Victor Gonzalez

The genome of melon (Cucumis melo L.)

We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site–leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.

Fluid generation and pathways beneath an active compressional orogen, the New Zealand Southern Alps, inferred from magnetotelluric data

[1] Forty-one wideband magnetotelluric (MT) soundings were collected in a 150-km-long transect across the Southern Alps of the central South Island of New Zealand, an active compressional orogen. Decomposed MT impedance tensors, vertical magnetic field relations, and reconnaissance soundings at two locations off line imply an approximately two-dimensional geometry here with average regional geoelectric strike of ∼N40°E, similar to surface geologic trends. Two independent, two-dimensional inversion algorithms were applied to the MT data, and both imply a concave-upward (U-shaped), middle to lower crustal conductive zone beneath the west central portion of the island. The average conductivity of this zone in the strike direction appears to be much higher than that required across strike and may represent anisotropy or along-strike conductive strands narrower than the transverse magnetic (cross-strike) mode MT data can resolve. The deep crustal conductor under the Southern Alps is interpreted to represent mainly a volume of fluids arising from prograde metamorphism within a thickening crust. Fluid interconnection and electrical conduction are promoted by shear deformation. The conductor rises northwestward toward the trace of the Alpine Fault but attains a near-vertical configuration at a depth of ∼10 km and reaches close to the surface 5-10 km inland of the fault trace itself. The transition to vertical orientation at this depth is interpreted to occur as fluids ascend across the brittle-ductile transition in uplifting schist and approach the surface through induced hydrofractures. The high-grade schist becomes resistive after depletion of fluids and continues to extrude toward the Alpine Fault. Shallow extensions of the deep high conductivity are coincident with modern, hydrothermal veining and gold mineralization interpreted to be of deep crustal provenance. To the southeast, high conductivity also reaches the surface coincident with a major back thrust fault zone of the doubly vergent Southern Alps orogen, which also exhibits evidence for expulsion of high-temperature fluids. The higher conductivity inferred along strike (possible anisotropy) could reflect more efficient fluid interconnection in this higher-strain direction, as well as possible contributions by sheared, fluid-deposited graphite. Conductivity of the uppermost mantle of the South Island is low, consistent with advection of cold mantle lithosphere into the underlying asthenosphere as suggested by P wave delay studies.

Geodetic and seismic constraints on some seismogenic zone processes in Costa Rica

New seismic and geodetic data from Costa Rica provide insight into seismogenic zone processes in Central America, where the Cocos and Caribbean plates converge. Seismic data are from combined land and ocean bottom deployments in the Nicoya peninsula in northern Costa Rica and near the Osa peninsula in southern Costa Rica. In Nicoya, inversion of GPS data suggests two locked patches centered at 14 ± 2 and 39 ± 6 km depth. Interplate microseismicity is concentrated in the more freely slipping intermediate zone, suggesting that small interseismic earthquakes may not accurately outline the updip limit of the seismogenic zone, the rupture zone for future large earthquakes, at least over the short (∼1 year) observation period. We also estimate northwest motion of a coastal “sliver block” at 8 ± 3 mm/yr, probably related to oblique convergence. In the Osa region to the south, convergence is orthogonal to the trench. Cocos-Caribbean relative motion is partitioned here, with ∼8 cm/yr on the Cocos-Panama block boundary (including a component of permanent shortening across the Fila Costena fold and thrust belt) and ∼1 cm/yr on the Panama block–Caribbean boundary. The GPS data suggest that the Cocos plate–Panama block boundary is completely locked from ∼10–50 km depth. This large locked zone, as well as associated forearc and back-arc deformation, may be related to subduction of the shallow Cocos Ridge and/or younger lithosphere compared to Nicoya, with consequent higher coupling and compressive stress in the direction of plate convergence.

