Comparative genomics reveals thousands of novel chemosensory genes and massive changes in chemoreceptor repertories across chelicerates

Chemoreception is a widespread biological function that is essential for the survival, reproduction, and social communication of animals. Though the molecular mechanisms underlying chemoreception are relatively well known in insects, they are poorly studied in the other major arthropod lineages. Current availability of a number of chelicerate genomes constitutes a great opportunity to better characterize gene families involved in this important function in a lineage that emerged and colonized land independently of insects. At the same time, that offers new opportunities and challenges for the study of this interesting animal branch in many translational research areas. Here, we have performed a comprehensive comparative genomics study that explicitly considers the high fragmentation of available draft genomes and that for the first time included complete genome data that cover most of the chelicerate diversity. Our exhaustive searches exposed thousands of previously uncharacterized chemosensory sequences, most of them encoding members of the gustatory and ionotropic receptor families. The phylogenetic and gene turnover analyses of these sequences indicated that the whole-genome duplication events proposed for this subphylum would not explain the differences in the number of chemoreceptors observed across species. A constant and prolonged gene birth and death process, altered by episodic bursts of gene duplication yielding lineage-specific expansions, has contributed significantly to the extant chemosensory diversity in this group of animals. This study also provides valuable insights into the origin and functional diversification of other relevant chemosensory gene families different from receptors, such as odorant-binding proteins and other related molecules

Chromosome-Level Genome Assembly of the Common Chaffinch (Aves: Fringilla coelebs): A Valuable Resource for Evolutionary Biology

The common chaffinch, Fringilla coelebs, is one of the most common, widespread, and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa, and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing in combination with Chicago and Hi-C libraries. The final genome is a 994.87-Mb chromosome-level assembly, with 98% of the sequence data located in chromosome scaffolds and a N50 statistic of 69.73 Mb. Our genome assembly shows high completeness, with a complete BUSCO score of 93.9% using the avian data set. Around 7.8% of the genome contains interspersed repetitive elements. The structural annotation yielded 17,703 genes, 86.5% of which have a functional annotation, including 7,827 complete universal single-copy orthologs out of 8,338 genes represented in the BUSCO avian data set. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian, and vertebrate evolution

The first genome of the Balearic shearwater (Puffinus mauretanicus) provides a valuable resource for conservation genomics and sheds light on adaptation to a pelagic lifestyle

The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe and a member of the most speciose group of pelagic seabirds, the order Procellariiformes, which exhibit extreme adaptations to a pelagic lifestyle. The fossil record suggests that human colonisation of the Balearic Islands resulted in a sharp decrease of the Balearic shearwater population size. Currently, populations of the species continue to be decimated mainly due to predation by introduced mammals and bycatch in longline fisheries, with some studies predicting its extinction by 2070. Here, using a combination of short and long reads, we generate the first high-quality reference genome for the Balearic shearwater, with a completeness amongst the highest across available avian species. We used this reference genome to study critical aspects relevant to the conservation status of the species and to gain insights into the adaptation to a pelagic lifestyle of the order Procellariiformes. We detected relatively high levels of genome-wide heterozygosity in the Balearic shearwater despite its reduced population size. However, the reconstruction of its historical demography uncovered an abrupt population decline potentially linked to a reduction of the neritic zone during the Penultimate Glacial Period (∼194-135 ka). Comparative genomics analyses uncover a set of candidate genes that may have played an important role into the adaptation to a pelagic lifestyle of Procellariiformes, including those for the enhancement of fishing capabilities, night vision, and the development of natriuresis. The reference genome obtained will be the crucial in the future development of genetic tools in conservation efforts for this Critically Endangered species

The Tetragnatha kauaiensis genome sheds light on the origins of genomic novelty in spider

