Liang-Hu Qu

Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes

Phylogenetic relationships of members of the salamander family Salamandridae were examined using complete mitochondrial genomes collected from 42 species representing all 20 salamandrid genera and five outgroup taxa. Weighted maximum parsimony, partitioned maximum likelihood, and partitioned Bayesian approaches all produce an identical, well-resolved phylogeny; most branches are strongly supported with greater than 90% bootstrap values and 1.0 Bayesian posterior probabilities. Our results support recent taxonomic changes in finding the traditional genera Mertensiella, Euproctus, and Triturus to be non-monophyletic species assemblages. We successfully resolved the current polytomy at the base of the salamandrid tree: the Italian newt genus Salamandrina is sister to all remaining salamandrids. Beyond Salamandrina, a clade comprising all remaining newts is separated from a clade containing the true salamanders. Among these newts, the branching orders of well-supported clades are: primitive newts (Echinotriton, Pleurodeles, and Tylototriton), New World newts (Notophthalmus-Taricha), Corsica-Sardinia newts (Euproctus), and modern European newts (Calotriton, Lissotriton, Mesotriton, Neurergus, Ommatotriton, and Triturus) plus modern Asian newts (Cynops, Pachytriton, and Paramesotriton).Two alternative sets of calibration points and two Bayesian dating methods (BEAST and MultiDivTime) were used to estimate timescales for salamandrid evolution. The estimation difference by dating methods is slight and we propose two sets of timescales based on different calibration choices. The two timescales suggest that the initial diversification of extant salamandrids took place in Europe about 97 or 69Ma. North American salamandrids were derived from their European ancestors by dispersal through North Atlantic Land Bridges in the Late Cretaceous ( approximately 69Ma) or Middle Eocene ( approximately 43Ma). Ancestors of Asian salamandrids most probably dispersed to the eastern Asia from Europe, after withdrawal of the Turgai Sea ( approximately 29Ma).

Mitogenomic Perspectives on the Origin and Phylogeny of Living Amphibians

Establishing the relationships among modern amphibians (lissamphibians) and their ancient relatives is necessary for our understanding of early tetrapod evolution. However, the phylogeny is still intractable because of the highly specialized anatomy and poor fossil record of lissamphibians. Paleobiologists are still not sure whether lissamphibians are monophyletic or polyphyletic, and which ancient group (temnospondyls or lepospondyls) is most closely related to them. In an attempt to address these problems, eight mitochondrial genomes of living amphibians were determined and compared with previously published amphibian sequences. A comprehensive molecular phylogenetic analysis of nucleotide sequences yields a highly resolved tree congruent with the traditional hypotheses (Batrachia). By using a molecular clock-independent approach for inferring dating information from molecular phylogenies, we present here the first molecular timescale for lissamphibian evolution, which suggests that lissamphibians first emerged about 330 million years ago. By observing the fit between molecular and fossil times, we suggest that the temnospondyl-origin hypothesis for lissamphibians is more credible than other hypotheses. Moreover, under this timescale, the potential geographic origins of the main living amphibian groups are discussed: (i) advanced frogs (neobatrachians) may possess an Africa-India origin; (ii) salamanders may have originated in east Asia; (iii) the tropic forest of the Triassic Pangaea may be the place of origin for the ancient caecilians. An accurate phylogeny with divergence times can be also helpful to direct the search for missing fossils, and can benefit comparative studies of amphibian evolution.

Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post-embryogenic development

In vitro cultured embryogenic callus was employed as a model to investigate microRNAs (miRNAs) associated with embryogenesis and post‐embryonic development. Thirty‐one miRNAs including 16 novel species were identified from a large number of small RNAs which were cloned from both differentiated and undifferentiated rice embryogenic calli. Four target genes of the miRNAs were further validated. A set of the miRNAs, including miR397 and miR156, exhibited intriguing expression patterns during the transition from undifferentiated to differentiated calli. By exploiting the correlations between the differential expression patterns of these miRNAs and their targets, the regulatory roles of the miRNAs on meristem maintenance and embryogenesis were indicated.

Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia

Giardia lamblia is an early diverging and evolutionarily successful protozoan as it can enter into a dormant cyst stage from a vegetative trophozoite. During dormant stage, its metabolic rate decreases dramatically. However, to date, the regulatory molecules participating in the initiation and maintenance of this process have not been fully investigated. In this study, we have identified a class of abundant small RNAs named sitRNAs, which are ∼46 nucleotides in length and accumulate in G. lamblia encysting cultures. Remarkably, they are derived from the 3′ portion of fully matured tRNAs by cleavage of the anticodon left arm, with the 3′ terminal CCA triplex still connected. During differentiation, only a limited portion of mature tRNAs is cleaved, but this cleavage occurs almost in the entire tRNA family. sitRNAs begin to accumulate as early as 3 h after initiation of encystation and are maintained at a relatively stable level during the whole process, exhibiting an expression peak at around 24 hr. Our studies further show that sitRNAs can be induced by several other stress factors, and in the case of serum deprivation, both tRNAs and sitRNAs degrade rapidly, with the accumulation of tRNA being halved. Our results may provide new insight into a novel mechanism for stressed G. lamblia to regulate gene expression globally.

The complete mitochondrial genome of a relic salamander, Ranodon sibiricus (Amphibia: Caudata) and implications for amphibian phylogeny.

The Amphibia were the dominant land Vertebrates in the Carboniferous and were certainly the stock from which the reptiles and in turn the mammals and birds evolved. Although two major groups of extinct amphibians, the Labyrinthodontia and the Lepospondyli did not last beyond the Triassic, amphibian lines evidently continued and are represented today by the three distinctly different groups of modern Amphibia (Lissamphibia), the Caudata, Anura, and Gymnophiona. The monophyly of the Lissamphibia and their phylogenetic relationships are still debated. The most widely accepted hypothesis, based on morphological data, supports the monophyletic origin in the Late Paleozoic (300myr) of the three living amphibian orders and a sister-group relationship between Anura and Caudata (the Batrachia hypothesis) (Laurin and Reisz, 1997; Trueb and Cloutier, 1991). However, Jarvik (1980) has suggested that Lissamphibia is not a natural group and hypothesized a polyphyletic origin of the three living orders. Carroll and coworkers (Carroll, 1988; Carroll and Holmes, 1980) have advocated a close phylogenetic relationship between salamanders and caecilians. According to these authors, frogs would have evolved from temnospondyl amphibians (Apsidospondyli) whereas salamanders and caecilians originated from different lineages of microsaurs (Lepospondyli). The affinity between salamanders and caecilians is also supported by several morphological (Bolt, 1991) and molecular (Feller and Hedges, 1998; Hedges et al., 1990) phylogenetic

MiR397b regulates both lignin content and seed number in Arabidopsis via modulating a laccase involved in lignin biosynthesis

Plant laccase (LAC) enzymes belong to the blue copper oxidase family and polymerize monolignols into lignin. Recent studies have established the involvement of microRNAs in this process; however, physiological functions and regulation of plant laccases remain poorly understood. Here, we show that a laccase gene, LAC4, regulated by a microRNA, miR397b, controls both lignin biosynthesis and seed yield in Arabidopsis. In transgenic plants, overexpression of miR397b (OXmiR397b) reduced lignin deposition. The secondary wall thickness of vessels and the fibres was reduced in the OXmiR397b line, and both syringyl and guaiacyl subunits are decreased, leading to weakening of vascular tissues. In contrast, overexpression of miR397b-resistant laccase mRNA results in an opposite phenotype. Plants overexpressing miR397b develop more than two inflorescence shoots and have an increased silique number and silique length, resulting in higher seed numbers. In addition, enlarged seeds and more seeds are formed in these miR397b overexpression plants. The study suggests that miR397-mediated development via regulating laccase genes might be a common mechanism in flowering plants and that the modulation of laccase by miR397 may be potential for engineering plant biomass production with less lignin.

Identification and Functional Analysis of 20 Box H/ACA Small Nucleolar RNAs (snoRNAs) from Schizosaccharomyces pombe

Considering all small nucleolar RNAs (snoRNAs) enriched in the nucleolus, we generated a specialized cDNA library of small nuclear RNAs from Schizosaccharomyces pombe and isolated, for the first time, 20 novel box H/ACA snoRNAs. Thirteen of these were characterized as novel guides that were predicted to direct 19 pseudouridylations in 18 S and 25 S rRNAs. The remaining seven snoRNAs were considered as orphan guides that lack sequence complementarity to either rRNAs or snRNAs. We have experimentally demonstrated the function of the 10 novel snoRNAs by gene deletion in the fission yeast. The snoRNAs were shown to be dispensable for the viability of S. pombe, although an impact of snR94 depletion on yeast growth, especially at 23 °C, was revealed. A total of 30 pseudouridylation sites were precisely mapped in the S. pombe rRNAs, showing a distinctive pseudouridylation pattern in the budding yeast. Interestingly, the absence of pseudouridylation on U2347 in S. pombe 25 S rRNA pointed out a critical role for Ψ2345 in conferring a growth advantage for yeast. In contrast to the intron-encoded box C/D sno-RNAs in yeast, all box H/ACA snoRNAs appeared to be transcribed independently from intergenic regions between two protein-coding genes, except for snR35, which was nested in an open reading frame encoding for a hypothetical protein, although expressed from the opposite strand. Remarkably, snR90 was cotranscribed with an intron-encoded box C/D snoRNA, and this is the first demonstration of a non-coding RNA gene that encodes two different types of snoRNAs by its exon and intron. A detailed comparison of the S. pombe snoRNAs, with their functional homologues in diverse organisms, suggests a mechanism by which the snoRNAs have evolved in coordination with rRNAs to preserve the post-transcriptional modification sites among distant eukaryotes.

