The Cyclically Seasonal Drosophila subobscura Inversion O Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes

Chromosome inversions are important contributors to standing genetic variation in Drosophila subobscura. Presently, the species is experiencing a rapid replacement of high-latitude by low-latitude inversions associated with global warming. Yet not all low-latitude inversions are correlated with the ongoing warming trend. This is particularly unexpected in the case of O because it shows a regular seasonal cycle that peaks in summer and rose with a heatwave. The inconsistent behavior of O across components of the ambient temperature suggests that is causally more complex than simply due to temperature alone. In order to understand the dynamics of O, high-quality genomic data are needed to determine both the breakpoints and the genetic content. To fill this gap, here we generated a PacBio long read-based chromosome-scale genome assembly, from a highly homozygous line made isogenic for an O chromosome. Then we isolated the complete continuous sequence of O by conserved synteny analysis with the available reference genome. Main findings include the following: (i) the assembled O inversion stretches 9.936 Mb, containing > 1,000 annotated genes; (ii) O had a complex origin, involving multiple breaks associated with non-B DNA-forming motifs, formation of a microinversion, and ectopic repair in trans with the two homologous chromosomes; (iii) the O breakpoints carry a pre-inversion record of fragility, including a sequence insertion, and transposition with later inverted duplication of an Attacin immunity gene; and (iv) the O inversion relocated the major insulin signaling forkhead box subgroup O (foxo) gene in tight linkage with its antagonistic regulatory partner serine/threonine-protein kinase B (Akt1) and disrupted concerted evolution of the two inverted Attacin duplicates, reattaching them to dFOXO metabolic enhancers. Our findings suggest that O exerts antagonistic pleiotropic effects on reproduction and immunity, setting a framework to understand its relationship with climate change. Furthermore, they are relevant for fragility in genome rearrangement evolution and for current views on the contribution of breakage versus repair in shaping inversion-breakpoint junctions

Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH

The neutrality theory predicts that the rate of neutral molecular evolution is constant over time, and thus that there is a molecular clock for timing evolutionary events. It has been observed that the variance of the rate of evolution is generally larger than expected according to the neutrality theory, which has raised the question of how reliable the molecular clock is or, indeed, whether there is a molecular clock at all. We have carried out an extensive investigation of three proteins, glycerol-3-phosphate dehydrogenase (GPDH), superoxide dismutase (SOD), and xanthine dehydrogenase (XDH). We have observed that (i) the three proteins evolve erratically through time and across lineages and (ii) the erratic patterns of acceleration and deceleration differ from locus to locus, so that one locus may evolve faster in one than another lineage, whereas the opposite may be the case for another locus. The observations are inconsistent with the predictions made by various subsidiary hypotheses proposed to account for the overdispersion of the molecular clock.F.R.-T. has received support from the Spanish Council for Scientific Research (Contrato Temporal de Investigación) and Grant AGL2000- 1073 from the Ministerio de Ciencia y Tecnología to A. Ballester. Research was supported by National Institutes of Health Grant GM42397 (to F.J.A.).Peer Reviewe

‘Costa da Morte’ ataxia is spinocerebellar ataxia 36: clinical and genetic characterization

Spinocerebellar ataxia 36 has been recently described in Japanese families as a new type of spinocerebellar ataxia with motor neuron signs. It is caused by a GGCCTG repeat expansion in intron 1 of NOP56. Family interview and document research allowed us to reconstruct two extensive, multigenerational kindreds stemming from the same village (Costa da Morte in Galicia, Spain), in the 17th century. We found the presence of the spinocerebellar ataxia 36 mutation co-segregating with disease in these families in whom we had previously identified an ∼0.8 Mb linkage region to chromosome 20 p. Subsequent screening revealed the NOP56 expansion in eight additional Galician ataxia kindreds. While normal alleles contain 5–14 hexanucleotide repeats, expanded alleles range from ∼650 to 2500 repeats, within a shared haplotype. Further expansion of repeat size was frequent, especially upon paternal transmission, while instances of allele contraction were observed in maternal transmissions. We found a total of 63 individuals carrying the mutation, 44 of whom were confirmed to be clinically affected; over 400 people are at risk. We describe here the detailed clinical picture, consisting of a late-onset, slowly progressive cerebellar syndrome with variable eye movement abnormalities and sensorineural hearing loss. There were signs of denervation in the tongue, as well as mild pyramidal signs, but otherwise no signs of classical amyotrophic lateral sclerosis. Magnetic resonance imaging findings were consistent with the clinical course, showing atrophy of the cerebellar vermis in initial stages, later evolving to a pattern of olivo-ponto-cerebellar atrophy. We estimated the origin of the founder mutation in Galicia to have occurred ∼1275 years ago. Out of 160 Galician families with spinocerebellar ataxia, 10 (6.3%) were found to have spinocerebellar ataxia 36, while 15 (9.4%) showed other of the routinely tested dominant spinocerebellar ataxia types. Spinocerebellar ataxia 36 is thus, so far, the most frequent dominant spinocerebellar ataxia in this region, which may have implications for American countries associated with traditional Spanish emigration