Spiders (Araneae) have a diverse spectrum of morphologies, behaviors, and physiologies. Attempts to understand the genomic-basis of this diversity are often hindered by their large, heterozygous, and AT-rich genomes with high repeat content resulting in highly fragmented, poor-quality assemblies. As a result, the key attributes of spider genomes, including gene family evolution, repeat content, and gene function, remain poorly understood. Here, we used Illumina and Dovetail Chicago technologies to sequence the genome of the long-jawed spider Tetragnatha kauaiensis, producing an assembly distributed along 3,925 scaffolds with an N50 of ∼2 Mb. Using comparative genomics tools, we explore genome evolution across available spider assemblies. Our findings suggest that the previously reported and vast genome size variation in spiders is linked to the different representation and number of transposable elements. Using statistical tools to uncover gene-family level evolution, we find expansions associated with the sensory perception of taste, immunity, and metabolism. In addition, we report strikingly different histories of chemosensory, venom, and silk gene families, with the first two evolving much earlier, affected by the ancestral whole genome duplication in Arachnopulmonata (∼450 Ma) and exhibiting higher numbers. Together, our findings reveal that spider genomes are highly variable and that genomic novelty may have been driven by the burst of an ancient whole genome duplication, followed by gene family and transposable element expansion

Genómica de la adaptación en artrópodos: estudio del sistema quimiosensorial y de la radiación del género Dysdera (Araneae) en Canarias

Los artrópodos, durante su historia evolutiva, han colonizado múltiples y diversos hábitats, incluyendo eventos de terrestrialización independientes en los distintos subfilos, e implicando en algunas ocasiones radiaciones adaptativas asociadas a eventos de especialización trófica. A pesar de que el sistema quimiosensorial probablemente tuvo un papel crítico en muchas de estas adaptaciones, algunos aspectos importantes sobre el origen y evolución de las familias multigénicas que median la quimiopercepción en artrópodos aún están en discusión. En esta tesis, nuestro objetivo principal es profundizar en el conocimiento de los mecanismos evolutivos involucrados en la diversificación de los quelicerados, y en particular, el papel de la selección natural en este proceso. Para ello, hemos estudiado la evolución de las familias multigénicas del sistema quimiosensorial en quelicerados mediante el análisis de genómica y transcriptómica comparativa. En primer lugar, hemos desarrollado una herramienta bioinformática (BITACORA) para la identificación y anotación de miembros de familias multigénicas en ensamblajes genómicos. Mediante el uso de esta herramienta, hemos identificado miembros de las dos principales familias multigénicas de quimiorreceptores en quelicerados (GRs e IRs) y hemos encontrando algunos de sus miembros expresados en los apéndices quimiosensoriales de la araña Dysdera silvatica, sugiriendo su implicación en la quimiopercepción de estos organismos. Estas familias han evolucionado bajo un modelo dinámico de nacimiento y muerte de genes, con la presencia de expansiones episódicas originadas por duplicaciones génicas y que han generado expansiones específicas de linaje. Sorprendentemente, hemos caracterizado una familia multigénica en quelicerados y miriápodos que presenta homología remota con las OBPs de insectos, sugiriendo que el origen de esta familia es mucho más antiguo de lo previamente reportado. También identificamos en arañas una nueva familia que codifica pequeñas proteínas globulares, y que podría ser una familia candidata a participar en la respuesta quimiosensorial en este grupo. A su vez, hemos verificado la ausencia de la familia de las CSPs en quelicerados, y discutimos la posible función de las NPC2 relacionada con la quimiopercepción. De forma paralela, hemos estudiado la radiación adaptativa del género de arañas Dysdera en las Islas Canarias, donde la diversificación de sus especies ha ocurrido de forma concomitante con eventos repetidos de especialización trófica. Hemos detectado cambios genéticos asociados a esta adaptación convergente y que están relacionados con la secreción y detoxificación de metales pesados, el metabolismo de nutrientes esenciales y componentes del veneno. Estos cambios genéticos convergentes se presentan a distintos niveles jerárquicos, incluyendo los mismos genes, funciones génicas, o incluso posiciones aminoacídicas, y alguno de ellos han evolucionado por selección positiva. En términos generales, nuestros resultados proporcionan nuevos conocimientos sobre la base molecular de los procesos adaptativos y la repetitividad de la evolución.During their evolutionary history, arthropods have diversified adapting to different habitats, including several independent colonizations of land, and sometimes implicating rapid radiations coupled with dietary specializations. Although the chemosensory system likely played a critical role in many of these adaptations, the origin and evolution of the gene families that mediate chemoperception in arthropods is still discussed in some important aspects. The main objective of this thesis is to gain insights into the molecular evolution of chelicerate diversification and, specifically, to determine the role of natural selection in this process. On one hand, we studied the evolution of the chemosensory gene families in chelicerates using comparative transcriptome and genome analyses. We first developed a bioinformatic pipeline (BITACORA) for the identification and annotation of gene families in genome assemblies. Using this tool, we identified members of two of the major arthropod chemoreceptor gene families (GRs and IRs) in chelicerates, being some of them expressed in the chemosensory appendages of the spider Dysdera silvatica, which supports its role in chemoperception. These families evolved under a dynamic gene birth and death model influenced by episodic bursts of gene duplication yielding lineage-specific expansions. Noticeably, we characterized in chelicerates a gene family distantly related to insect OBPs, suggesting a more ancient origin of these soluble carriers than previously thought, and a new gene family encoding small globular secreted proteins, which is a good chemosensory gene family candidate. In addition, we discuss the absence of the CSP family in chelicerates, and the putative role of NPC2 members in chemoperception. On the other hand, we studied the radiation of the spider genus Dysdera in the Canary Islands, where species diversification occurs concomitant with repeated events of trophic specialization. We identified a number of genetic changes likely associated with this convergent adaptation, including some related to heavy metal detoxification and homeostasis, metabolism of important nutrients and venom toxins. We uncovered the specific molecular substrates of these changes at different hierarchical levels, including same genes, gene functions or amino acid positions, some of them promoted by positive selection. Globally, our results increase the knowledge about the molecular basis of adaptation and provide new insights into the predictability of evolution

