西太平洋浮游有孔虫Globigerinita glutinata种内SSU rDNA多样性研究
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摘要
有孔虫分子鉴定和分子多样性研究多基于SSU rDNA序列片段分析,但某些浮游种内可能存在基因组内rDNA变化,影响分类学和分子生态学的研究结果。为了研究浮游有孔虫物种内是否存在rDNA多样性,本工作以采自热带西太平洋的浮游有孔虫Globigerinita glutinata活体标本作为研究对象,经形态学鉴定后,利用单细胞PCR和克隆技术,获得5个虫体的20条SSU rDNA目的片段(300—400 bp),同时对其序列结构进行了研究。结果显示,同种G.glutinata出现了四类不同的SSU rDNA核酸类型。序列成对分析显示,该种遗传距离差异最长可达0.249,远高于其它物种。此外,同一样本不同克隆片段中,出现了高达四个不同的SSU rDNA核酸型。序列的差异主要集中在三个不同的高变异区,高可变区的长度范围为21 bp到63 bp。从差异序列的间隔分布推断,核糖体基因簇的重组可能是不同SSU rDNA核酸型出现的原因。本工作在国内首次揭示了热带西太平洋浮游有孔虫G.glutinata种内的SSU rD NA核酸型,研究结果表明G.glutinata的种内SSU rDNA变异性极大,复杂的生活史以及假基因的存在或许是造成该现象的原因。
SSU rDNA are widely used as molecular marker for classification and diversity of foraminifera. Some planktonic foraminifera may have varieties in intra-genomic SSU rDNA, which will affect the results of studies on taxo-nomy and molecular ecology. In order to understand the intra-specific SSU rDNA diversity in planktonic foraminifera, we studied 5 living individuals of Globigerinita glutinata from the western Pacific Ocean. After morphological identification, single-cell PCR and cloning, totally 20 partial SSU rDNA sequences were obtained. Sequencing analyses results showed that there were 4 different ribosomal types occurred in the 5 individuals. Genetic distance between each paired up to 0.249, and it is much higher than that in the other species. Unexpectedly,4 ribosomal types were existed in the same individual. In addition, the sequence differences of G. glutinata mainly occurred in 3 highly variable regions which were ranged from 21 bp to 63 bp. Recombination of ribosome gene cluster in G. glutinata may lead to mosaic distribution of high variable region, and cause the variety of SSU rDNA. Our research results indicated that the intra-specific SSU rDNA variability of G. glutinata was rather large. We presumed that the complex life history and the existence of "pseudogene" might contribute the increasing variability of SSU rDNA in G. glutinata.
SSU rDNA are widely used as molecular marker for classification and diversity of foraminifera. Some planktonic foraminifera may have varieties in intra-genomic SSU rDNA, which will affect the results of studies on taxo-nomy and molecular ecology. In order to understand the intra-specific SSU rDNA diversity in planktonic foraminifera, we studied 5 living individuals of Globigerinita glutinata from the western Pacific Ocean. After morphological identification, single-cell PCR and cloning, totally 20 partial SSU rDNA sequences were obtained. Sequencing analyses results showed that there were 4 different ribosomal types occurred in the 5 individuals. Genetic distance between each paired up to 0.249, and it is much higher than that in the other species. Unexpectedly,4 ribosomal types were existed in the same individual. In addition, the sequence differences of G. glutinata mainly occurred in 3 highly variable regions which were ranged from 21 bp to 63 bp. Recombination of ribosome gene cluster in G. glutinata may lead to mosaic distribution of high variable region, and cause the variety of SSU rDNA. Our research results indicated that the intra-specific SSU rDNA variability of G. glutinata was rather large. We presumed that the complex life history and the existence of "pseudogene" might contribute the increasing variability of SSU rDNA in G. glutinata.
引文
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李小艳,翦知湣,石学法等,2012.全新世东海内陆架泥质区有孔虫特征及其古环境意义.海洋地质与第四纪地质,32(4):61-71
李保华,李铁刚ERTAN K T等,2007.西北太平洋浮游有孔虫的SSU rDNA序列及其古海洋学意义.自然科学进展,17(3):391-395
李铁刚,江波,孙荣涛等,2007.末次冰消期以来东黄海暖流系统的演化.第四纪研究,27(6):945-954
杨艺萍,唐灵刚,向荣等,2017.东沙西南海域表层沉积物底栖有孔虫群落特征及其对冷泉活动的指示意义.微体古生物学报,34(3):237-246
杨晓玲,施苏华,唐恬,2010.新一代测序技术的发展及应用前景.生物技术通报,(10):76-81
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张彤,方汉平,2003.微生物分子生态技术:16S rRNA/DNA方法.微生物学通报,30(2):97-101
赵泉鸿,翦知湣,张在秀等,2009.东海内陆架泥质沉积区全新世古环境变迁:有孔虫证据.海洋地质与第四纪地质,(2):79-86
翦知湣,李保华,王吉良等,2003.从微体化石看西太平洋暖池的形成与演化.第四纪研究,23(2):185-192
翦知湣,陈荣华,李保华等,1996.冲绳海槽南部20ka来深水底栖有孔虫的古海洋学记录.中国科学:地球科学,(5):467-473
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GRIBBLE K,ANDERSON D,2007.High individual,intraspecific,interspecific variability in large-subunit ribosomal DNA in the heterotrophic dinoflagellates Protoperidinium,Diplosalis,and Preperidinium (Dinophyceae).Phycologia,46(3):315-324
