Comparative Genomic Analysis of Delftia tsuruhatensis MTQ3 and the Identification of Functional NRPS Genes for Siderophore Production.

Plant growth-promoting rhizobacteria (PGPR) are a group of rhizosphere bacteria that promote plant growth. Delftia tsuruhatensis MTQ3 is a member of PGPR that produces siderophores. The draft genome sequence of MTQ3 has been reported. Here, we analyzed the genome sequence of MTQ3 and performed a comparative genome analysis of four sequenced Delftia strains, revealing genetic relationships among these strains. In addition, genes responsible for bacteriocin and nonribosomal peptide synthesis were detected in the genomes of each strain. To reveal the functions of NRPS genes in siderophore production in D. tsuruhatensis MTQ3, three NRPS genes were knocked out to obtain the three mutants MTQ3-Δ1941, MTQ3-Δ1945, and MTQ3-Δ1946, which were compared with the wild-type strain. In qualitative and quantitative analyses using CAS assay, the mutants failed to produce siderophores. Accordingly, the NRPS genes in MTQ3 were functionally related to siderophore production. These results clarify one mechanism by which plant growth is promoted in MTQ3 and have important applications in agricultural production.

Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations.

Indexing individual template molecules with a unique identifier (UID) before PCR and deep sequencing is promising for detecting low frequency mutations, as true mutations could be distinguished from PCR errors or sequencing errors based on consensus among reads sharing same index. In an effort to develop a robust assay to detect from urine low-abundant bladder cancer cells carrying well-documented mutations, we have tested the idea first on a set of mock templates, with wild type and known mutants mixed at defined ratios. We have measured the combined error rate for PCR and Illumina sequencing at each nucleotide position of three exons, and demonstrated the power of a UID in distinguishing and correcting errors. In addition, we have demonstrated that PCR sampling bias, rather than PCR errors, challenges the UID-deep sequencing method in faithfully detecting low frequency mutation.

High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin.

Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.

Genome-wide identification and evolutionary analysis of B7-H3.

B7-H3 is an immune co-stimulatory molecule of the B7 family that contains a set of immunoglobulin-V (IgV) and immunoglobulin-C (IgC) domains. To explore the evolutionary process of B7-H3 gene, we conducted a genome-wide structure and phylogenetic analysis of B7-H3 genes in currently sequenced genomes. On the basis of the available data, 17 mammalian B7-H3 genes were predicted to have tandemly duplicated 4Ig domains. The analysis of gene structure and phylogenesis reveal that these 4IgB7-H3 genes resulted from domain duplication. Nevertheless, no difference in function has been observed between the two isoforms. It is more likely that domain duplication in 4IgB7-H3 leads to functional redundancy.

[Analysis of horizontal transfer gene of Bombyx mori NPV].

For research on genetic characters and evolutionary origin of the genome of baculoviruses, a comprehensive homology search and phylogenetic analysis of the complete genomes of Bombyx mori NPV and Bombyx mori were used. Three horizontally transferred genes (inhibitor of apoptosis, chitinase, and UDP-glucosyltransferase) were identified, and there was evidence that all of these genes were derived from the insect host. The results of analysis showed lots of differences between the features of horizontal transferred genes and the ones of whole genomic genes, such as nucleotide composition, codon usagebias and selection pressure. These results reconfirmed that the horizontally transferred genes are exogenous. The analysis of gene function suggested that horizontally transferred genes acquired from an ancestral host insect can increase the efficiency of baculoviruses transmission.

The complete mitogenome and phylogenetic analysis of Bombyx mandarina strain Qingzhou.

The complete nucleotide sequence of the mitogenome of Bombyx mandarina strain Qingzhou was determined. The circular genome is 15,717 bp long and has the typical gene organization and order of lepidopteran mitogenomes. All protein-coding sequences are initiated with a typical ATN codon, except the COI gene, which has a 4-bp TTAG putative initiator codon. Eleven of the 13 protein-coding gene have a complete termination codon (all TAA), but the remaining two genes terminate with incomplete codons. All transfer RNAs (tRNAs) have a clover-leaf structure typical of the mitochondrial tRNAs, and some of them have a mismatch in the four-stem-and-loop structure. The length of the A + T rich region of B. mandarina strain Qingzhou is 495 bp, shorter than that of B. mandarina strain Tsukuba (747 bp) but similar to that of Bombyx mori. Phylogenetic analysis based on the whole mitochondrial genome sequences of the available sequenced species (B. mori strains C-108, Aojuku, Backokjam, and Xiafang, B. mandarina strains Tsukuba, Ankang, and Qingzhou, and Antheraea pernyi) shows the origin of the domesticated silkmoth B. mori to be the Chinese B. mandarina. Nuclear mitochondrial pseudogene sequences were detected in the nuclear genome of B. mori with the MEGA BLAST search program. A phylogenetic analysis of these nuclear mitochondrial pseudogene sequences suggests that B. mori was domesticated independently in different areas and periods.