PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II’s sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

Ocean acidification may negatively impact the early life stages of some marine invertebrates including corals. Although reduced growth of juvenile corals in acidified seawater has been reported, coral larvae have been reported to demonstrate some level of tolerance to reduced pH. We hypothesize that the observed tolerance of coral larvae to low pH may be partly explained by reduced metabolic rates in acidified seawater because both calcifying and non-calcifying marine invertebrates could show metabolic depression under reduced pH in order to enhance their survival. In this study, after 3-d and 7-d exposure to three different pH levels (8.0, 7.6, and 7.3), we found that the oxygen consumption of Acropora digitifera larvae tended to be suppressed with reduced pH, although a statistically significant difference was not observed between pH conditions. Larval metamorphosis was also observed, confirming that successful recruitment is impaired when metamorphosis is disrupted, despite larval survival. Results also showed that the metamorphosis rate significantly decreased under acidified seawater conditions after both short (2 h) and long (7 d) term exposure. These results imply that acidified seawater impacts larval physiology, suggesting that suppressed metabolism and metamorphosis may alter the dispersal potential of larvae and subsequently reduce the resilience of coral communities in the near future as the ocean pH decreases.

Here, we report the complete genome sequences of low-passage virulent and high-passage avirulent variants of pathogenic Leptospira interrogans serovar Manilae strain UP-MMC-NIID, a major causative agent of leptospirosis. While there were no major differences between the genome sequences, the levels of base modifications were higher in the avirulent variant.

Abstract. Increasing the acidity of ocean waters will directly threaten calcifying marine organisms such as reef-building scleractinian corals, and the myriad of species that rely on corals for protection and sustenance. Ocean pH has already decreased by around 0.1 pH units since the beginning of the industrial revolution, and is expected to decrease by another 0.2–0.4 pH units by 2100. This study mimicked the pre-industrial, present, and near-future levels of pCO2 using a precise control system (± 5% pCO2), to assess the impact of ocean acidification on the calcification of recently settled primary polyps of Acropora digitifera, both with and without symbionts, and adult fragments with symbionts. The increase in pCO2 of ~100 μatm between the pre-industrial period and the present had more effect on the calcification rate of adult A. digitifera than the anticipated future increases of several hundreds of micro-atmospheres of pCO2. The primary polyps with symbionts showed higher calcification rates than primary polyps without symbionts, suggesting that: (i) primary polyps housing symbionts are more tolerant to near-future ocean acidification than organisms without symbionts, and (ii) corals acquiring symbionts from the environment (i.e., broadcasting species) will be more vulnerable to ocean acidification than corals that maternally acquire symbionts.

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