RESUMO
Sex chromosomes are evolutionarily labile in many animals and sometimes fuse with autosomes, creating so-called neo-sex chromosomes. Fusions between sex chromosomes and autosomes have been proposed to reduce sexual conflict and to promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery of such fusions across the tree of life. Here, we discovered multiple fusions leading to neo-sex chromosomes in the sapho subclade of the classical adaptive radiation of Heliconius butterflies. Heliconius butterflies generally have 21 chromosomes with very high synteny. However, the five Heliconius species in the sapho subclade show large variation in chromosome number ranging from 21 to 60. We find that the W chromosome is fused with chromosome 4 in all of them. Two sister species pairs show subsequent fusions between the W and chromosomes 9 or 14, respectively. These fusions between autosomes and sex chromosomes make Heliconius butterflies an ideal system for studying the role of neo-sex chromosomes in adaptive radiations and the degeneration of sex chromosomes over time. Our findings emphasize the capability of short-read resequencing to detect genomic signatures of fusion events between sex chromosomes and autosomes even when sex chromosomes are not explicitly assembled.
Assuntos
Borboletas , Evolução Molecular , Cromossomos Sexuais , Animais , Borboletas/genética , Cromossomos Sexuais/genética , Feminino , Masculino , Filogenia , Genômica/métodos , Sintenia , Cromossomos de Insetos/genética , Genoma de InsetoRESUMO
YABBY genes encode specific TFs of seed plants involved in development and formation of leaves, flowers, and fruit. In the present work, genome-wide and expression analyses of the YABBY gene family were performed in six species of the Fragaria genus: Fragaria × ananassa, F. daltoniana, F. nilgerrensis, F. pentaphylla, F. viridis, and F. vesca. The chromosomal location, synteny pattern, gene structure, and phylogenetic analyses were carried out. By combining RNA-seq data and RT-qPCR analysis we explored specific expression of YABBYs in F. × ananassa and F. vesca. We also analysed the promoter regions of FaYABBYs and performed MeJA application to F. × ananassa fruit to observe effects on gene expression. We identified and characterized 25 YABBY genes in F. × ananassa and six in each of the other five species, which belong to FIL/YAB3 (YABBY1), YAB2 (YABBY2), YAB5 (YABBY5), CRC, and INO clades previously described. Division of the YABBY1 clade into YABBY1.1 and YABBY1.2 subclades is reported. We observed differential expression according to tissue, where some FaYABBYs are expressed mainly in leaves and flowers and to a minor extent during fruit development of F. × ananassa. Specifically, the FaINO genes contain jasmonate-responsive cis-acting elements in their promoters which may be functional since FaINOs are upregulated in F. × ananassa fruit under MeJA treatment. This study suggests that YABBY TFs play an important role in the development- and environment-associated responses of the Fragaria genus.
Assuntos
Ciclopentanos , Diploide , Fragaria , Regulação da Expressão Gênica de Plantas , Oxilipinas , Filogenia , Proteínas de Plantas , Fatores de Transcrição , Fragaria/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Ciclopentanos/metabolismo , Ciclopentanos/farmacologia , Oxilipinas/farmacologia , Oxilipinas/metabolismo , Frutas/genética , Frutas/crescimento & desenvolvimento , Poliploidia , Acetatos/farmacologia , Regiões Promotoras Genéticas/genética , Sintenia , Família MultigênicaRESUMO
The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and noncoding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole-genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared with other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared with a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.
Assuntos
Cavernas , Characidae , Cromossomos , Animais , Characidae/genética , Cromossomos/genética , Filogenia , Genoma , Genômica/métodos , Variação Genética , Locos de Características Quantitativas , Sintenia , FenótipoRESUMO
Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87â Gb distributed in 327 scaffolds, with an N50 of 279â Mb and an L50 of 3. Approximately 98.4% of the genome is contained in 14 scaffolds, with 6 large scaffolds (334-127â Mb) representing macrochromosomes and 8 small scaffolds (63-22â Mb) representing microchromosomes. Using standard gene modeling and transcriptomic data, we predicted 17,902 protein-coding genes on the genome. The repeat content is characterized by a large proportion of long interspersed nuclear elements that are relatively old. Synteny analysis revealed some microchromosomes with high repeat content are more prone to rearrangements but that both macro- and microchromosomes are well conserved across reptiles. We identified scaffold 14 as the X chromosome. This microchromosome presents perfect dosage compensation where the single X of males has the same expression levels as two X chromosomes in females. Finally, we estimated the effective population size for U. nigricaudus was extremely low, which may reflect a reduction in polymorphism related to it becoming a peninsular endemic.
