Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: implications for phylogenetic inference

In order to maximise the positional homology in the primary sequence alignment of the second internal transcribed spacer for 30 species of equine strongyloid nematodes, the secondary structures of the precursor ribosomal RNA were predicted using an approach combining an energy minimisation method and comparative sequence analysis. The results indicated that a common secondary structure model of the second internal transcribed spacer of these nematodes was maintained, despite significant interspecific differences (2–56%) in primary sequences. The secondary structure model was then used to refine the primary second internal transcribed spacer sequence alignment. The “manual” and “structure” alignments were both subjected to phylogenetic analysis using three different tree-building methods to compare the effect of using different sequence alignments on phylogenetic inference. The topologies of the phylogenetic trees inferred from the manual second internal transcribed spacer alignment were usually different to those derived from the structure second internal transcribed spacer alignment. The results suggested that the positional homology in the second internal transcribed spacer primary sequence alignment was maximised when the secondary structure model was taken into consideration.     

Molecular characterization of a 14-3-3 zeta gene from Plodia interpunctella: A potential marker for phylogenetic inference

The 14-3-3 proteins are a large family of approximately 30 kDa acidic proteins and acting in the regulation of many biological processes. In this study, a 14-3-3 zeta (Pi14-3-3z) gene from the Indian meal moth, Plodia interpunctella (Lepidoptera, Pyralidae) was isolated and characterized. The full-length cDNA of Pi14-3-3z is 1382 bp, including a 5'-untranslated region (UTR) of 141 bp, 3′-UTR of 497 bp and an open reading frame (ORF) of 744 bp encoding a polypeptide of 247 amino acids which contains a 14-3-3 homologues domain (PF00244). The deduced Pi14-3-3z protein sequence has 81%–100% identity with the homologues in comparison to with other individuals. qPCR analysis revealed that Pi14-3-3z was expressed at the four developmental stages and in all tissues tested. Based on the amino acid of 14-3-3z, phylogenetic analysis demonstrated a similar topology with the traditional classification, suggesting 14-3-3z protein has the potential value in phylogenetic inference.     

基于k-mer组分信息的系统发生树构建方法

随着越来越多基因组的测序完成,基于全基因组的非比对的系统发生分析已成为研究热点。不同的生物物种或个体基因组之间的核酸组分不完全相同。遗传语言-DNA序列的信息很大程度上反映在其k—mer频数中。基于基因组序列k-mer频数的系统发生树则从新的角度为我们提供物种之间的亲缘关系。本文定义基于k-mer,频数的信息参数,并用它表征基因组序列,计算不同基因组之间信息参数的距离,用邻接法对84个病毒构建了系统发生树,发现构建的系统发生树很大程度上与已有的系统发生树相吻合。     

The first complete mitogenome of Picumnus innominatus (Aves,Piciformes, Picidae) and phylogenetic inference within the Picidae

The avian family Picidae, which is nearly global in distribution, contains the piculets (Picumninae and Nesoctitinae), the woodpeckers (Picinae), and the wrynecks (Jynginae). However, the phylogenetic relationships within the Picidae remain obscure for most genera. In the present study, the complete mitochondrial genome of Picumnus innominatus was determined and described, which was the first complete mitogenome reported in the Picumnus. The circular mitogenome of P. innominatus was 17,180 bp in size and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNA genes, a control region (CR), and a noncoding region. The gene order and arrangement of the P. innominatus mitogenome were identical to other mitogenomes of the Picidae. Moreover, strikingly large tandem repeats were found in the noncoding region of the P. innominatus mitogenome, which have not yet been covered in other picid species to date. At the family level (Picidae), the highest dN/dS ratio was detected for the ND1 gene (1.38726) among 13 PCGs, indicating that positive selection was powerful for this gene. Bayesian and Maximum Likelihood phylogenetic analyses based on the combination of 12S rRNA and CYTB gene supported strongly that the Picumninae is monophyletic.     

