Draft genomes of three closely related low light-adapted <i>Prochlorococcus</i>

OBJECTIVES: The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism's vast wild diversity in sequence collections, we performed a set of isolation efforts targeting low light-adapted Prochlorococcus. Three genomes resulting from this larger body of work are described here.DATA DESCRIPTION: We present draft-quality Prochlorococcus genomes from enrichment cultures P1344, P1361, and P1363, sampled in the North Pacific. The genomes were built from Illumina paired reads assembled de novo. Supporting datasets of raw reads, assessments, and sequences from co-enriched heterotrophic marine bacteria are also provided. These three genomes represent members of the low light-adapted LLIV Prochlorococcus clade that are closely related, with 99.9% average nucleotide identity between pairs, yet vary in gene content. Expanding the powerful toolkit of Prochlorococcus genomes, these sequences provide an opportunity to study fine-scale variation and microevolutionary processes.</p

Physiology and evolution of nitrate acquisition in Prochlorococcus

Prochlorococcus is the numerically dominant phototroph in the oligotrophic subtropical ocean and carries out a significant fraction of marine primary productivity. Although field studies have provided evidence for nitrate uptake by Prochlorococcus, little is known about this trait because axenic cultures capable of growth on nitrate have not been available. Additionally, all previously sequenced genomes lacked the genes necessary for nitrate assimilation. Here we introduce three Prochlorococcus strains capable of growth on nitrate and analyze their physiology and genome architecture. We show that the growth of high-light (HL) adapted strains on nitrate is ~17% slower than their growth on ammonium. By analyzing 41 Prochlorococcus genomes, we find that genes for nitrate assimilation have been gained multiple times during the evolution of this group, and can be found in at least three lineages. In low-light adapted strains, nitrate assimilation genes are located in the same genomic context as in marine Synechococcus. These genes are located elsewhere in HL adapted strains and may often exist as a stable genetic acquisition as suggested by the striking degree of similarity in the order, phylogeny and location of these genes in one HL adapted strain and a consensus assembly of environmental Prochlorococcus metagenome sequences. In another HL adapted strain, nitrate utilization genes may have been independently acquired as indicated by adjacent phage mobility elements; these genes are also duplicated with each copy detected in separate genomic islands. These results provide direct evidence for nitrate utilization by Prochlorococcus and illuminate the complex evolutionary history of this trait.Gordon and Betty Moore Foundation (Grant GBMF495)National Science Foundation (U.S.) (Grant OCE-1153588)National Science Foundation (U.S.) (Grant DBI-0424599

A Framework for Prioritizing the TESS Planetary Candidates Most Amenable to Atmospheric Characterization

A key legacy of the recently launched TESS mission will be to provide the astronomical community with many of the best transiting exoplanet targets for atmospheric characterization. However, time is of the essence to take full advantage of this opportunity. JWST, although delayed, will still complete its nominal five year mission on a timeline that motivates rapid identification, confirmation, and mass measurement of the top atmospheric characterization targets from TESS. Beyond JWST, future dedicated missions for atmospheric studies such as ARIEL require the discovery and confirmation of several hundred additional sub-Jovian size planets (R_p < 10 R_Earth) orbiting bright stars, beyond those known today, to ensure a successful statistical census of exoplanet atmospheres. Ground-based ELTs will also contribute to surveying the atmospheres of the transiting planets discovered by TESS. Here we present a set of two straightforward analytic metrics, quantifying the expected signal-to-noise in transmission and thermal emission spectroscopy for a given planet, that will allow the top atmospheric characterization targets to be readily identified among the TESS planet candidates. Targets that meet our proposed threshold values for these metrics would be encouraged for rapid follow-up and confirmation via radial velocity mass measurements. Based on the catalog of simulated TESS detections by Sullivan et al. (2015), we determine appropriate cutoff values of the metrics, such that the TESS mission will ultimately yield a sample of $\sim300$ high-quality atmospheric characterization targets across a range of planet size bins, extending down to Earth-size, potentially habitable worlds.Comment: accepted to PAS

The First Habitable Zone Earth-Sized Planet From TESS II: Spitzer Confirms TOI-700 d

