Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha

Autor: Marina Marcet-Houben, Fernando Cruz, Jèssica Gómez-Garrido, Irene Julca, Tyler Alioto, Toni Gabaldón, Leonor Frias, John Spencer Johnston, André Corvelo, Carlos Vargas-Chávez, Amparo Latorre, Francisco Camara, Damian Loska, Marta Gut
Přispěvatelé: Battistuzzi, Fabia Ursula, European Commission, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, European Research Council, Instituto de Salud Carlos III, Barcelona Supercomputing Center
Jazyk: angličtina
Rok vydání: 2019
Předmět:
0106 biological sciences
Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC]
Gene duplication
Aphidomorpha
Lineage (evolution)
010603 evolutionary biology
01 natural sciences
Genome
Synteny
DNA sequencing
Filogènia
Evolution
Molecular
03 medical and health sciences
sequencia genómica
Species Specificity
Phylogenomics
Bioinformatica
Genetics
Adelgidae
Animals
Molecular Biology
Ecology
Evolution
Behavior and Systematics
Discoveries
Phylogeny
030304 developmental biology
Segmental duplication
0303 health sciences
Aphid
biology
Whole Genome Sequencing
Gene Expression Profiling
gene duplication
food and beverages
High-Throughput Nucleotide Sequencing
Afidomorfa
biochemical phenomena
metabolism
and nutrition
biology.organism_classification
aphids
Genòmica
Gene Expression Regulation
Evolutionary biology
Aphids
Insect Proteins
Genètica
Zdroj: Molecular Biology and Evolution
UPCommons. Portal del coneixement obert de la UPC
Universitat Politècnica de Catalunya (UPC)
Digital.CSIC. Repositorio Institucional del CSIC
instname
ISSN: 1537-1719
0737-4038
2018-0993
Popis: Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106–227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings.
This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union’s Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF).
Databáze: OpenAIRE
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