Assuntos
Lagartos , Animais , Feminino , Masculino , Lagartos/genética , México , Cromossomos , Genoma , SinteniaRESUMO
In comparative genomics, the study of synteny can be a powerful method for exploring genome rearrangements, inferring genomic ancestry, defining orthology relationships, determining gene and genome duplications, and inferring gene positional conservation patterns across taxa. In this chapter, we present a step-by-step protocol for microsynteny network (SynNet) analysis, as an alternative to traditional methods of synteny comparison, where nodes in the network represent protein-coding genes and edges represent the pairwise syntenic relationships. The SynNet pipeline consists of six main steps: (1) pairwise genome comparisons between all the genomes being analyzed, (2) detection of inter- and intrasynteny blocks, (3) generation of an entire synteny database (i.e., edgelist), (4) network clustering, (5) phylogenomic profiling of the gene family of interest, and (6) evolutionary inference. The SynNet approach facilitates the rapid analysis and visualization of synteny relationships (from specific genes, specific gene families up to all genes) across a large number of genomes.
Assuntos
Genoma , Genômica , Evolução Molecular , Genômica/métodos , Filogenia , Plantas/genética , SinteniaRESUMO
Serrasalmidae has high morphological and chromosomal diversity. Based on molecular hypotheses, the family is currently divided into two subfamilies, Colossomatinae and Serrasalminae, with Serrasalminae composed of two tribes: Myleini (comprising most of pacus species) and Serrasalmini (represented by Metynnis, Catoprion, and remaining piranha's genera). This study aimed to analyze species of the tribes Myleini (Myloplus asterias, M. lobatus, M. rubripinnis, M. schomburgki, and Tometes camunani) and Serrasalmini (Metynnis cuiaba, M. hypsauchen, and M. longipinnis) using classical and molecular cytogenetic techniques in order to understand the chromosomal evolution of the family. The four species of the genus Myloplus and T. camunani presented 2n = 58 chromosomes, while the species of Metynnis presented 2n = 62 chromosomes. The distribution of heterochromatin occurred predominantly in pericentromeric regions in all species. Tometes camunani and Myloplus spp. presented only one site with 5S rDNA. Multiple markers of 18S rDNA were observed in T. camunani, M. asterias, M. lobatus, M. rubripinnis, and M. schomburgkii. For Metynnis, however, synteny of the 18S and 5S rDNA was observed in the three species, in addition to an additional 5S marker in M. longipinnis. These data, when superimposed on the phylogeny of the family, suggest a tendency to increase the diploid chromosome number from 54 to 62 chromosomes, which occurred in a nonlinear manner and is the result of several chromosomal rearrangements. In addition, the different karyotype formulas and locations of ribosomal sequences can be used as cytotaxonomic markers and assist in the identification of species.
Assuntos
Caraciformes/genética , Citogenética , Evolução Molecular , Filogenia , Animais , Caraciformes/classificação , DNA Ribossômico/genética , Heterocromatina/genética , Cariótipo , RNA Ribossômico 18S/genética , RNA Ribossômico 5S/genética , Sintenia/genéticaRESUMO
BACKGROUND: 6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-coding RNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB) constitute a group of microorganisms with strong biotechnological relevance, often exploited as starter cultures for industrial products through fermentation. Some strains are used as probiotics while others represent potential pathogens. Occasional reports of 6S RNA within this group already indicate striking metabolic implications. A conceivable idea is that LAB with 6S RNA defects may metabolize nutrients faster, as inferred from studies of Echerichia coli. This may accelerate fermentation processes with the potential to reduce production costs. Similarly, elevated levels of secondary metabolites might be produced. Evidence for this possibility comes from preliminary findings regarding the production of surfactin in Bacillus subtilis, which has functions similar to those of bacteriocins. The prerequisite for its potential biotechnological utility is a general characterization of 6S RNA in LAB. RESULTS: We provide a genomic annotation of 6S RNA throughout the Lactobacillales order. It laid the foundation for a bioinformatic characterization of common 6S RNA features. This covers secondary structures, synteny, phylogeny, and product RNA start sites. The canonical 6S RNA structure is formed by a central bulge flanked by helical arms and a template site for product RNA synthesis. 6S RNA exhibits strong syntenic conservation. It is usually flanked by the replication-associated recombination protein A and the universal stress protein A. A catabolite responsive element was identified in over a third of all 6S RNA genes. It is known to modulate gene expression based on the available carbon sources. The presence of antisense transcripts could not be verified as a general trait of LAB 6S RNAs. CONCLUSIONS: Despite a large number of species and the heterogeneity of LAB, the stress regulator 6S RNA is well-conserved both from a structural as well as a syntenic perspective. This is the first approach to describe 6S RNAs and short 6S RNA-derived transcripts beyond a single species, spanning a large taxonomic group covering multiple families. It yields universal insights into this regulator and complements the findings derived from other bacterial model organisms.