The Vein Patterning 1 (VEP1) Gene Family Laterally Spread through an Ecological Network

Lateral gene transfer (LGT) is a major evolutionary mechanism in prokaryotes. Knowledge about LGT— particularly, multicellular— eukaryotes has only recently started to accumulate. A widespread assumption sees the gene as the unit of LGT, largely because little is yet known about how LGT chances are affected by structural/functional features at the subgenic level. Here we trace the evolutionary trajectory of VEin Patterning 1, a novel gene family known to be essential for plant development and defense. At the subgenic level VEP1 encodes a dinucleotide-binding Rossmann-fold domain, in common with members of the short-chain dehydrogenase/reductase (SDR) protein family. We found: i) VEP1 likely originated in an aerobic, mesophilic and chemoorganotrophic α-proteobacterium, and was laterally propagated through nets of ecological interactions, including multiple LGTs between phylogenetically distant green plant/fungi-associated bacteria, and five independent LGTs to eukaryotes. Of these latest five transfers, three are ancient LGTs, implicating an ancestral fungus, the last common ancestor of land plants and an ancestral trebouxiophyte green alga, and two are recent LGTs to modern embryophytes. ii) VEP1's rampant LGT behavior was enabled by the robustness and broad utility of the dinucleotide-binding Rossmann-fold, which provided a platform for the evolution of two unprecedented departures from the canonical SDR catalytic triad. iii) The fate of VEP1 in eukaryotes has been different in different lineages, being ubiquitous and highly conserved in land plants, whereas fungi underwent multiple losses. And iv) VEP1-harboring bacteria include non-phytopathogenic and phytopathogenic symbionts which are non-randomly distributed with respect to the type of harbored VEP1 gene. Our findings suggest that VEP1 may have been instrumental for the evolutionary transition of green plants to land, and point to a LGT-mediated ‘Trojan Horse’ mechanism for the evolution of bacterial pathogenesis against plants. VEP1 may serve as tool for revealing microbial interactions in plant/fungi-associated environments

Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

Background: Drosophila subobscura has long been a central model in evolutionary genetics. Presently, its use is hindered by the lack of a reference genome. To bridge this gap, here we used PacBio long-read technology, together with the available wealth of genetic marker information, to assemble and annotate a high-quality nuclear and complete mitochondrial genome for the species. With the obtained assembly, we performed the first synteny analysis of genome structure evolution in the subobscura subgroup. Results: We generated a highly-contiguous ~ 129 Mb-long nuclear genome, consisting of six pseudochromosomes corresponding to the six chromosomes of a female haploid set, and a complete 15,764 bp-long mitogenome, and provide an account of their numbers and distributions of codifying and repetitive content. All 12 identified paracentric inversion differences in the subobscura subgroup would have originated by chromosomal breakage and repair, with some associated duplications, but no evidence of direct gene disruptions by the breakpoints. Between lineages, inversion fixation rates were 10 times higher in continental D. subobscura than in the two small oceanic-island endemics D. guanche and D. madeirensis. Within D. subobscura, we found contrasting ratios of chromosomal divergence to polymorphism between the A sex chromosome and the autosomes. Conclusions: We present the first high-quality, long-read sequencing of a D. subobscura genome. Our findings generally support genome structure evolution in this species being driven indirectly, through the inversions' recombination-suppression effects in maintaining sets of adaptive alleles together in the face of gene flow. The resources developed will serve to further establish the subobscura subgroup as model for comparative genomics and evolutionary indicator of global change

Cambios de las frecuencias alélicas en un compuesto de maíz a través de tres ciclos de selección recurrente

4 páginas, 2 tablas.- Trabajo presentado en el II Congreso de Mejora Genética de Plantas, celebrado en León (España) del 21 al 24 de septiembre de 2004.Sesamia nonagrioides Lèfevbre es la principal plaga del maíz en el área mediterránea (Cordero et al. 1998). De entre los materiales evaluados para resistencia a dicha plaga destacaron diversas poblaciones provenientes del valle del Ebro y el compuesto EPS7 (Malvar et al. 1993) que fue construido con cuatro poblaciones del valle del Ebro y del este peninsular (Ordás et al. 1991). Este compuesto fue sometido a tres ciclos de selección recurrente intrapoblacional para mejorar su rendimiento y el compuesto mejorado fue denominado EPS12. Basándose en trabajos previos que determinaron que la herencia de la resistencia a S. nonagrioides era básicamente aditiva (Butrón et al. 1999, Cartea et al. 1999), se diseñó un programa de mejora intrapoblacional para aumentar la resistencia del compuesto EPS12. En dicho programa también se tuvo en cuenta el rendimiento como carácter secundario de mejora porque, cuando el carácter de selección es la resistencia a insectos, es común que el progreso en la selección se haga a expensas de otros caracteres agronómicos como el rendimiento (Klenke et al. 1988). Se pueden seguir los cambios a nivel molecular asociados al proceso de selección y determinar cuáles de dichos cambios podrían ser producto de la selección direccional encaminada a aumentar la frecuencia de los alelos favorables en loci involucrados en la resistencia a S. nonagrioides. Dichos cambios direccionales que no puedan ser explicados por fenómenos de deriva genética serían un indicativo de la posible presencia, en las cercanías del marcador considerado, de QTLs (loci para caracteres cuantitativos) involucrados en el carácter o caracteres de selección. Los objetivos de este trabajo fueron: identificar cambios en las frecuencias alélicas de ciertos microsatélites asociados al proceso de selección e identificar regiones del genoma que pudieran estar involucradas en la herencia de los caracteres de selección.Este trabajo ha sido financiado por el proyecto del Ministerio de Ciencia y Tecnología AGL2000-00961.Peer reviewe

