Articles selected by Faculty of 1000: plant comparative mitochondrial genomics; open source proteomics database; identifying disease-associated enzymes; predicting microRNA targets; genome annotation using polymorphisms

Background

Phylogenetic analysis of human complete mitochondrial DNA sequences has largely contributed to resolving phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this haplogroup to precisely characterize the lineages and unravel their intricate phylogeny.

Results

The phylogenetic tree constructed from sequencing information of twenty four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the formulation of a new lineage M30, distinguished by the presence of 12007 transition, and comprises of the recently defined M18 and a potential new sub-lineage possessing substitution at 16223 and 16300. M30 further branches into M30a sub-lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage M* with HVSI sequence 16223,16325. No new substitutions were found in M25 and the M3 mt DNA genome could only be tentatively rooted by 16126 mutation. M4 and M*(16251, 16267) lineages could not be resolved distinctly.

Conclusions

This study describes seven new basal mutations and fourteen lineages that substantially contribute to the present understanding of superhaplogroup M. The phylogenetic tree supported by median-joining network helps in distinctly identifying the genetic relation between different M lineages that could not be achieved solely by control region sequence information. Although high control region diversity has been reported in the different M lineages distributed in India, complete sequencing of M* and defined lineages suggests that these mt DNA genomes emerged from a limited number of branches arising from the M trunk.     

Articles selected by Faculty of 1000: proteomics of PH domains; machine-learning prediction of RNA-binding proteins; coated vesicle proteomics; classifying protein domain combinations; amino acid usage within proteomes

A selection of evaluations from Faculty of 1000 covering the proteomics of PH domains; machine-learning prediction of RNA-binding proteins; coated vesicle proteomics; classifying protien domain combinations; amino acid usage within proteomes.     

Articles selected by Faculty of 1000: p53 gene silencing; duplications in the Arabidopsis genome; RNA interference and disease protection; arraying environmental gene diversity; predicting RNA folding patterns.

A selection of evaluations from Faculty of 1000 covering several post-genomic studies in C. elegans, the use of 'integrative genomics' in disease gene identification and a comparison of mouse and human genomes.     

Articles selected by Faculty of 1000 Biology: yeast metabolite profiling; high-frequency homologous recombination; functional RNA motifs; phylogeny of Oryzeae; genomic variability within an organism.

A selection of evaluations from Faculty of 1000 Biology Genetically identical SNPs; detailed histone modification mapping; plant gene-expression diversity; photosynthesis gene evolution; ε-Proteobacteria diversity.     

Articles selected by Faculty of 1000 Biology: yeast metabolite profiling; high-frequency homologous recombination; functional RNA motifs; phylogeny of Oryzeae; genomic variability within an organism.

A selection of evaluations from Faculty of 1000 Biology: yeast metabolite profiling; high-frequency homologous recombination; functional RNA motifs; phylogeny of Oryzeae; genomic variability within an organism.     

Articles selected by Faculty of 1000: Neurospora crassa genome sequence; human c-Myc target genes; prokaryote genome annotation database; diversity of marine eukaryotes; transcriptional regulation by a pseudogene

A selection of evaluations from Faculty of 1000 covering the synthesis of sugar arrays, C. elegans ORFeome v1.1, a novel method for identifying tRNA genes, a step towards analysis of the human serum proteome and rates of molecular divergence in rearranged chromosomes.     

Articles selected by Faculty of 1000 Biology: genetically identical SNPs; detailed histone modification mapping; plant gene-expression diversity; photosynthesis gene evolution; ε-Proteobacteria diversity.

A selection of evaluations from Faculty of 1000 Biology Genetically identical SNPs; detailed histone modification mapping; plant gene-expression diversity; photosynthesis gene evolution; ε-Proteobacteria diversity.     

Articles selected by Faculty of 1000: enhancer evolution in flies; modeling nuclear import; cell-cycle kinase substrates; transgenic plants change little; early embryo epigenetics

A selection of evaluations from Faculty of 1000 covering similar embryos from divergent genomes; gene expression variation in twins; the E. coli stress response network; adaptive immune system evolution; alloployploid tobacco evolution.     

Articles selected by Faculty of 1000: phage receptor-binding proteins; genetic diversity in Toxoplasma; ribosome biogenesis and cell size; gene regulation by retrotransposons; manipulation of the cancer epigenome

A selection of evaluations from Faculty of 1000 covering phage receptor-binding proteins; genetic diversity in Toxoplasma; ribosome biogenesis and cell size; gene regulation by retrotransposons; manipulation of the cancer epigenome.     

Articles selected by Faculty of 1000: single-cell neuronal expression analysis; array analysis of chick hair cells; coiled-coil protein arrays; high-throughput identification of plasmodesmata-interacting proteins; multicompenent therapeutics

A selection of evaluations from Faculty of 1000 covering yeast metabolomics, genome-wide threading-based predictions of protein-protein interactions, genetic analysis of filamentous growth in C. albicans, the production of knockout rats and genome-wide mutagenesis of humoral immune responses.     

Articles selected by Faculty of 1000: the quantification of proteins and phosphoproteins; haplotype structure in Arabidopsis; genomewide analysis of small interfering RNAs; screening newborns for inborn errors of metabolism; and profiling vaccinia virus infection of human HeLa cells

A selection of evaluations from Faculty of 1000 covering the identification of cereal cell wall biosynthetic genes, off-target gene regulation by RNAi, protoemics of lipid rafts, a mating-type gene in Aspergillus fumigatus and genomic identification of hyperthermophiles.