Strong along-arc variations in attenuation in the mantle wedge beneath Costa Rica and Nicaragua

Attenuation structure in the Central American subduction zone was imaged using local events recorded by the Tomography Under Costa Rica and Nicaragua array, a 20-month-long deployment (July 2004 until March 2006) of 48 seismometers that spanned the fore-arc, arc, and back-arc regions of Nicaragua and Costa Rica. P and S waveforms were inverted separately for the corner frequency and moment of each event and for the path-averaged attenuation operator (t*) of each event-station pair, assuming attenuation is slightly frequency-dependent ( = 0.27). Then, tomographic inversions were performed for S and P attenuation (Q S ?1 and Q P ?1). Since P wave amplitudes reflect both shear and the bulk moduli, tomographic inversions were also performed to determine shear and bulk attenuation (Q S ?1 and Q ?1), the loss of energy per cycle owing to shearing and uniform compression, respectively. Damping and other inversion tomographic parameters were systematically varied. As is typical in subduction zone attenuation studies, a less attenuating slab, upper plate, and wedge corner and a more attenuating mantle wedge were imaged. In addition, first-order differences between the mantles beneath Nicaragua and Costa Rica were observed. The slab in Nicaragua is more attenuating than the slab in Costa Rica. A larger zone of higher shear attenuation also characterizes the Nicaraguan mantle wedge. Within the wedge, maximum attenuation values at 1 Hz correspond to Qs = 38–73 beneath Nicaragua and Qs = 62–84 beneath Costa Rica, and average values are Qs = 76–78 and Qs = 84–88, respectively. Attenuation variations correlate with along-arc trends in geochemical indicators that suggest that melting beneath Nicaragua occurs at more hydrated conditions, and possibly to greater extents and depths, relative to northern Costa Rica. Shear attenuation dominates over bulk attenuation in the well-resolved regions of the wedge. The more extensive zones of greater shear attenuation observed in the Nicaraguan wedge could be explained by higher temperatures and/or greater hydration, but comparison with petrological data suggests that hydration variations play a larger role. Average wedge attenuation values are comparable to estimates for the Andes and Japan, greater than those for Alaska, and less than those for Tonga-Lau.

Seismic tomography and earthquake locations in the Nicaraguan and Costa Rican upper mantle

The Central American subduction zone exhibits large variations in geochemistry, downgoing plate roughness and dip, and volcano locations over a short distance along the arc. Results from joint inversions for Vp, Vp/Vs, and hypocenters from the Tomography Under Costa Rica and Nicaragua (TUCAN) experiment give insight into its geometry and structure. In both Costa Rica and Nicaragua, the intermediate-depth seismic zone is a single layer no more than 10 to 20 km thick. Tomographic images show that throughout Nicaragua and Costa Rica the slowest mantle P wave velocities appear below and behind the volcanic front, indicating likely zones of highest temperature extending 80 to 120 km depth. A sheet of high Vp/Vs, thought to be caused by melt, is imaged directly beneath the Nicaraguan volcanoes, whereas a weaker, broader anomaly is imaged beneath the Costa Rican volcanoes, potentially indicating a greater extent of melting beneath Nicaragua. Within the downgoing plate, anomalously low velocities occur at least 20–30 km below Wadati-Benioff zone seismicity, to depths of 140 km beneath Nicaragua and to 60 km depth beneath Costa Rica. They indicate 10–20% serpentinized upper mantle of the downgoing plate beneath Nicaragua, similar to that inferred from refraction seaward of the trench, but continuing to subarc depths. This unusually hydrated lithosphere may introduce more water into the Nicaraguan mantle, initiating increased amount of melting and fluid flux to the arc.

The March 25, 1990 (Mw = 7.0, ML = 6.8), earthquake at the entrance of the Nicoya Gulf, Costa Rica: Its prior activity, foreshocks, aftershocks, and triggered seismicity