拽线法:一个构建系统发育树的新算法

这篇文章要讨论的拽线法（DL）是贪婪算法的一种。和Fitch—Margoliash（FM）一样,DL也是基于距离矩阵构建系统发育树,但是和FM算法相比,DL具有低复杂度、较高的容错性和准确度高的优点。当存在误差时,DL算法只是加大了不在同一个父节点下的基因序列的距离,但能够准确的判断序列的亲缘关系,进而得到完美的进化树拓扑结构;相比之下,FM算法让各个基因序列间的距离均摊了这种误差,从而有可能将本应该具有相同父节点的基因序列分到不同的分支。     

Molecular phylogenetic analysis of actin genic regions fromAchlya bisexualis (Oomycota) andCostaria costata (Chromophyta)

Summary Actin genic regions were isolated and characterized from the heterokont-flagellated protists,Achlya bisexualis (Oomycota) andCostaria costata (Chromophyta). Restriction enzyme and cloning experiments suggested that the genes are present in a single copy and sequence determinations revealed the existence of two introns in theC. costata actin genic region. Phylogenetic analyses of actin genic regions using distance matrix and maximum parsimony methods confirmed the close evolutionary relationship ofA. bisexualis andC. costata suggested by ribosomal DNA (rDNA) sequence comparisons and reproductive cell ultrastructure. The higher fungi, green plants, and animals were seen as monophyletic groups; however, a precise order of branching for these assemblages could not be determined. Phylogenetic frameworks inferred from comparisons of rRNAs were used to assess rates of evolution in actin genic regions of diverse eukaryotes. Actin genic regions had nonuniform rates of nucleotide substitution in different lineages. Comparison of rates of actin and rDNA sequence divergence indicated that actin genic regions evolve 2.0 and 5.3 times faster in higher fungi and flowering plants, respectively, than their rDNA sequences. Conversely, animal actins evolve at approximately one-fifth the rate of their rDNA sequences.     

A phylogenetic analysis of Myriapoda (Arthropoda) using two nuclear protein-encoding genes

Nucleotide and inferred amino acid sequences from two nuclear protein-encoding genes, elongation factor-aα and RNA polymerase II, were obtained from 34 myriapods and 14 other arthropods to determine phylogenetic relationships among and within the myriapod classes. Phylogenetic analyses using maximum parsimony and maximum likelihood methods recovered all three represented myriapod classes (Chilopoda, Diplopoda, Symphyla) and all multiply sampled chilopod and diplopod orders, often with high node support. In contrast, relationships between classes and between orders were recovered less consistently and node support was typically lower. The temporal structure of phylogenetic diversification in Myriapoda may explain this apparent pattern of the phylogenetic recovery.     

The larval head of Raphidia (Raphidioptera, Insecta) and its phylogenetic significance

External and internal head structures of larval representatives of Raphidiidae are described. The obtained data were compared to characters of other neuropterid larvae and to larval characters of representatives of other endopterygote lineages. Characters potentially relevant for phylogenetic reconstruction are listed and discussed. The larvae of Raphidioptera differ distinctly from other neuropterid larvae in their morphology. They are mainly characterised by autapomorphic and plesiomorphic character states and few features indicate systematic affinities with other groups. Endopterygote groundplan features maintained in Raphidioptera are the complete tentorium, the free labrum, the full set of labral muscles, the presence of four extrinsic antennal muscles, the three-segmented labial palpi, the presence of a full set of extrinsic maxillary and labial muscles, the presence of a salivarium, and possibly the high number of stemmata. Apomorphies likely correlated with predaceous habits are the long gula, the protracted maxillae, the longitudinal arrangement of extrinsic maxillary muscles, and the elongated prepharyngeal tube. Highly unusual, potentially autapomorphic features are the presence of a dorsal ligament of the tentorium and paired gland-like structures below the pharynx. A prognathous or very slightly inclined head and slender mandibles without mola are features shared by larvae of all orders of Neuropterida. The parallel-sided head is a potential synapomorphy of Raphidioptera and Megaloptera. A fully prognathous head with anteriorly shifted posterior tentorial grooves and the presence of a parietal ridge and a distinct neck region are features shared with Corydalidae. Characters of the larval head are not sufficient for a reliable placement of Raphidioptera.     