Resistencia de poblaciones precoces de maíz dulce al taladro

Comunicación presentada al X Congreso Nacional de Ciencias Hortícolas, celebrado en Pontevedra en mayo de 2003En los países mediterráneos, la principal plaga del maíz (Zea mays L.) es el taladro, causado por varias especies de lepidópteros, principalmente Sesamia nonagrioides Lef y, en menor medida, Ostrinia nubilalis Hbn. (Cordero y otros, 1998). En el noroeste de España, el número de larvas de S. nonagrioides es mayor y más variable que el de O. nubilalis en las mazorcas de maíz dulce (Velasco y otros 1999a). El daño del taladro en maíz depende de factores genéticos y otros tales como la fecha de siembra, la temperatura o la pluviosidad del periodo de cultivo. El daño en maíz dulce es más grave que en maíz grano por tratarse de un producto de consumo humano y porque el maíz dulce es menos resistente al taladro que el maíz grano. Velasco y otros (1999b) encontraron resistencia variable en diversas poblaciones de maíz dulce precoces, además algunas estuvieron entre las menos dañadas en 1996 y entre las más dañadas en 1997. El objetivo de este trabajo fue investigar la relación entre la resistencia al taladro y la fecha de infestación y el estado de madurez de la planta.Peer reviewe

Assessment of bedload equations using data obtained with tracers in two coarse-bed mountain streams (Narcea River basin, NW Spain)

International audienceThis paper evaluates the predictive power of nine bedload equations, comparing the results provided by the equations with the bedload rates obtained in a previous field-based tracer experiment accomplished in River Piguena and River Coto, two coarse bed streams from NW Spain. Rivers from NW Spain draining the northern watershed of the Cantabrian Mountain range flow into the Bay of Biscay in a short path (50-60 km). In this region, they are developed forested catchments featured by fluvial networks with relatively steep slopes, single-thread sinuous channels, and where bed sediment is typically coarse (cobble and gravel). Tagged stones were used to trace bed sediment movement during flood events in River Piguena and River Coto, the two main tributaries of the Narcea River basin. With the tracer results, bedload transport rates between 02 and 4.0 kg/s were estimated for six flood episodes. The tracer-based bedload discharges were compared with the bedload rates estimated with the bedload formulae (DuBoys-Straub, Schoklitsch, Meyer Peter-Muller, Bagbold, Einstein, Parker-Klingeman-McLean, Parker-Klingeman, Parker and Wilcock-Crowe). Our assessment shows that all of the bedload equations tend to overestimate when compared with the tracer-based results, with the Wilcock and Crowe (2003) equation the only exception in River Piguena. We linked these results to the particular geomorphology of coarse-bed rivers in humid and forested mountain environments. Within these rivers, armored textures and structural arrangements in the bed are ubiquitous; these features, together with a low sediment supply coming from upstream forested reaches, define a supply-limited condition for these channels limiting the potential use of bedload equations. The Wilcock and Crowe (2003) equation introduces complex corrections into the 'hiding function', and this could explain why it performs better

Alternative splicing: a missing piece in the puzzle of intron gain.

Spliceosomal introns, a hallmark of eukaryotic gene organization, were an unexpected discovery. After three decades, crucial issues such as when and how introns first appeared in evolution remain unsettled. An issue yet to be answered is how intron positions arise de novo. Phylogenetic investigations concur that intron positions continue to emerge, at least in some lineages. Yet genomic scans for the sources of introns occupying new positions have been fruitless. Two alternative solutions to this paradox are: (i) formation of new intron positions halted before the recent past and (ii) it continues to occur, but through processes different from those generally assumed. One process generally dismissed is intron sliding--the relocation of a preexisting intron over short distances--because of supposed associated deleterious effects. The puzzle of intron gain arises owing to a pervasive operational definition of introns, which sees them as precisely demarcated segments of the genome separated from the neighboring nonintronic DNA by unmovable limits. Intron homology is defined as position homology. Recent studies of pre-mRNA processing indicate that this assumption needs to be revised. We incorporate recent advances on the evolutionarily frequent process of alternative splicing, by which exons of primary transcripts are spliced in different patterns, into a new model of intron sliding that accounts for the diversity of intron positions. We posit that intron positional diversity is driven by two overlapping processes: (i) background process of continuous relocation of preexisting introns by sliding and (ii) spurts of extensive gain/loss of new intron sequences