On March 25, 1990 a large earthquake (Mw = 7.0, ML = 6.8) occurred at the entrance of the Nicoya Gulf, Costa Rica, at 1322:55.6 UTC, producing considerable damage in central Costa Rica and generating much interest about whether or not the Nicoya seismic gap (Nishenko, 1989) had broken. The local country-wide seismographic network recorded 6 years of activity prior to this large earthquake, 16 hours of foreshocks, the mainshock, and its aftershocks. This network is operated jointly by the Costa Rica Volcanological and Seismological Observatory at the National University (OVSICORI-UNA), and the Charles F. Richter Seismological Laboratory at the University of California, Santa Cruz (CFRSL-UCSC). We obtained high resolution locations from this network and located the mainshock at 9°38.5′N, 84°55.6′W (depth is 20.0 km) and the largest foreshock (Mw = 6.0, March 25, 1990, at 1316:05.8 UTC) at 9°36.4′N, 84°57.1′W (depth is 22.4 km). We find that the aftershock zone abuts the southeast boundary of the Nicoya seismic gap, suggesting that the seismic gap did not rupture. Since the installation of the local network in April 1984 to March 24, 1990, nearly 1900 earthquakes with magnitudes from 1.7 to 4.8 (318 with magnitude 3.0 or larger) have been located at the entrance of the Nicoya Gulf, one of the most active regions in Costa Rica. The March 25 earthquake occurred at the northwest edge of this region, where a sequence of foreshocks began 16 hours prior to the mainshock. The spatial-temporal distribution of aftershocks and directivity analysis of the mainshock rupture process using teleseismic records both indicate a southeast propagating rupture. The mainshock ruptured an asperity of approximately 600 km2 of area, with this area expanding to 4000 km2 after 7 days. We present evidence that suggests that the ruptured asperity is produced by the subduction of a seamount. Inversion of teleseismic broadband and long-period P and SH waves yields a thrust faulting mechanism with the shallow plane striking 292°, dipping 26°, and with a rake of 88°, in agreement with the subduction of the Cocos plate under the Caribbean plate. Local first motions for the largest foreshock and the mainshock agree with this solution. We also present evidence suggesting that the March 25, 1990, earthquake triggered and reactivated several seismic swarms in central Costa Rica and temporally decreased the activity in the epicentral area of the July 3, 1983 (Ms = 6.2), Perez Zeledon earthquake.

Conjugative Transfer of p42a from Rhizobium etli CFN42, Which Is Required for Mobilization of the Symbiotic Plasmid, Is Regulated by Quorum Sensing

Rhizobium etli CFN42 contains six plasmids. Only one of them, p42a, is self-conjugative at high frequency. This plasmid is strictly required for mobilization of the symbiotic plasmid (pSym). To study the transfer mechanism of p42a, a self-transmissible cosmid clone containing its transfer region was isolated. Its sequence showed that most of the tra genes are highly similar to genes of Agrobacterium tumefaciens pTiC58 and other related plasmids. Four putative regulatory genes were identified; three of these (traI, traR, and cinR) belong to the LuxR-LuxI family. Mutagenesis of these genes confirmed their requirement for p42a transfer. We found that the conjugative transfer of p42a is dependent on quorum sensing, and consequently pSym transfer also was found to be similarly regulated, establishing a complex link between environmental conditions and pSym transfer. Although R. etli has been shown to produce different N-acyl-homoserine lactones, only one of them, a 3-oxo-C(8)-homoserine lactone encoded by the traI gene described here, was involved in transfer. Mutagenesis of the fourth regulatory gene, traM, had no effect on transfer. Analysis of transcriptional fusions of the regulatory genes to a reporter gene suggests a complex regulation scheme for p42a conjugative transfer. Conjugal transfer gene expression was found to be directly upregulated by TraR and the 3-oxo-C(8)-homoserine lactone synthesized by TraI. The traI gene was autoregulated by these elements and positively regulated by CinR, while cinR expression required traI. Finally, we did not detect expression of traM, indicating that in p42a TraM may be expressed so weakly that it cannot inhibit conjugal transfer, leading to the unrepressed transfer of p42a.