Virus-encoded miR-155 ortholog is an important potential regulator but not essential for the development of lymphomas induced by very virulent Marek's disease virus.

The microRNA (miRNA) mdv1-miR-M4, a functional miR-155 ortholog encoded by oncogenic Mareks disease virus (MDV), has previously been suggested to be involved in MDV pathogenesis. Using the technique of bacterial artificial chromosome mutagenesis, we have presently evaluated the potential role of mdv1-miR-M4 in the oncogenesis of the very virulent (vv) MDV strain GX0101. Unexpectedly, deletions of the Meq-cluster or mdv1-miR-M4 alone from the viral genome strongly decreased rather than abolished its oncogenicity. Compared to GX0101, mortalities of mutants GXΔmiR-M4 and GXΔMeq-miRs were reduced from 100% to 18% and 4%, coupled with the gross tumor incidence reduction from 28% to 22% and 8%, respectively. Our data suggests that the mdv1-miR-M4 is possibly an important regulator in the development of Mareks disease (MD) lymphomas but is not essential for the oncogenicity of vvMDV. In addition, some of the other Meq-clustered miRNAs may also play potentially critical roles in vvMDV induction of lymphomas.

Marek's disease virus-encoded analog of microRNA-155 activates the oncogene c-Myc by targeting LTBP1 and suppressing the TGF-β signaling pathway.

Mareks disease virus (MDV) is a representative alpha herpes virus able to induce rapid-onset T-cell lymphoma in its natural host and regarded as an ideal model for the study of virus-induced tumorigenesis. Recent studies have shown that the mdv1-miR-M4-5p, a viral analog of cellular miR-155, is critical for MDV׳s oncogenicity. However, the precise mechanism whereby it was involved in MD lymphomagenesis remained unknown. We have presently identified the host mRNA targets of mdv1-miR-M4-5 and identified the latent TGF-β binding protein 1 (LTBP1) as a critical target for it. We found that during MDV infection, down-regulation of LTBP1 expression by mdv1-miR-M4-5p led to a significant decrease of the secretion and activation of TGF-β1, with suppression of TGF-β signaling and a significant activation of expression of c-Myc, a well-known oncogene which is critical for virus-induced tumorigenesis. Our findings reveal a novel and important mechanism of how mdv1-miR-M4-5p potentially contributes to MDV-induced tumorigenesis.

Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs

BackgroundSmall nucleolar RNAs (snoRNAs) represent one of the largest groups of functionally diverse trans-acting non-protein-coding (npc) RNAs currently known in eukaryotic cells. Chicken snoRNAs have been very poorly characterized when compared to other vertebrate snoRNAs. A genome-wide analysis of chicken snoRNAs is therefore of great importance to further understand the functional evolution of snoRNAs in vertebrates.ResultsTwo hundred and one gene variants encoding 93 box C/D and 62 box H/ACA snoRNAs were identified in the chicken genome and are predicted to guide 86 2-O-ribose methylations and 69 pseudouridylations of rRNAs and spliceosomal RNAs. Forty-four snoRNA clusters were grouped into four categories based on synteny characteristics of the clustered snoRNAs between chicken and human. Comparative analyses of chicken snoRNAs revealed extensive recombination and separation of guiding function, with cooperative evolution between the guiding duplexes and modification sites. The gas5-like snoRNA host gene appears to be a hotspot of snoRNA gene expansion in vertebrates. Our results suggest that the chicken is a good model for the prediction of functional snoRNAs, and that intragenic duplication and divergence might be the major driving forces responsible for expansion of novel snoRNA genes in the chicken genome.ConclusionWe have provided a detailed catalog of chicken snoRNAs that aids in understanding snoRNA gene repertoire differences between avians and other vertebrates. Our genome-wide analysis of chicken snoRNAs improves annotation of the darkness matter in the npcRNA world and provides a unique perspective into snoRNA evolution in vertebrates.