A molecular phylogenetic framework for the phylum Ctenophora using 18S rRNA genes.

This paper presents the first molecular phylogenetic analysis of the phylum Ctenophora, by use of 18S ribosomal RNA sequences from most of the major taxa. The ctenophores form a distinct monophyletic group that, based on this gene phylogeny, is most closely related to the cnidarians. Our results suggest that the ancestral ctenophore was tentaculate and cydippid-like and that the presently recognized order Cydippida forms a polyphyletic group. The other ctenophore orders that we studied (Lobata, Beroida, and Platyctenida) are secondarily derived from cydippid-like ancestors, a conclusion that is also supported by developmental and morphological data. The very short evolutionary distances between characterized ctenophore 18S rRNA gene sequences suggests that extant ctenophores are derived from a recent common ancestor. This has important consequences for future studies and for an understanding of the evolution of the metazoans.     

The complete mitochondrial genome of Diaphorina citri (Hemiptera: Psyllidae) and phylogenetic analysis

The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is the most serious pest of citrus as the vector of Huanglongbing (HLB), the citrus greening disease. In this study, the complete mitochondrial genome (mitogenome) of D. citri has been sequenced and annotated, and a comparative analysis is provided with known Psylloidea species. The mitogenome of D. citri is a typical circular molecular of 15,038 bp in length with an A + T content of 74.56%, contains the typical 37 genes and the gene order is identical to the other Psylloidea mitogenomes. The nucleotide composition and codon usage of D. citri are similar to the four Psylloidea species. All protein-coding genes (PCGs) use standard initiation codons (TAN), stop with TAA and TAG except ND2 and ND5 which stop with incomplete termination codon T. All tRNAs have the typical clover-leaf structure, with the exception of trnS1 lacking the dihydrouridine (DHU) arm. The control region is located between rrnL and the trnI gene with the highest A + T content among the five Psylloidea species. Phylogenetic analysis is conducted based on the 13 PCGs or/and 2 rRNAs of 23 Sternorrhycha mitogenomes. Both maximum likelihood (ML) and Bayesian inference (BI) analysis suggest a clear relationship of Psylloidea, Aleyrodoidea and Aphidoidea within Sternorrhycha, which support the traditional morphological classification.     

从18S rRNA基因序列探讨盾腹吸虫的系统发育关系

盾腹亚纲吸虫被认为是寄生扁形动物中古老的类群,包括盾腹科、多萼科、裂杯科和皱腹科,科间系统发育关系尚存争议。本研究收集GenBank数据库中所有的盾腹吸虫18S rRNA基因序列,测定了三种盾腹吸虫的相应序列,分别采用最大简约法和最大似然法构建分子系统发育树。结果显示,多萼科的分类地位不成立,多萼属应还原到盾腹科;盾腹科的盾腹亚科和杯盾亚科均非单系,吸槽列数可能是平行进化特征,不能反映盾腹科各亚科间的系统发育关系。建议将具有边缘器的吸槽型腹吸盘,以及不具边缘器的吸杯型和皱褶型腹吸盘分别鉴定为盾腹科、裂杯科和皱腹科种类的共裔性状。     

Quasispecies composition and phylogenetic analysis of feline coronaviruses (FCoVs) in naturally infected cats

Quasispecies composition and tissue distribution of feline coronaviruses (FCoVs) were studied in naturally infected cats. The genomic complexity of FCoVs was investigated using single-strand conformational polymorphism (SSCP) analysis of N and ORF7b amplicons, and the evolutionary process was investigated by sequence-based phylogenetic analysis. SSCP analysis showed high heterogeneity of the FCoV genome which was correlated with the seriousness of the clinical form. The two genomic regions analysed showed different levels of variation; the N region demonstrated significant heterogeneity as compared to ORF7b. Phylogenetic analysis of the nucleotide sequences showed the clear separation of sequences analysed on the basis of virulence and geographical origin. A maximum likelihood analysis of N and ORF7b data sets showed a situation of strong heterogeneity for the N region.     

