The Human Genome Project revealed that almost half of the human genome consists of transposable elements (TEs), which are also abundant in non-human primates. Various studies have confirmed the roles of different TE families in primate evolution. TEs such as endogenous retroviruses (ERVs), long terminal repeats (LTRs), long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs) all have numerous effects on the primate genome, including genomic rearrangement, regulatory functions and epigenetic mechanisms. This review offers an overview of research on TEs, including our current understanding of their presence in modern primate lineages, their evolutionary origins, and their regulatory and modifying effects on primate as well as human genomes. The information provided here should be useful for the study of primate genomics.

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Streptococcus criceti is a cariogenic organism that belongs to the mutans streptococci. Of the four S. criceti strains, strain OMZ 61 has been identified as being resistant to erythromycin. Antimicrobial susceptibility testing showed that strain OMZ 61 is also resistant to azithromycin, josamycin and clindamycin but susceptible to tetracycline and tiamulin. DNA hybridization analysis of the 23S rRNA genes revealed that the hybridization patterns in strain OMZ 61 differed from those in the other three strains. We further analyzed the nucleotide sequences of a ribosomal RNA operon, the rrnD operon, and the rpsJ−rpsQ region including rplC and rplD genes for ribosomal proteins L3 and L4, respectively, in the four strains studied. Nucleotide sequence analysis indicated that strain OMZ 61 contains an A-to-G substitution at nucleotide position 2059, equivalent to Escherichia coli numbering 2058, in a 23S rRNA gene (rrlD) and a G-to-A substitution at nucleotide position 439 in the rplC gene, suggesting an amino acid residue change at position 147 from valine to isoleucine, whereas no mutation in the rplD gene was found. DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism analysis showed that most or all of the 23S rRNA genes in strain OMZ 61 contain the A2059G mutation. These findings suggest that the resistance to erythromycin, azithromycin, josamycin and clindamycin in strain OMZ 61 is conferred by alterations in 23S rRNA and/or ribosomal protein L3. This is the first description of mutations in the 23S rRNA and rplC genes in mutans streptococci.

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AA genome species in the genus Oryza are valuable resources for improvement of cultivated rice. Oryza rufipogon and O. barthii were progenitors of two domesticated rice species, O. sativa and O. glaberrima, respectively. We used chloroplast single-nucleotide repeats (RCt1-10) to evaluate genetic diversity among AA genome species. Higher diversity was detected in the American species O. glumaepatula and the Asian species O. rufipogon. Other chloroplast sequences indicated that O. glumaepatula shares high similarity with O. longistaminata. Insertions of retrotransposable elements, however, showed a close relation between O. barthii and O. glumaepatula. To clarify phylogenetic relationships among AA genomes, whole-genome sequences obtained from different species were used to develop chloroplast INDEL markers. The INDEL patterns clearly showed multiple maternal origins of O. glumaepatula. The complicated origins have resulted in high genetic diversity in this species. In contrast, the Australian endemic species O. meridionalis tended to show narrower diversity than the other species. High variation in O. rufipogon, reconfirmed using the chloroplast INDELs, covered the variation in O. meridionalis and part of the variation in O. glumaepatula. Maternal lineages including O. barthii, O. longistaminata and the remainder of O. glumaepatula were phylogenetically close to each other and carried low genetic diversity. They were separated from independent lineages, suggesting that they had diverged from a single ancestral maternal lineage, but diverged later to keep gene flow within respective species, as SSR compositions suggested. Genetic relationships among AA genome species indicate how these species have evolved and become distributed across four continents.

