Evaluation of a novel 16S rRNA/tRNA mitochondrial marker for the identification and phylogenetic analysis of shrimp species belonging to the superfamily Penaeoidea

In this study, we infer the phylogenetic relationships within commercial shrimp using sequence data from a novel mitochondrial marker consisting of an approximately 530-bp region of the 16S ribosomal RNA (rRNA)/transfer RNA (tRNA)^Val genes compared with two other mitochondrial genes: 16S rRNA and cytochrome c oxidase I (COI). All three mitochondrial markers were considerably AT rich, exhibiting values up to 78.2% for the species Penaeus monodon in the 16S rRNA/tRNA^Val genes, notably higher than the average among other Malacostracan mitochondrial genomes. Unlike the 16S rRNA and COI genes, the 16S rRNA/tRNA^Val marker evidenced that Parapenaeus is more closely related to Metapenaeus than to Solenocera, a result that seems to be more in agreement with the taxonomic status of these genera. To our knowledge, our study using the 16S rRNA/tRNA^Val gene as a marker for phylogenetic analysis offers the first genetic evidence to confirm that Pleoticus muelleri and Solenocera agassizi constitute a separate group and that they are more related to each other than to genera belonging to the family Penaeidae. The 16S rRNA/tRNA^Val region was also found to contain more variable sites (56%) than the other two regions studied (33.4% for the 16S rRNA region and 42.7% for the COI region). The presence of more variable sites in the 16S rRNA/tRNA^Val marker allowed the interspecific differentiation of all 19 species examined. This is especially useful at the commercial level for the identification of a large number of shrimp species, particularly when the lack of morphological characteristics prevents their differentiation.     

Application of mitochondrial control region in population genetic studies of the shrimp Penaeus

This study reports a primer set for amplifying a partial fragment of about 610 bp in the fast mutating mitochondrial control region in shrimps of the genus Penaeus (Decapoda: Penaeidae). The utility of this amplified fragment for studying population differentiation and structuring, compared with more conservative mitochondrial genes (16S rRNA and COI), was explored in P. merguiensis populations over a vast geographical range based on sequence and RFLP analyses. The results indicate that the mitochondrial control region provides more informative sites and reveals more haplotypes, making it most useful for evaluating genetic variations within and between populations of Penaeus species.     

Phylogeny and biogeography of the freshwater crab genus Johora (Crustacea: Brachyura: Potamidae) from the Malay Peninsula, and the origins of its insular fauna

The phylogeny and biogeography of the Malayan freshwater crab genus Johora was studied using two mitochondrial genes, 16S rRNA (560 bp) and cytochrome oxidase subunit I (COI) (616 bp), and one nuclear gene, histone 3 (H3) (328 bp). Johora is shown to be monophyletic and composed of three clades that correspond with the topography of the Malay Peninsula. The three clades were estimated to be of similar age ( c . 11 million years ago (mya)). The Malayan island of Pulau Tioman (with five species) was determined to have been colonised independently by two separate clades (at c . 11 and 5 mya, respectively), one of which evolved semiterrestrial habits, possibly in response to competition by the second. A partitioned Bremer support (PBS) analysis reveals that most of the support for the phylogenetic tree comes from the COI gene fragment and that the nuclear protein-encoding genes H3 is useful for reconstructing the relationships of Johora .     

米尔顿姬小蜂线粒体16SrRNA与COI基因片段序列测定及分析

【背景】米尔顿姬小蜂是一种入侵我国台湾地区的植食性小蜂,能够严重影响水果的产量和食用价值。目前在我国大陆没有分布,由于其个体微小,与近似种区别较小,通过传统的形态学分类方法难以鉴定,因此有必要研究其基因片段序列,探讨分子鉴定方法。【方法】利用PCR方法扩增并测定了米尔顿姬小蜂线粒体16SrRNA和COI基因的部分序列,并对各序列的碱基组成进行了分析。然后根据COI基因部分序列,利用DNAMAN的MaximumLikelihood方法构建了米尔顿姬小蜂与膜翅目其他科的系统发育树。【结果】16SrRNA基因的PCR扩增产物为426bp,COI基因的PCR扩增产物为488bp。通过测序获得米尔顿姬小蜂16SrRNA和COI基因部分序列,序列分析表明,16SrRNA和COI基因的A＋T含量均较高,存在较强的A＋T偏向性。系统发育树显示,米尔顿姬小蜂与蚜小蜂科的Encarsiaberlesei亲缘关系最近,与姬小蜂科的Chrysocharisnautius、C．eurynota亲缘关系较远。【结论与意义】本研究为米尔顿姬小蜂的分子鉴定提供了依据。     

