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Background: It was reported that there is a majority profile for trinucleotide frequencies among genomes. And further study has revealed that two common profiles, rather than one majority profile, exist for genomic trinucleotide frequencies. However, the origins of the common/majority profile remain elusive. Moreover, it is not clear whether the features of common profile may be extended to oligonucleotides other than trinucleotides. Findings: We analyzed 571 prokaryotic genomes (chromosomes) and some selected eukaryotic nuclear genomes as well as other genetic systems to study their compositional features. We found that there are also two common profiles for genomic oligonucleotide frequencies: one is from low-GC content genomes, and the other is from high-GC content genomes. Furthermore, each common profile is highly correlated to the average profile of random sequences with corresponding GC content and generated according to first-order symmetry. Conclusions: The causes for the existence of two common profiles would mainly be GC content variations and strand symmetry of genomic sequences. Therefore, both GC content and strand symmetry would play important roles in genome evolution. [ABSTRACT FROM AUTHOR]

Background: Peptide transporter (PTR) family whose member can transport di-/tripeptides and nitrate is important for plant growth and development. Although the rice (Oryza sativa L.) genome has been sequenced for a few years, a genomic survey, characterization and expression profile analysis of the PTR family in this species has not been reported. Results: In this study, we report a comprehensive identification, characterization, phylogenetic and evolutionary analysis of 84 PTR family members in rice (OsPTR) as well as their whole-life expression patterns. Chromosomal distribution and sequence analysis indicate that nearly 70% of OsPTR members are involved in the tandem and segmental duplication events. It suggests that genome duplication might be a major mechanism for expansion of this family. Highly conserved motifs were identified in most of the OsPTR members. Meanwhile, expression profile of OsPTR genes has been analyzed by using Affymetrix rice microarray and real-time PCR in two elite hybrid rice parents, Minghui 63 and Zhenshan 97. Seven genes are found to exhibit either preferential or tissue-specific expression during different development stages of rice. Under phytohormone (NAA, GA3 and KT) and light/dark treatments, 14 and 17 OsPTR genes are differentially expressed respectively. Ka/Ks analysis of the paralogous OsPTR genes indicates that purifying selection plays an important role in function maintenance of this family. Conclusion: These investigations add to our understanding of the importance of OsPTR family members and provide useful reference for selecting candidate genes for functional validation studies of this family in rice. [ABSTRACT FROM AUTHOR]

Ketogulonicigenium vulgate is an industrial organism commonly used in the vitamin C industry. Here, we report the finished, annotated, and compared 3.28-Mbp high-quality genome sequence of Ketogulonicigenium vulgare WSH-001, a 2-keto-L-gulonic acid-producing industrial strain stocked in our laboratory. [ABSTRACT FROM AUTHOR]

Lactobacillus helveticus strain H10 was isolated from traditional fermented milk in Tibet, China. We sequenced the whole genome of strain H10 and compared it to the published genome sequence of Lactobacillus helveticus DPC4571. [ABSTRACT FROM AUTHOR]