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Hybrid chlorosis, one of the reproductive barriers between tetraploid wheat and its D-genome progenitor, Aegilops tauschii, inhibits normal growth of synthetic wheat hexaploids. Hybrid chlorosis appears to be due to an epistatic interaction of two loci from the AB and D wheat genomes. Our previous study assigned the causal D-genome gene for hybrid chlorosis, Hch1, to the short arm of chromosome 7D. Here, we constructed a fine map of 7DS near Hch1 using 280 F₂ individuals from a cross of two wheat synthetic lines, one showing normal growth and the other showing hybrid chlorosis. The hybrid chlorosis phenotype was controlled by a single dominant allele of the Hch1 locus in the synthetic hexaploids. Hch1 was closely linked to four new markers within 0.2 cM, and may be localized near or within the two Ae. tauschii scaffolds containing the linked markers on 7DS. Comparative analysis of the Hch1 chromosomal region for Ae. tauschii, barley and Brachypodium showed that a local inversion occurred in the region proximal to Hch1 during the divergence between barley and Ae. tauschii, and that the Hch1 region on wheat 7DS is syntenic to Brachypodium chromosome 1. These observations provide useful information for further studies toward map-based cloning of Hch1.

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Tubby proteins are highly conserved in a wide range of multicellular organisms. The Tubby gene family was first verified in obese mice. In plants, 11 Tubby genes have been identified in Arabidopsis, 14 in rice, and 11 in poplar. However, there is very little information about Tubby-like proteins in wheat. In this study, we identified four Tubby-like protein genes (TaTULP1-TaTULP4) in wheat. A comparison of the gene structure showed a conserved exon number pattern in TaTULPs, although the length of the introns differed. With the exception of TaTULP2, TaTULPs had four exons. To identify the chromosome localization of TaTULPs, BLASTn analyses were performed using the URGI database to predict the chromosomal location of TaTULP genes. TaTULP1, 2, 3 and 4 genes were localized on chromosomes 4, 5, 7 and 2. All TaTULPs harbor a Tubby domain in their C-terminal region and an F-box domain in the N terminus. We investigated protein–protein interactions between the F-box domain of TaTULPs and various wheat SKP1-like proteins (TaSKPs) using the yeast two-hybrid system. TaTULP1, TaTULP3 and TaTULP4 were found to interact with TaSKP1, TaSKP3 and TaSKP6, whereas TaTULP2 showed no interaction with TaSKP proteins. TaTULP proteins tagged with green fluorescent protein were targeted to the Golgi apparatus in plant cells. Our analysis of TaTULPs will aid in understanding the functions of TaTULPs in plants.

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With the advance of sequencing technologies, large-scale data of expressed sequence tags and full-length cDNA sequences have been reported for several conifer species. Comparative analyses of evolutionary rates among diverse taxa provide insights into taxon-specific molecular evolutionary features and into the origin of variation in evolutionary rates within genomes and between species. Here, we estimated evolutionary rates in two conifer species, Taxodium distichum and Cryptomeria japonica, to illuminate the molecular evolutionary features of these species, using hundreds of genes and employing Chamaecyparis obtusa as an outgroup. Our results show that the mutation rates based on synonymous substitution rates (dS) of T. distichum and C. japonica are approximately 0.67 × 10^–9 and 0.59 × 10^–9/site/year, respectively, which are 15–25 times lower than those of annual angiosperms. We found a significant positive correlation between dS and GC3. This implies that a local mutation bias, such as context dependency of the mutation bias, exists within the genomes of T. distichum and C. japonica, and/or that selection acts on synonymous sites in these species. In addition, the means of the ratios of synonymous to nonsynonymous substitution rate in the two species are almost the same, suggesting that the average intensity of functional constraint is constant between the lineages. Finally, we tested the possibility of positive selection based on the site model, and detected one candidate gene for positive selection.

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Protein complexes are aggregates of protein molecules that play important roles in biological processes. Detecting protein complexes from protein-protein interaction (PPI) networks is one of the most challenging problems in computational biology, and many computational methods have been developed to solve this problem. Generally, these methods yield high false positive rates. In this article, a semantic similarity measure between proteins, based on Gene Ontology (GO) structure, is applied to weigh PPI networks. Consequently, one of the well-known methods, COACH, has been improved to be compatible with weighted PPI networks for protein complex detection. The new method, WCOACH, is compared to the COACH, ClusterOne, IPCA, CORE, OH-PIN, HC-PIN and MCODE methods on several PPI networks such as DIP, Krogan, Gavin 2002 and MIPS. WCOACH can be applied as a fast and high-performance algorithm to predict protein complexes in weighted PPI networks. All data and programs are freely available at http://bioinformatics.aut.ac.ir/wcoach.

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