Molecular phylogenetic analysis of white prawns species and the existence of two clades in Penaeus merguiensis

Closely related species, Penaeus merguiensis and Penaeus silasi from Thai waters, were genetically examined using variation observed in 558 base pairs (bp) of sequence from cytochrome oxidase subunit I (COI) gene of mtDNA. The sequence divergences of COI between P. merguiensis and other Penaeus species were 5.76-6.15% (P. silasi), 13.17-13.97% (Penaeus indicus), 16.43% (Penaeus vannamei), 16.63% (Penaeus monodon), and 18.37% (Penaeus japonicus). From the alignment reported that there were four clades on phylogenetic tree, the distinction of the two monophyletic clades was referred as P. merguiensis, one monophyletic clade within P. silasi and P. indicus. These results point toward the possibility of P. merguiensis being a complex of two cryptic species or a single species with strong phylogeographic subdivision.     

Evolution, biogeography, and the utility of mitochondrial 16s and COI genes in phylogenetic analysis of the crab genus Austinixa (Decapoda: Pinnotheridae)

This study used molecular data (mitochondrial 16s and COI) for the first time to explore evolutionary relationships among species of the pinnotherid crab genus Austinixa. Low levels of phylogenetic signal were detected for COI. High levels of phylogenetic signal were detected for 16s, indicating it is a more useful marker for inferring species level phylogenies in Austinixa. Phylogeographic patterns among species of Austinixa are consistent with allopatric speciation due to numerous climatic and oceanographic fluctuations during the last 5-6 my. In addition, all but two species have been derived since the closure of the Isthmus of Panama, a pattern consistent with hypotheses that the marine biota of the Caribbean and southeastern North America underwent a pulse of biotic turnover within the last 2-3 my. Austinixa aidae and Austinixa hardyi had identical 16s sequences, and differed by only 2 bp in COI, raising questions about the validity of A. hardyi as a distinct species.     

日本囊对虾4个地理群体线粒体16S rRNA序列及遗传结构分析

对我国东南沿海日本囊对虾(Marsupenaeus japonicus)的4个地理群体广东群体(GD)、台湾群体(TW)、福建群体(FJ)和浙江群体(ZJ)的线粒体16S rRNA基因片段进行PCR扩增,对产物进行测序后分析。经比对获得470bp的核苷酸分析序列,发现了16个变异位点,得到了10种单倍型。广东、台湾、福建和浙江群体的核苷酸多样性依次分别为0.0008、0.0010、0.0051、0.0015,各群体均存在独有的单倍型和共有单倍型。群体遗传距离分析表明各群体间保持着一定的遗传差异,其中福建群体与其他群体之间存在着较远的遗传距离并保持了较高的遗传多样性。另外,利用其423bp的16S rRNA同源序列探讨了对虾科6个属共12种对虾的系统进化关系,囊对虾属与沟对虾属亲缘关系较近聚为一支,其他4个属的10种对虾聚为一支。     

Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians

BACKGROUND: Identifying species of organisms by short sequences of DNA has been in the center of ongoing discussions under the terms DNA barcoding or DNA taxonomy. A C-terminal fragment of the mitochondrial gene for cytochrome oxidase subunit I (COI) has been proposed as universal marker for this purpose among animals. RESULTS: Herein we present experimental evidence that the mitochondrial 16S rRNA gene fulfills the requirements for a universal DNA barcoding marker in amphibians. In terms of universality of priming sites and identification of major vertebrate clades the studied 16S fragment is superior to COI. Amplification success was 100% for 16S in a subset of fresh and well-preserved samples of Madagascan frogs, while various combination of COI primers had lower success rates.COI priming sites showed high variability among amphibians both at the level of groups and closely related species, whereas 16S priming sites were highly conserved among vertebrates. Interspecific pairwise 16S divergences in a test group of Madagascan frogs were at a level suitable for assignment of larval stages to species (1-17%), with low degrees of pairwise haplotype divergence within populations (0-1%). CONCLUSION: We strongly advocate the use of 16S rRNA as standard DNA barcoding marker for vertebrates to complement COI, especially if samples a priori could belong to various phylogenetically distant taxa and false negatives would constitute a major problem.     

