Evolution of multigene families in species with large genomes using Schistocerca grasshoppers as models
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2021-10-04
Autores
Martí, Emiliano
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Universidade Estadual Paulista (Unesp)
Resumo
As famílias multigênicas são componentes essenciais dos genomas eucarióticos e desempenham papéis-chave tanto estrutural como funcional. Seus modos de evolução permanecem elusivos mesmo na era da genômica, pois múltiplas sequências de famílias multigênicas coexistem em genomas, particularmente em grandes genomas repetitivos. Aqui, eu estudo os padrões de evolução das famílias multigênicas 18S rDNA, U2 snDNA, e histona H3 em dez espécies de Schistocerca, um gênero de gafanhotos com genomas grandes e repetitivos. Usando genomas sequenciados e mapeamento com FISH, encontrei diferenças substanciais entre as famílias multigênicas, incluindo o número de grupos cromossômicos, alterações na abundância e composição de nucleotídica, pseudogenização e associação com elementos transponíveis (TEs). A análise intragenômica de S. gregaria empregando sequenciamento de long-reads e montagem do genoma revela alta conservação na histona H3, assim como recorrente pseudogenização nas famílias genicas 18S rDNA e U2 snDNA, provavelmente promovida pela associação com TEs. Notavelmente, os TEs que estavam associados frequentemente com cópias truncadas revelaram características de atividade recente. Nossos resultados sugerem um efeito combinado dos modelos de evolução concertada e de nascimento e morte na evolução de famílias multigênicas em Schistocerca nos últimos oito milhões de anos, e a ocorrência de rearranjos intra e intercromossômicos modificando os padrões de distribuição cromossômica. Apesar do cariótipo conservado em Schistocerca, nossa análise destaca a extensa reorganização dos DNAs repetitivos no genero, contribuindo para o avanço da genômica comparativa para este importante gênero de gafanhotos.
Multigene families are essential components of eukaryotic genomes and play structural and functional. Their modes of evolution remain elusive even in the era of genomics, because multiple multigene family sequences coexist in genomes, particularly in large repetitive genomes. Here, we investigate how the multigene families 18S rDNA, U2 snDNA, and H3 histone evolved in ten species of Schistocerca grasshoppers with very large and repeat-enriched genomes. Using sequenced genomes and FISH mapping, we find substantial differences for the multigene families, including the number of chromosomal clusters, changes in sequence abundance and nucleotide composition, pseudogenization, and association with transposable elements (TEs). The intra-genomic analysis of S. gregaria using long-read sequencing and genome assembly unveils conservation for H3 histone and recurrent pseudogenization for 18S rDNA and U2 snDNA, likely promoted by association with TEs and sequence truncation. Remarkably, TEs were frequently associated with truncated copies and were also among the most abundant in the genome, and revealed signatures of recent activity. Our findings suggest a combined effect of concerted and birth-and-death models driving the evolution of multigene families in Schistocerca over the last eight million years, and the occurrence of intra- and inter-chromosomal rearrangements shaping their chromosomal distribution. Despite the conserved karyotype in Schistocerca, our analysis highlights the extensive reorganization of repetitive DNAs, contributing to the advance of comparative genomics for this important grasshopper genus.
Multigene families are essential components of eukaryotic genomes and play structural and functional. Their modes of evolution remain elusive even in the era of genomics, because multiple multigene family sequences coexist in genomes, particularly in large repetitive genomes. Here, we investigate how the multigene families 18S rDNA, U2 snDNA, and H3 histone evolved in ten species of Schistocerca grasshoppers with very large and repeat-enriched genomes. Using sequenced genomes and FISH mapping, we find substantial differences for the multigene families, including the number of chromosomal clusters, changes in sequence abundance and nucleotide composition, pseudogenization, and association with transposable elements (TEs). The intra-genomic analysis of S. gregaria using long-read sequencing and genome assembly unveils conservation for H3 histone and recurrent pseudogenization for 18S rDNA and U2 snDNA, likely promoted by association with TEs and sequence truncation. Remarkably, TEs were frequently associated with truncated copies and were also among the most abundant in the genome, and revealed signatures of recent activity. Our findings suggest a combined effect of concerted and birth-and-death models driving the evolution of multigene families in Schistocerca over the last eight million years, and the occurrence of intra- and inter-chromosomal rearrangements shaping their chromosomal distribution. Despite the conserved karyotype in Schistocerca, our analysis highlights the extensive reorganization of repetitive DNAs, contributing to the advance of comparative genomics for this important grasshopper genus.
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Palavras-chave
Birth-and-death, Concerted evolution, FISH, Large genomes, Repetitive DNAs, Transposable elements, Nascimento-e-morte, Evolução concertada, Genomas grandes, DNA repetitivo, Elementos de transposição