We present Spitzer 4.5 μm observations of the transit of TOI-700 d, a habitable-zone Earth-sized planet in a multiplanet system transiting a nearby M-dwarf star (TIC 150428135, 2MASS J06282325–6534456). TOI-700 d has a radius of 1.144^(+0.062)_(-0.061) R⊕ and orbits within its host star's conservative habitable zone with a period of 37.42 days (T_(eq) ~ 269 K). TOI-700 also hosts two small inner planets (R_b = 1.037^(+0.0065)_(-0.064) R⊕ and R_c = 2.65^(+0.16)_(-0.15) R⊕) with periods of 9.98 and 16.05 days, respectively. Our Spitzer observations confirm the Transiting Exoplanet Survey Satellite (TESS) detection of TOI-700 d and remove any remaining doubt that it is a genuine planet. We analyze the Spitzer light curve combined with the 11 sectors of TESS observations and a transit of TOI-700 c from the LCOGT network to determine the full system parameters. Although studying the atmosphere of TOI-700 d is not likely feasible with upcoming facilities, it may be possible to measure the mass of TOI-700 d using state-of-the-art radial velocity (RV) instruments (expected RV semiamplitude of ~70 cm s⁻¹)

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments

Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography

TOI 122b and TOI 237b: Two Small Warm Planets Orbiting Inactive M Dwarfs Found by TESS

peer reviewedWe report the discovery and validation of TOI 122b and TOI 237b, two warm planets transiting inactive M dwarfs observed by the Transiting Exoplanet Survey Satellite (TESS). Our analysis shows that TOI 122b has a radius of 2.72 ± 0.18 R[SUB]⊕[/SUB] and receives 8.8 ± 1.0 times Earth's bolometric insolation, and TOI 237b has a radius of 1.44±0.12 R⊕ and receives 3.7 ± 0.5 times Earth's insolation, straddling the 6.7 × Earth insolation that Mercury receives from the Sun. This makes these two of the cooler planets yet discovered by TESS, even on their 5.08 and 5.43 day orbits. Together, they span the small-planet radius valley, providing useful laboratories for exploring volatile evolution around M dwarfs. Their relatively nearby distances (62.23 ± 0.21 pc and 38.11 ± 0.23 pc, respectively) make them potentially feasible targets for future radial velocity follow-up and atmospheric characterization, although such observations may require substantial investments of time on large telescopes

The First Habitable-zone Earth-sized Planet from TESS. II. Spitzer Confirms TOI-700 d

We present Spitzer 4.5 μm observations of the transit of TOI-700 d, a habitable-zone Earth-sized planet in a multiplanet system transiting a nearby M-dwarf star (TIC 150428135, 2MASS J06282325-6534456). TOI-700 d has a radius of 1.144-0.061+0.062R⊕ and orbits within its host star's conservative habitable zone with a period of 37.42 days (T eq ∼ 269 K). TOI-700 also hosts two small inner planets (R b = 1.037-0.064+0.065R⊕and R c = 2.65-0.15+0.16R⊕) with periods of 9.98 and 16.05 days, respectively. Our Spitzer observations confirm the Transiting Exoplanet Survey Satellite (TESS) detection of TOI-700 d and remove any remaining doubt that it is a genuine planet. We analyze the Spitzer light curve combined with the 11 sectors of TESS observations and a transit of TOI-700 c from the LCOGT network to determine the full system parameters. Although studying the atmosphere of TOI-700 d is not likely feasible with upcoming facilities, it may be possible to measure the mass of TOI-700 d using state-of-the-art radial velocity (RV) instruments (expected RV semiamplitude of ∼70 cm s-1)

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

TESS Discovery of an Ultra-short-period Planet around the Nearby M Dwarf LHS 3844

Data from the newly commissioned Transiting Exoplanet Survey Satellite has revealed a 'hot Earth' around LHS 3844, an M dwarf located 15 pc away. The planet has a radius of R ⊕ and orbits the star every 11 hr. Although the existence of an atmosphere around such a strongly irradiated planet is questionable, the star is bright enough (I = 11.9, K = 9.1) for this possibility to be investigated with transit and occultation spectroscopy. The star's brightness and the planet's short period will also facilitate the measurement of the planet's mass through Doppler spectroscopy