Detection of hepatopancreatic parvovirus (HPV) in wild shrimp from India by nested polymerase chain reaction (PCR)

The prevalence of hepatopancreatic parvovirus (HPV) in wild penaeid shrimp samples from India was studied by nested polymerase chain reaction (PCR) using primers designed in our laboratory. The virus could be detected in 9 out of 119 samples by non-nested PCR. However, by nested PCR 69 out of 119 samples were positive. The PCR results were confirmed by hybridization with digoxigenin-labelled DNA probe. Shrimp species positive by non-nested PCR included Penaeus monodon, Penaeus indicus and Penaeus semisulcatus and by nested PCR Parapenaeopsis stylifera, Penaeus japonicus, Metapenaeus monoceros, M. affinis, M. elegans, M. dobsoni, M. ensis and Solenocera choprai. This is the first report on the prevalence of HPV in captured wild shrimp from India.     

Molecular phylogeny of penaeid shrimps inferred from two mitochondrial markers

Penaeid shrimps are an important resource in crustacean fisheries, representing more than the half of the gross production of shrimp worldwide. In the present study, we used a sample of wide-ranging diversity (41 shrimp species) and two mitochondrial markers (758 bp) to clarify the evolutionary relationships among Penaeidae genera. Three different methodologies of tree reconstruction were employed in the study: maximum likelihood, neighbor joining and Bayesian analysis. Our results suggest that the old Penaeus genus is monophyletic and that the inclusion of the Solenocera genus within the Penaeidae family remains uncertain. With respect to Metapenaeopsis monophyly, species of this genus appeared clustered, but with a nonsignificant bootstrap value. These results elucidate some features of the unclear evolution of Penaeidae and may contribute to the taxonomic characterization of this family.     

Molecular phylogeny of a red-snow-crab species complex using mitochondrial and nuclear DNA markers

Nucleotide sequence variation of mitochondrial DNA COI and nuclear rRNA gene regions was used to reconstruct phylogenetic relationships for the red-snow-crab species complex, including the red snow crab, Chionoecetes japonicus, its nominal subspecies, C. japonicus pacificus, and the triangle tanner crab, C. angulatus. The topologies of the Bayesian and neighbor-joining (NJ) trees of the COI and of NJ trees of rRNA sequences placed C. japonicus and C. angulatus in a single clade. The net sequence divergence between these taxa was d(net) = 0.000 in COI, and strongly suggests that these taxa represent a single species. In contrast, haplotypes in C. j. pacificus clustered separately from the C. japonicus - C. angulatus clade. Net sequence divergence from C. japonicus - C. angulatus to C. j. pacificus was d(net) = 0.026 in COI, indicating that C. j. pacificus should be elevated to a separate species, C. pacificus. A 165 bp insert appeared in the rRNA gene of C. j. pacificus, but was absent in the remaining species of Chionoecetes. This autapomorphic condition in C. j. pacificus adds support for an independent evolution of this taxon. Evolutionary divergences between these taxa may reflect contrasting evolutionary process influenced by ocean bathymetry.     

The phylogeny of the genus Nitrobacter based on comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene sequence analysis

Strains of Nitrobacter mediate the second step in the nitrification process by oxidizing nitrite to nitrate. The phylogenetic diversity of the genus is currently not well investigated. In this study, a rep-PCR profile and the nearly complete 16S rRNA gene sequence of 30 strains, comprising a wide physiological as well as ecological diversity and encompassing representatives of the four species, were determined. The sequence diversity of the 16S rRNA gene between different species was low, indicating the need for additional phylogenetic markers. Therefore, primers were developed for amplifying the complete nxrX gene and a 380bp fragment of the nxrB1 gene, which are both genes involved in the nitrite oxidation process. These genes confirmed the division into phylogenetic groups revealed by the 16S rRNA gene but showed a better discriminatory power. They can be a valuable additional tool for phylogenetic analysis within the genus Nitrobacter and can assist in the identification of new Nitrobacter isolates.     

澳洲宝石鲈线粒体DNA COI基因的克隆与序列分析

对澳洲宝石鲈线粒体DNA细胞色素氧化酶Ⅰ亚基(cytochrome oxidase subunit Ⅰ,COI)基因进行了扩增、克隆和测序,并对COI序列进行了分析.结果显示,澳洲宝石鲈COI基因序列长度为631 bp,其中A、T、G和C 4种碱基的含量分别为27.7%,23.6%,29.8%和18.9%.与从GenBank中查到的其他4种蜊科鱼类的同源序列比对,邻接法(neighbor-joining)构建系统进化树.结果显示,5种蜊科鱼类聚在一起,分为两个大的支系,其中花身蜊与条纹蜊首先聚成一支,然后与詹氏弱棘鯻和银锯眶鯻聚成的一支共同组成一个支系;而高体革鯻单独聚为一个支系,所得的聚类结果与传统的分类结果基本一致.     