Genómica de la adaptación en artrópodos: estudio del sistema quimiosensorial y de la radiación del género Dysdera (Araneae) en Canarias

[spa] Los artrópodos, durante su historia evolutiva, han colonizado múltiples y diversos hábitats, incluyendo eventos de terrestrialización independientes en los distintos subfilos, e implicando en algunas ocasiones radiaciones adaptativas asociadas a eventos de especialización trófica. A pesar de que el sistema quimiosensorial probablemente tuvo un papel crítico en muchas de estas adaptaciones, algunos aspectos importantes sobre el origen y evolución de las familias multigénicas que median la quimiopercepción en artrópodos aún están en discusión. En esta tesis, nuestro objetivo principal es profundizar en el conocimiento de los mecanismos evolutivos involucrados en la diversificación de los quelicerados, y en particular, el papel de la selección natural en este proceso. Para ello, hemos estudiado la evolución de las familias multigénicas del sistema quimiosensorial en quelicerados mediante el análisis de genómica y transcriptómica comparativa. En primer lugar, hemos desarrollado una herramienta bioinformática (BITACORA) para la identificación y anotación de miembros de familias multigénicas en ensamblajes genómicos. Mediante el uso de esta herramienta, hemos identificado miembros de las dos principales familias multigénicas de quimiorreceptores en quelicerados (GRs e IRs) y hemos encontrando algunos de sus miembros expresados en los apéndices quimiosensoriales de la araña Dysdera silvatica, sugiriendo su implicación en la quimiopercepción de estos organismos. Estas familias han evolucionado bajo un modelo dinámico de nacimiento y muerte de genes, con la presencia de expansiones episódicas originadas por duplicaciones génicas y que han generado expansiones específicas de linaje. Sorprendentemente, hemos caracterizado una familia multigénica en quelicerados y miriápodos que presenta homología remota con las OBPs de insectos, sugiriendo que el origen de esta familia es mucho más antiguo de lo previamente reportado. También identificamos en arañas una nueva familia que codifica pequeñas proteínas globulares, y que podría ser una familia candidata a participar en la respuesta quimiosensorial en este grupo. A su vez, hemos verificado la ausencia de la familia de las CSPs en quelicerados, y discutimos la posible función de las NPC2 relacionada con la quimiopercepción. De forma paralela, hemos estudiado la radiación adaptativa del género de arañas Dysdera en las Islas Canarias, donde la diversificación de sus especies ha ocurrido de forma concomitante con eventos repetidos de especialización trófica. Hemos detectado cambios genéticos asociados a esta adaptación convergente y que están relacionados con la secreción y detoxificación de metales pesados, el metabolismo de nutrientes esenciales y componentes del veneno. Estos cambios genéticos convergentes se presentan a distintos niveles jerárquicos, incluyendo los mismos genes, funciones génicas, o incluso posiciones aminoacídicas, y alguno de ellos han evolucionado por selección positiva. En términos generales, nuestros resultados proporcionan nuevos conocimientos sobre la base molecular de los procesos adaptativos y la repetitividad de la evolución.