A tremor and slip event on the Cocos-Caribbean subduction zone as measured by a global positioning system (GPS) and seismic network on the Nicoya Peninsula, Costa Rica

In May 2007 a network of global positioning systems (GPS) and seismic stations on the Nicoya Peninsula, of northern Costa Rica, recorded a slow-slip event accompanied by seismic tremor. The close proximity of the Nicoya Peninsula to the seismogenic part of the Cocos-Caribbean subduction plate boundary makes it a good location to study such events. Several centimeters of southwest motion were recorded by the GPS stations over a period of several days to several weeks, and the seismic stations recorded three distinct episodes of tremor during the same time span. Inversion of the surface displacement data for the depth and pattern of slip on the plate interface shows peak slip at a depth of 25–30 km, downdip of the main seismogenic zone. Estimated temperatures here are ∼250°–300°C, lower than in other subduction zones where events of this nature have been previously identified. There may also be a shallower patch of slip at ∼6 km depth. These results are significant in that they are the first to suggest that slow slip can occur at the updip transition from stick slip to stable sliding, and that a critical temperature threshold is not required for slow slip. Tremor and low-frequency earthquake locations are more difficult to determine. Our results suggest they occur on or near the plate interface at the same depth range as the deep slow slip, but not spatially colocated.

Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin

BackgroundThe melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and genetic studies. Despite similar nuclear and chloroplast genome sizes, cucurbits show great variation when their mitochondrial genomes are compared. The melon possesses the largest plant mitochondrial genome, as much as eight times larger than that of other cucurbits.ResultsThe nucleotide sequences of the melon chloroplast and mitochondrial genomes were determined. The chloroplast genome (156,017 bp) included 132 genes, with 98 single-copy genes dispersed between the small (SSC) and large (LSC) single-copy regions and 17 duplicated genes in the inverted repeat regions (IRa and IRb). A comparison of the cucumber and melon chloroplast genomes showed differences in only approximately 5% of nucleotides, mainly due to short indels and SNPs. Additionally, 2.74 Mb of mitochondrial sequence, accounting for 95% of the estimated mitochondrial genome size, were assembled into five scaffolds and four additional unscaffolded contigs. An 84% of the mitochondrial genome is contained in a single scaffold. The gene-coding region accounted for 1.7% (45,926 bp) of the total sequence, including 51 protein-coding genes, 4 conserved ORFs, 3 rRNA genes and 24 tRNA genes. Despite the differences observed in the mitochondrial genome sizes of cucurbit species, Citrullus lanatus (379 kb), Cucurbita pepo (983 kb) and Cucumis melo (2,740 kb) share 120 kb of sequence, including the predicted protein-coding regions. Nevertheless, melon contained a high number of repetitive sequences and a high content of DNA of nuclear origin, which represented 42% and 47% of the total sequence, respectively.ConclusionsWhereas the size and gene organisation of chloroplast genomes are similar among the cucurbit species, mitochondrial genomes show a wide variety of sizes, with a non-conserved structure both in gene number and organisation, as well as in the features of the noncoding DNA. The transfer of nuclear DNA to the melon mitochondrial genome and the high proportion of repetitive DNA appear to explain the size of the largest mitochondrial genome reported so far.

Crustal structure along the southern Central American volcanic front

Subduction alters continents several ways, including accretion, magmatic addition, mantle wedge serpentinization, and crustal differentiation. These changes affect seismic velocities, so characterizing upper plate crust establishes a baseline for composition and continental growth. Teleseismic P and PP arrivals from a temporary deployment of broadband seismometers in Central America have been used to estimate crustal thickness and Vp/Vs ratio from receiver functions and to image crust across the active arc. Crustal thickness ranges from 25 to 44 km with formal errors of 1.6–9.2 km. The thinnest crust (24.6 ± 3.5 km) lies directly beneath the Nicaraguan arc, whereas the thickest crust lies in the Nicaraguan back arc (43.5 ± 2.5 km) and beneath the Costa Rican arc (37.9 ± 5.2 km). Crustal structure and Vp/Vs show sharp transitions at terrane boundaries. The Moho exhibits strong velocity contrasts throughout the study area of ∼0.5–1.0 km/s, even beneath arc and fore arc, precluding extensive serpentinization or ponded melt below the Moho. Crust is thicker beneath the Costa Rican arc, consistent with 10–23 km3/km/Ma crustal growth. The crust is thinner by 11–18 km beneath the large depression in central Nicaragua, with the thinnest crust beneath the arc. There, the relationship between thin crust, arc location, and deeper seismic velocities suggests that upper plate structure plays a critical role in focusing magma to the surface.