机选取81对引物进行微卫星标记验证,最终获得27个具有多态性的微卫星标记。对30个青蛤进行多态性位点检测和评价,共扩增到等位基因99个,每个位点的等位基因数Na为2~6个,期望杂合度He为0.0333~0.8085,观测杂合度Ho为0.0000~0.6786,多态信息含量(PIC)为0.0323~0.7645,有19个位点显著偏离Hardy-Weinberg平衡(p<0.01)。本研究开发的微卫星标记为青蛤的分子遗传学研究、种质鉴定和自然种群资源保护等研究提供了基础数据。     

不同饵料对植食性海水鱼——黄斑蓝子鱼的内脏器官特性及消化酶活性的影响

黄斑蓝子鱼（Siganus canaliculatus）是可养殖的少数植食性海水鱼之一。为进一步了解黄斑蓝子鱼的消化生理特征,以及将海藻更科学地应用于配合饲料中,本研究采用不同类型饵料：冰鲜杂鱼（Raw fish,RF）、配方饲料（Formulated diet,FD）、浒苔（Enteromorpha prolifra,EP）和龙须菜（Gracilaria lemaneiformis,GL）饲喂黄斑篮子鱼8周,分析鱼内脏特征及其消化酶活性的变化情况。研究结果显示：RF组和FD组鱼的肝体比和脏体比,以及EP组和GL组鱼的肠长比（Relative intestine length,RIL）,都显著高于其他组。此外,分析不同处理组鱼的肝和前肠组织形态结构,发现RF组肝细胞核被脂滴挤到细胞边缘,两海藻组前肠黏膜的皱褶程度最高。养殖前三周,鱼的消化酶活性变化波动明显,而之后消化酶活性趋于平稳。消化道的蛋白酶,脂肪酶和α-淀粉酶的水平分别随着日粮中蛋白质,脂肪和碳水化合物水平的变化而变化。虽然,海藻饵料显著降低了黄斑篮子鱼的胃蛋白酶活性,但是提高了机体RIL和前肠黏膜的皱褶程度以弥补其对胃蛋白酶的负面影响。以上结果表明黄斑蓝子鱼的消化系统可较好地适应不同类型的饵料,其适应时间大约为三周。因此,本研究结果也暗示黄斑蓝子鱼也具有一些杂食性鱼类的属性。     

中国海域长眼寄居蟹属两个新记录种

在我国南海海域大型底栖生物进行分类和多样性研究中,发现我国长眼寄居蟹属2个新记录种,紫斑长眼寄居蟹(Paguristes gonagrus)和条纹长眼寄居蟹(Paguristes runyanae),并对其进行描述。紫斑长眼寄居蟹采集自海南岛,主要特征为：螯足和步足密布刚毛,第一触角柄未达到角膜基部,螯足腕节、掌节背面刺和突起密集而发达,螯足和第二、三步足长节末端有紫色色斑;条纹长眼寄居蟹采集于西沙群岛,主要特征为：右螯足略大于左螯足,第一触角柄短,长度仅为眼柄长度的1/2,螯足和第二、三步足背腹面均有黄色条纹。     

浙江洞头岛自由生活线虫两个优势种的形态描述及其系统发育分析

为了了解浙江洞头岛自由生活线虫(Nematoda)的种类和多样性, 作者对该海域线虫进行分类研究, 发现了2个优势种并进行了重新描述。其中, 丑萨巴线虫(Sabatieria foetida Gagarin & Nguyen Vu Thanh, 2008)为一新纪录种, 主要特征为: 表皮具环状排列的小点, 有较大的点组成的侧装饰, 4根头刚毛较短(3~4 μm), 化感器呈螺旋状(2.5~3.0圈), 交接刺细长, 近端略膨大, 中间开始至远端变细(65~69 μm), 引带具直的引带突(20~25 μm), 具13~15个小的乳突状肛前辅器; 厦门后菱光线虫(Metachromadora xiamenensis Zhou, Zeng, Cai, Fu & Tan, 2020)特征为: 表皮具明显环纹, 4根头刚毛短且粗, 脊线由食道中部延伸至尾中部, 双环状化感器位于身体最前端, 交接刺近端具头状膨大(58~65 μm), 肛前辅器细管状(15个), 尾为短圆锥形。同时, 获得了两种线虫核糖体大亚基(LSU)的D2-D3片段序列数据, 构建了两种线虫基于贝叶斯推论法(Bayesian inference, BI)和最大似然法(maximum likelihood, ML)的系统发育树, 结果表明萨巴线虫属和后菱光线虫属表现出了多系进化的趋势。     

南极红藻Iridaea cordata和Curdiea racovitzae转录组分析及其极端光环境适应相关基因的挖掘

南极红藻具有重要的生态学功能和开发利用价值。南极极端环境赋予了其独特的生理耐受机制,也是发现新基因和代谢途径的理想材料。我们测序分析了南极产胶红藻Iridaea cordata (Turner) Bory和Curdiea racovitzae Hariot的转录组序列,并与其常温近缘种进行了比较,同时挖掘了其与光限制和强紫外线辐射等光环境适应相关的基因。I. cordata和C. racovitzae的转录组序列分别拼接成了14 055条和12 006条非冗余基因,平均长度分别为1 473 bp和1 448 bp。在I. cordata转录组中发现多条与绿藻基因同源的捕光复合物LHC基因Lhca2、Lhca6和Lhcb,并且在两种南极红藻中都各发现了1条编码结合岩藻黄质和Chl a/c蛋白的Lhcf基因,目前尚未在其他红藻中发现这类基因。光裂解酶修复紫外线诱导DNA损伤,在I. cordata的转录组序列中发现了6-4光裂解酶,光裂解酶CPD Ⅰ和CPD Ⅱ基因,而C. racovitzae转录组序列中仅找到了光裂解酶CPD Ⅱ基因。尽管南极红藻中这些特有基因的功能有待进一步的验证,但...     

Phylogenomic analysis of transcriptomic sequences of mitochondria and chloroplasts of essential brown algae (Phaeophyceae) in China

The chloroplast and mitochondrion of brown algae （Class Phaeophyceae of Phylum Ochrophyta） may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their evolutionary lineages by using algal RNA-seq datasets of the 1 000 Plants （1KP） Project and publicly available complete genomes of mitochondria and chloroplasts of Kingdom Chromista. We have found that there is a split between Class Phaeophyceae of Phylum Ochrophyta and the others （Phylum Cryptophyta and Haptophyta） in Kingdom Chromista, and identified more diversity in chloroplast genes than mitochondrial ones in their phylogenetic trees. Taxonomy resolution for Class Phaeophyceae showed that it was divided into Laminariales-Ectocarpales clade and Fucales clade, and phylogenetic positions of Kjellmaniella crassi-folia, Hizikia fusifrome and Ishige okamurai were confirmed. Our analysis provided the basic phylogenetic relationships of Chromista algae, and demonstrated their potential ability to study endosymbiotic events.