[eng] During their evolutionary history, arthropods have diversified adapting to different habitats, including several independent colonizations of land, and sometimes implicating rapid radiations coupled with dietary specializations. Although the chemosensory system likely played a critical role in many of these adaptations, the origin and evolution of the gene families that mediate chemoperception in arthropods is still discussed in some important aspects. The main objective of this thesis is to gain insights into the molecular evolution of chelicerate diversification and, specifically, to determine the role of natural selection in this process. On one hand, we studied the evolution of the chemosensory gene families in chelicerates using comparative transcriptome and genome analyses. We first developed a bioinformatic pipeline (BITACORA) for the identification and annotation of gene families in genome assemblies. Using this tool, we identified members of two of the major arthropod chemoreceptor gene families (GRs and IRs) in chelicerates, being some of them expressed in the chemosensory appendages of the spider Dysdera silvatica, which supports its role in chemoperception. These families evolved under a dynamic gene birth and death model influenced by episodic bursts of gene duplication yielding lineage-specific expansions. Noticeably, we characterized in chelicerates a gene family distantly related to insect OBPs, suggesting a more ancient origin of these soluble carriers than previously thought, and a new gene family encoding small globular secreted proteins, which is a good chemosensory gene family candidate. In addition, we discuss the absence of the CSP family in chelicerates, and the putative role of NPC2 members in chemoperception. On the other hand, we studied the radiation of the spider genus Dysdera in the Canary Islands, where species diversification occurs concomitant with repeated events of trophic specialization. We identified a number of genetic changes likely associated with this convergent adaptation, including some related to heavy metal detoxification and homeostasis, metabolism of important nutrients and venom toxins. We uncovered the specific molecular substrates of these changes at different hierarchical levels, including same genes, gene functions or amino acid positions, some of them promoted by positive selection. Globally, our results increase the knowledge about the molecular basis of adaptation and provide new insights into the predictability of evolution

Bitacora: A comprehensive tool for the identification and annotation of gene families in genome assemblies

Gene annotation is a critical bottleneck in genomic research, especially for the comprehensive study of very large gene families in the genomes of nonmodel organisms. Despite the recent progress in automatic methods, state‐of‐the‐art tools used for this task often produce inaccurate annotations, such as fused, chimeric, partial or even completely absent gene models for many family copies, errors that require considerable extra efforts to be corrected. Here we present bitacora , a bioinformatics solution that integrates popular sequence similarity‐based search tools and Perl scripts to facilitate both the curation of these inaccurate annotations and the identification of previously undetected gene family copies directly in genomic DNA sequences. We tested the performance of bitacora in annotating the members of two chemosensory gene families with different repertoire size in seven available genome sequences, and compared its performance with that of augustus‐ppx , a tool also designed to improve automatic annotations using a sequence similarity‐based approach. Despite the relatively high fragmentation of some of these drafts, bitacora was able to improve the annotation of many members of these families and detected thousands of new chemoreceptors encoded in genome sequences. The program creates general feature format (GFF) files, with both curated and newly identified gene models, and FASTA files with the predicted proteins. These outputs can be easily integrated in genomic annotation editors, greatly facilitating subsequent manual annotation and downstream evolutionary analyses