Human NAT10 Is an ATP-dependent RNA Acetyltransferase Responsible for N4-Acetylcytidine Formation in 18 S Ribosomal RNA (rRNA)

Human N-acetyltransferase 10 (NAT10) is known to be a lysine acetyltransferase that targets microtubules and histones and plays an important role in cell division. NAT10 is highly expressed in malignant tumors, and is also a promising target for therapies against laminopathies and premature aging. Here we report that NAT10 is an ATP-dependent RNA acetyltransferase responsible for formation of N⁴-acetylcytidine (ac⁴C) at position 1842 in the terminal helix of mammalian 18 S rRNA. RNAi-mediated knockdown of NAT10 resulted in growth retardation of human cells, and this was accompanied by high-level accumulation of the 30 S precursor of 18 S rRNA, suggesting that ac⁴C1842 formation catalyzed by NAT10 is involved in rRNA processing and ribosome biogenesis.     

Complete mitochondrial genome of spined sleeper Eleotris oxycephala (Perciformes,Eleotridae) and phylogenetic consideration

The complete mitochondrial genome of Eleotris oxycephala was determined to be 16,527 bp in length with (A + T) content of 53%, and it consists of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the E. oxycephala complete mtDNA were identical to most of other vertebrates. Phylogenetic analysis based on different sequences of species of the Gobioidei suborder and different methods showed that E. oxycephala formed a cluster with Eleotris acanthopoma and Eleotridae were divided into two clades. Furthermore, extensive taxon sampling and more molecular information are needed to confirm the phylogenetic relationships among the Gobioidei.     

The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes

With efficient sequencing techniques, full mitochondrial genomes are rapidly replacing other widely used markers, such as the nuclear rRNA genes, for phylogenetic analysis but their power to resolve deep levels of the tree remains controversial. We studied phylogenetic relationships of leaf beetles (Chrysomelidae) in the tribes Galerucini and Alticini (root worms and flea beetles) based on full mitochondrial genomes (103 newly sequenced), and compared their performance to the widely sequenced nuclear rRNA genes (full 18S, partial 28S). Our results show that: (i) the mitogenome is phylogenetically informative from subtribe to family level, and the per‐nucleotide contribution to nodal support is higher than that of rRNA genes, (ii) the Galerucini and Alticini are reciprocally monophyletic sister groups, if the classification is adjusted to accommodate several ‘problematic genera’ that do not fit the dichotomy of lineages based on the presence (Alticini) or absence (Galerucini) of the jumping apparatus, and (iii) the phylogenetic results suggest a new classification system of Galerucini with eight subtribes: Oidina, Galerucina, Hylaspina, Metacyclina, Luperina, Aulacophorina, Diabroticina and Monoleptina.     

The mitochondrial genome of Gatzara jezoensis (Neuroptera: Myrmeleontidae) and phylogenetic analysis of Neuroptera

Phylogenetic relationship within Neuroptera is controversial, particularly for the various hypotheses based on both morphological and molecular evidence. In the present study, we determined the complete mitochondrial genome (mitogenome) of Gatzara jezoensis, which is the second representative of the tribe Dendroleontini. The G. jezoensis mitogenome contained the conserved set of 37 mitochondrial genes and a putative control region, with a conserved gene arrangement which was similar to that of most sequenced neuropteran mitogenomes. All transfer RNAs exhibited the canonical cloverleaf secondary structure, except for trnS^(AGN). The control region contained two conserved elements (ploy-T stretch and ATGGTTCAAYAAAATAAYYCYCTC motif) and abundant microsatellite-like elements. The phylogenetic analysis of sequenced neuropteran mitogenomes using the concatenated protein-coding genes (PCGs) and ribosomal genes recovered the monophyly of Myrmeleontidae, which revealed this dataset could generate the more robust phylogeny of Neuroptera than that of 13 PCGs dataset.