Assuntos
Regulação Bacteriana da Expressão Gênica , Lactobacillales/genética , RNA Bacteriano/genética , RNA não Traduzido/genética , Bacillus subtilis/genética , Sequência Conservada/genética , Humanos , Sintenia/genéticaRESUMO
Abstract Introduction: Climatic variables show a seasonal pattern in the central Amazon, but the intra-annual variability effect on tree growth is still unclear. For variables such as relative humidity (RH) and air vapor pressure deficit (VPD), whose individual effects on tree growth can be underestimated, we hypothesize that such influences can be detected by removing the effect of collinearity between regressors. Objective: This study aimed to determine the collinearity-free effect of climatic variability on tree growth in the central Amazon. Methods: Monthly radial growth was measured in 325 trees from January 2013 to December 2017. Irradiance, air temperature, rainfall, RH, and VPD data were also recorded. Principal Component Regression was used to assess the effect of micrometeorological variability on tree growth over time. For comparison, standard Multiple Linear Regression (MLR) was also used for data analysis. Results: Tree growth increased with increasing rainfall and relative humidity, but it decreased with rising maximum VPD, irradiance, and maximum temperature. Therefore, trees grew more slowly during the dry season, when irradiance, temperature and VPD were higher. Micrometeorological variability did not affect tree growth when MLR was applied. These findings indicate that ignoring the correlation between climatic variables can lead to imprecise results. Conclusions: A novelty of this study is to demonstrate the orthogonal effect of maximum VPD and minimum relative humidity on tree growth.
Resumen Introducción: Las variables climáticas muestran un patrón estacional en la Amazonía central, pero el efecto de la variabilidad intra-anual en el crecimiento de los árboles aún no está claro. Para variables como la humedad relativa (HR) y el déficit de presión de vapor (VPD), cuyo efecto individual en el crecimiento de los árboles puede ser subestimada, planteamos la hipótesis de que tales influencias pueden detectarse eliminando el efecto de colinealidad entre regresores. Objetivo: Este estudio tuvo como objetivo determinar el efecto libre de colinealidad de la variabilidad climática sobre el crecimiento de los árboles en la Amazonía central. Métodos: Se midió el crecimiento radial mensual en 325 árboles desde enero 2013 hasta diciembre 2017. También se registraron datos de irradiancia (PAR), temperatura del aire, lluvia, humedad relativa (RH) y déficit de presión de vapor de aire (VPD). Se utilizó la regresión de componentes principales para evaluar el efecto de la variabilidad micrometeorológica a lo largo del tiempo sobre el crecimiento de los árboles. Para comparación, también se utilizó la regresión lineal múltiple (MLR) estándar para el análisis de datos. Resultados: El crecimiento de los árboles incrementó con el aumento de las precipitaciones y la humedad relativa, y disminuyó con el aumento de la VPD máxima, la irradiancia y la temperatura máxima. Por lo tanto, los árboles crecieron más lentamente durante la estación seca, cuando la irradiancia, la temperatura y la VPD eran más altas. La variabilidad micrometeorológica no afectó el crecimiento de los árboles cuando se aplicó MLR. Estos hallazgos indican que ignorar la correlación entre las variables climáticas puede conducir a resultados imprecisos. Conclusiones: Una novedad de este estudio es demostrar el efecto ortogonal del VPD máximo y la humedad relativa mínima sobre el crecimiento de los árboles.
Assuntos
Árvores/crescimento & desenvolvimento , Ecossistema Amazônico , SinteniaRESUMO
Cytogenomic resources have accelerated synteny and chromosome evolution studies in plant species, including legumes. Here, we established the first cytogenetic map of V. angularis (Va, subgenus Ceratotropis) and compared this new map with those of V. unguiculata (Vu, subgenus Vigna) and P. vulgaris (Pv) by BAC-FISH and oligopainting approaches. We mapped 19 Vu BACs and 35S rDNA probes to the 11 chromosome pairs of Va, Vu, and Pv. Vigna angularis shared a high degree of macrosynteny with Vu and Pv, with five conserved syntenic chromosomes. Additionally, we developed two oligo probes (Pv2 and Pv3) used to paint Vigna orthologous chromosomes. We confirmed two reciprocal translocations (chromosomes 2 and 3 and 1 and 8) that have occurred after the Vigna and Phaseolus divergence (~9.7 Mya). Besides, two inversions (2 and 4) and one translocation (1 and 5) have occurred after Vigna and Ceratotropis subgenera separation (~3.6 Mya). We also observed distinct oligopainting patterns for chromosomes 2 and 3 of Vigna species. Both Vigna species shared similar major rearrangements compared to Pv: one translocation (2 and 3) and one inversion (chromosome 3). The sequence synteny identified additional inversions and/or intrachromosomal translocations involving pericentromeric regions of both orthologous chromosomes. We propose chromosomes 2 and 3 as hotspots for chromosomal rearrangements and de novo centromere formation within and between Vigna and Phaseolus. Our BAC- and oligo-FISH mapping contributed to physically trace the chromosome evolution of Vigna and Phaseolus and its application in further studies of both genera.
Assuntos
Phaseolus , Vigna , Cromossomos de Plantas/genética , Phaseolus/genética , Sintenia , Translocação Genética , Vigna/genéticaRESUMO
Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.