Comparative genomics reveals thousands of novel chemosensory genes and massive changes in chemoreceptor repertories across chelicerates

Chemoreception is a widespread biological function that is essential for the survival, reproduction, and social communication of animals. Though the molecular mechanisms underlying chemoreception are relatively well known in insects, they are poorly studied in the other major arthropod lineages. Current availability of a number of chelicerate genomes constitutes a great opportunity to better characterize gene families involved in this important function in a lineage that emerged and colonized land independently of insects. At the same time, that offers new opportunities and challenges for the study of this interesting animal branch in many translational research areas. Here, we have performed a comprehensive comparative genomics study that explicitly considers the high fragmentation of available draft genomes and that for the first time included complete genome data that cover most of the chelicerate diversity. Our exhaustive searches exposed thousands of previously uncharacterized chemosensory sequences, most of them encoding members of the gustatory and ionotropic receptor families. The phylogenetic and gene turnover analyses of these sequences indicated that the whole-genome duplication events proposed for this subphylum would not explain the differences in the number of chemoreceptors observed across species. A constant and prolonged gene birth and death process, altered by episodic bursts of gene duplication yielding lineage-specific expansions, has contributed significantly to the extant chemosensory diversity in this group of animals. This study also provides valuable insights into the origin and functional diversification of other relevant chemosensory gene families different from receptors, such as odorant-binding proteins and other related molecules

Comparative genomics reveals thousands of novel chemosensory genes and massive changes in chemoreceptor repertories across chelicerates

Chemoreception is a widespread biological function that is essential for the survival, reproduction, and social communication of animals. Though the molecular mechanisms underlying chemoreception are relatively well known in insects, they are poorly studied in the other major arthropod lineages. Current availability of a number of chelicerate genomes constitutes a great opportunity to better characterize gene families involved in this important function in a lineage that emerged and colonized land independently of insects. At the same time, that offers new opportunities and challenges for the study of this interesting animal branch in many translational research areas. Here, we have performed a comprehensive comparative genomics study that explicitly considers the high fragmentation of available draft genomes and that for the first time included complete genome data that cover most of the chelicerate diversity. Our exhaustive searches exposed thousands of previously uncharacterized chemosensory sequences, most of them encoding members of the gustatory and ionotropic receptor families. The phylogenetic and gene turnover analyses of these sequences indicated that the whole-genome duplication events proposed for this subphylum would not explain the differences in the number of chemoreceptors observed across species. A constant and prolonged gene birth and death process, altered by episodic bursts of gene duplication yielding lineage-specific expansions, has contributed significantly to the extant chemosensory diversity in this group of animals. This study also provides valuable insights into the origin and functional diversification of other relevant chemosensory gene families different from receptors, such as odorant-binding proteins and other related molecules

Comparative analysis of tissue-specific transcriptomes in the funnel web spider Macrothele calpeiana (Araneae, Hexathelidae)

The funnel-web spider Macrothele calpeiana is a charismatic Mygalomorph with a great interest in basic, applied and translational research. Nevertheless, current scarcity of genomic and transcriptomic data of this species clearly limits the research in this non-model organism. To overcome this limitation, we launched the first tissue-specific enriched RNA-seq analysis in this species using a subtractive hybridization approach, with two main objectives, to characterize the specific transcriptome of the putative chemosensory appendages (palps and first pair of legs), and to provide a new set of DNA markers for further phylogenetic studies. We have characterized the set of transcripts specifically expressed in putative chemosensory tissues of this species, much of them showing features shared by chemosensory system genes. Among specific candidates, we have identified some members of the iGluR and NPC2 families. Moreover, we have demonstrated the utility of these newly generated data as molecular markers by inferring the phylogenetic position M. calpeina in the phylogenetic tree of Mygalomorphs. Our results provide novel resources for researchers interested in spider molecular biology and systematics, which can help to expand our knowledge on the evolutionary processes underlying fundamental biological questions, as species invasion or biodiversity origin and maintenance