基于COI基因5′端与3′端序列田间常见粉虱的分子鉴定

【目的】粉虱种类繁多,个体微小,其种类识别与鉴定常需借助分子生物学技术。本研究旨在明确线粒体COI基因(mitochondrial cytochrome c oxidase subunit I gene) 5′端和3′端序列对常见种类粉虱识别鉴定的可行性。【方法】以我国田间常见的16种粉虱为对象,以COI基因5′端(641 bp)和3′端(738 bp)序列为靶标进行比对分析,以MEGA 5.10软件的K2-P模型计算种内与种间遗传距离,以邻接法(NJ法)构建进化树并进行系统发育分析。【结果】当以5′端为靶标时,16种粉虱的种内平均遗传距离为0.0015,种间平均遗传距离为0.2897,种间遗传距离为种内遗传距离的193.1倍;而且种内、种间遗传距离没有重叠区域。当以3′端为靶标时种内平均遗传距离为0.0007,种间平均遗传距离为0.2817,种间遗传距离为种内遗传距离的402.4倍;但桑粉虱Pealius mori与烟粉虱Bemisia tabaci Asia II 1的种内和种间遗传距离重叠。系统发育分析结果显示,以5′端为靶标时,16种粉虱可以形成独立的进化分支;以3′端为靶标时,除桑粉虱与传统分类学不一致外,其余种类均可形成独立的分支。【结论】结果表明,5′端序列更适用于基于DNA条形码技术的物种识别鉴定研究。     

Genetic diversity and population connectivity of the Asian green mussel Perna viridis in South China Sea,inferred from mitochondria DNA markers

The Asian green mussel Perna viridis is ecologically and economically important in the coastal regions of China. In order to characterize the genetic diversity and population connectivity of P. viridis in South China Sea, a 664 bp region of mitochondrial COI gene and a 293 bp region of 16S rRNA gene were sequenced and analyzed for 78 and 92 individuals from four populations in South China Sea, respectively. A total of 15 haplotypes were defined by 14 variable nucleotide sites in COI gene, and 7 haplotypes by 6 variable nucleotide sites in 16S rRNA gene. High haplotype diversity and low nucleotide diversity were observed in COI gene, while moderate haplotype diversity and low nucleotide diversity were observed in 16S rRNA gene. Pairwise F_ST values of COI gene were all negative and those of 16S rRNA gene ranged from −0.01409 to 0.10289. The results showed that no significant genetic divergence (or shallow genetic structure) and high levels of population connectivity among the four populations of P. viridis in South China Sea.     

Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes

Operational taxonomic units (OTUs) are conventionally defined at a phylogenetic distance (0.03—species, 0.05—genus, 0.10—family) based on full-length 16S rRNA gene sequences. However, partial sequences (700 bp or shorter) have been used in most studies. This discord may affect analysis of diversity and species richness because sequence divergence is not distributed evenly along the 16S rRNA gene. In this study, we compared a set each of bacterial and archaeal 16S rRNA gene sequences of nearly full length with multiple sets of different partial 16S rRNA gene sequences derived therefrom (approximately 440-700 bp), at conventional and alternative distance levels. Our objective was to identify partial sequence region(s) and distance level(s) that allow more accurate phylogenetic analysis of partial 16S rRNA genes. Our results showed that no partial sequence region could estimate OTU richness or define OTUs as reliably as nearly full-length genes. However, the V1-V4 regions can provide more accurate estimates than others. For analysis of archaea, we recommend the V1-V3 and the V4-V7 regions and clustering of species-level OTUs at 0.03 and 0.02 distances, respectively. For analysis of bacteria, the V1-V3 and the V1-V4 regions should be targeted, with species-level OTUs being clustered at 0.04 distance in both cases.     