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刘健,王红,李绍全等,2004.南黄海北部泥质沉积区冰后期海侵沉积记录.海洋地质与第四纪地质,24(3):1-10
孙荣涛,李铁刚,常凤鸣等,2015.基于底栖有孔虫转换函数的南黄海近岸古环境演化过程定量重建.中国科学:地球科学,45(9):1383-1393
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李保华,李铁刚ERTAN K T等,2007.西北太平洋浮游有孔虫的SSU rDNA序列及其古海洋学意义.自然科学进展,17(3):391-395
李铁刚,江波,孙荣涛等,2007.末次冰消期以来东黄海暖流系统的演化.第四纪研究,27(6):945-954
杨艺萍,唐灵刚,向荣等,2017.东沙西南海域表层沉积物底栖有孔虫群落特征及其对冷泉活动的指示意义.微体古生物学报,34(3):237-246
杨晓玲,施苏华,唐恬,2010.新一代测序技术的发展及应用前景.生物技术通报,(10):76-81
汪品先,1988.东海底质中的有孔虫和介形虫.海洋出版社.1-307
宋岩,1983.浮游有孔虫具有惊人的再生能力.海洋科学,3:10
张彤,方汉平,2003.微生物分子生态技术:16S rRNA/DNA方法.微生物学通报,30(2):97-101
赵泉鸿,翦知湣,张在秀等,2009.东海内陆架泥质沉积区全新世古环境变迁:有孔虫证据.海洋地质与第四纪地质,(2):79-86
翦知湣,李保华,王吉良等,2003.从微体化石看西太平洋暖池的形成与演化.第四纪研究,23(2):185-192
翦知湣,陈荣华,李保华等,1996.冲绳海槽南部20ka来深水底栖有孔虫的古海洋学记录.中国科学:地球科学,(5):467-473
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ANDRé A,QUILLéVéRé F,MORARD R et al.,2014.SSU rDNA divergence in planktonic foraminifera:molecular taxonomy and biogeographic implications.Plos One,9(8):e104641
AURAHS R,GRIMM G W,HEMLEBEN V et al.,2009.Geographical distribution of cryptic genetic types in the planktonic foraminifer Globigerinoides ruber.Molecular Ecology,18(8):1692-1706
BASS D,HOWE A T,MYLNIKOV A P et al.,2009.Phylogeny and classification of Cercomonadida (Protozoa,Cercozoa):Cercomonas,Eocercomonas,Paracercomonas,and Cavernomonas gen.nov.Protist,160(4):483
CARON D A,COUNTWAY P D,SAVAI P et al.,2009.Defining DNA-based operational taxonomic units for microbial-eukaryote ecology.Applied & Environmental Microbiology,75(18):5797-5808
CIARDO D E,SCH?R G,B?TTGER E C et al.,2006.Internal transcribed spacer sequencing versus biochemical profiling for identification of medically important yeasts.Journal of Clinical Microbiology,44(1):77-84
COLLINS N E,ALLSOPP B A,1999.Theileria parva ribosomal internal transcribed spacer sequences exhibit extensive polymorphism and mosaic evolution:application to the characterization of parasites from cattle and buffalo.Parasitology,118(Pt 6)(6):541
DOVER G,1982.Molecular drive:a cohesive mode of species evolution.Nature,299(5879):111-117
FIORE-DONNO A M,2010.Invalidation of Hyperamoeba by transferring its species to other genera of Myxogastria.Journal of Eukaryotic Microbiology,57(2):189-196
GL?CKNER G,HüLSMANN N,SCHLEICHER M et al.,2014.The genome of the foraminiferan Reticulomyxa filosa.Current Biology,24(1):11-18
GONG J,DONG J,LIU X et al.,2013.Extremely high copy numbers and polymorphisms of the rDNA operon estimated from single cell analysis of oligotrich and peritrich ciliates.Protist,164(3):369
GRIBBLE K,ANDERSON D,2007.High individual,intraspecific,interspecific variability in large-subunit ribosomal DNA in the heterotrophic dinoflagellates Protoperidinium,Diplosalis,and Preperidinium (Dinophyceae).Phycologia,46(3):315-324
GROSHENY D,1989.Modern planktonic foraminifera.Geobios,22(4):545
GUNDERSON J H,SOGIN M L,WOLLETT G et al.,1987.Structurally distinct,stage-specific ribosomes occur in Plasmodium.Science,238(4829):933-937
GUPTAB,BARUN K,2003.Modern Foraminifera.Dordrecht:Kluwer Academic Publishers.1-368
HOLZMANN M,PAWLOWSKI J,1996a.Preservation of Forami-nifera for DNA extraction and PCR amplification.Journal of Foraminiferal Research,26(3):264-267
HOLZMANN M,PILLER W,PAWLOWSKI J,1996b.Sequence variations in the large-subunit ribosomal RNA gene of Ammonia (Foraminifera,Protozoa) and their evolutionary implications.Journal of Molecular Evolution,43(2):145-151
JIAN Z,CHEN R,LI B,1996.Paleoceanographic records of benthic foraminifera from deep water in the southern Okinawa since 20ka.Scientia Sinica Terrae,(5):467-473(in Chinese)
JIAN Z,LI B,WANG J,2003.Formation and evolution of the western pacific warm pool recorded by microfossils.Quaternary Sciences,23(2):185-192(in Chinese)
JOSEPH S,GUPTA A K,1999.New Species of benthic foramini-fera from the neogene sequence of ODP sites 757B and 758A,northeastern Indian Ocean.Micropaleontology,45(2):221-224
LEFFERS H,ANDERSEN A H,1993.The sequence of 28S ribosomal RNA varies within and between human cell lines.Nucleic Acids Research,21(6):1449
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