大黄鱼16SrRNA和18SrRNA基因的测定与序列分析

利用多对引物,扩增并测定出大黄鱼16SrRNA基因和18SrRNA基因的部分序列,其长度分别为1202bp和1275bp,16SrRNA基因序列的GC含量为46．12％,18SrRNA基因的Gc含量为53．oo％。将大黄鱼16SrRNA基因序列与GenBank中15种硬骨鱼类的同源序列结合,同时将其18SrRNA基因序列与GenBank中9种脊索动物的同源序列相结合,运用软件获得各自序列间差异百分比,转换和颠换数值等信息。基于这两种基因序列,利用NJ法和BI法,分别构建16种硬骨鱼类和10种脊索动物的分子系统树。18SrRNA构建的系统树包括三大支,一支为哺乳类、鸟类和爬行类共6个物种,一支为两栖类的1个物种,另一支为2种硬骨鱼类。16SrRNA构建的系统树显示大黄鱼所在的石首鱼科与鲈科和盖刺鱼科亲缘关系较近。此外还讨论了这两个基因的序列特征。     

Complete sequence and gene organization of the Nosema heliothidis ribosomal RNA gene region

By sequencing the entire ribosomal RNA (rRNA) gene region of Nosema heliothidis isolated from cotton bollworm (Helicoverpa armigera), we showed that its gene organization is similar to the type species, Nosema bombycis: the 5'-large subunit rRNA (2,490 bp)-internal transcribed spacer (192 bp)-small subunit rRNA (1,232 bp)-intergenic spacer (274 bp)-5S rRNA (115 bp)-3'. We constructed two phylogenetic trees, analyzed phylogenetic relationships, examined rRNA organization of microsporidia, and compared the secondary structure of small subunit rRNA with closely related microsporidia. The latter two features may provide important information for the classification and phylogenetic analysis of microsporidia.     

Sperm ultrastructure of shrimps from the family Penaeidae (Crustacea: Dendrobranchiata) in a phylogenetic context

We describe the sperm ultrastructure of six penaeid species, including at least one member of each tribe (Penaeini, Parapenaeini and Trachypenaeini). Fragments of the vas deferens of the Penaeidae Farfantepenaeus brasiliensis, Farfantepenaeus paulensis, Litopenaeus schmitti, Parapenaeus americanus, Rimapenaeus constrictus and Xiphopenaeus kroyeri were fixed and processed according to the routine for transmission electron microscopy. The morphological results were contextualized in an evolutionary perspective using molecular markers for the phylogenetic reconstruction of this group. A phylogram was proposed by Bayesian inference based on 1007 bp of 33 sequences of the combined genes (16S rDNA and COI mtDNA) from 27 dendrobranchiate specimens. Our findings show that morphological differences in the sperm ultrastructures of members among the tribes of Penaeidae can be used as a baseline to understand their evolutionary relationships. Individuals from the Penaeini tribe show plesiomorphic characteristics in the sperm ultrastructure compared to the Trachypenaeini tribe from which they were derived, such as shrimp from family Sicyoniidae. The morphological complexity of the sperm of the different penaeid members corroborated with the genetic phylogeny, which showed different clades for each tribe and the close relationship with Sicyoniidae. The sperm features of the selected species studied here reflected their evolutionary history. These features confirm the previous phylogenetic hypothesis and question the monophyly of Penaeidae, which should be verified in the future with a more complete set of representative members of each tribe.     

A broad-host-range, generalized transducing phage (SN-T) acquires 16S rRNA genes from different genera of bacteria

Genomic analysis has revealed heterogeneity among bacterial 16S rRNA gene sequences within a single species; yet the cause(s) remains uncertain. Generalized transducing bacteriophages have recently gained recognition for their abundance as well as their ability to affect lateral gene transfer and to harbor bacterial 16S rRNA gene sequences. Here, we demonstrate the ability of broad-host-range, generalized transducing phages to acquire 16S rRNA genes and gene sequences. Using PCR and primers specific to conserved regions of the 16S rRNA gene, we have found that generalized transducing phages (D3112, UT1, and SN-T), but not specialized transducing phages (D3), acquired entire bacterial 16S rRNA genes. Furthermore, we show that the broad-host-range, generalized transducing phage SN-T is capable of acquiring the 16S rRNA gene from two different genera: Sphaerotilus natans, the host from which SN-T was originally isolated, and Pseudomonas aeruginosa. In sequential infections, SN-T harbored only 16S rRNA gene sequences of the final host as determined by restriction fragment length polymorphism analysis. The frequency of 16S rRNA gene sequences in SN-T populations was determined to be 1 x 10(-9) transductants/PFU. Our findings further implicate transduction in the horizontal transfer of 16S rRNA genes between different species or genera of bacteria.