The nuclear and mitochondrial genomes of Frieseomelitta varia – a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste

BMC Genomics

Carlos A. M. Cardoso-Júnior¹  Mário S. Cervoni¹  Douglas E. Santos¹  Carolina G. Santos¹  Klaus Hartfelder¹  Livia M. Moda²  Joseana Vieira²  Angel R. Barchuk²  Zilá L. P. Simões³  Fernanda Dalarmi³  Márcia M. G. Bitondi³  Leonardo Nascimento³  Matheus Pedrino⁴  Marco A. Del Lama⁴  Kátia M. Ferreira⁴  Paula S. Gória⁴  Michael C. Jaskot⁴  Flávia C. de Paula Freitas⁵  Fabiano C. P. Abreu⁵  Fábio O. Barbin⁵  Fernanda C. Sanches⁵  Thiago S. Depintor⁵  Luana Bataglia⁵  Franciene Rabiço Oliveira⁵  Danielle Luna-Lucena⁵  Anete P. Lourenço⁵  Denyse C. Lago⁵  Francis M. F. Nunes⁵  Saura R. Silva⁶  Daniel G. Pinheiro⁶  Alexandre R. Paschoal⁷ 

[1] Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo;Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas;Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo;Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos;Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo;Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”;Universidade Tecnológica Federal do Paraná;

关键词: Social insect;    Meliponini;    Illumina sequencing;    Genome assembly;    Synteny;    Repetitive elements;   

DOI  :  10.1186/s12864-020-06784-8

来源: DOAJ

【 摘 要 】

Abstract Background Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonomically and biologically more diverse Meliponini, a full genome sequence was so far available for a single Melipona species only. We present here the genome sequence of Frieseomelitta varia, a stingless bee that has, as a peculiarity, a completely sterile worker caste. Results The assembly of 243,974,526 high quality Illumina reads resulted in a predicted assembled genome size of 275 Mb composed of 2173 scaffolds. A BUSCO analysis for the 10,526 predicted genes showed that these represent 96.6% of the expected hymenopteran orthologs. We also predicted 169,371 repetitive genomic components, 2083 putative transposable elements, and 1946 genes for non-coding RNAs, largely long non-coding RNAs. The mitochondrial genome comprises 15,144 bp, encoding 13 proteins, 22 tRNAs and 2 rRNAs. We observed considerable rearrangement in the mitochondrial gene order compared to other bees. For an in-depth analysis of genes related to social biology, we manually checked the annotations for 533 automatically predicted gene models, including 127 genes related to reproductive processes, 104 to development, and 174 immunity-related genes. We also performed specific searches for genes containing transcription factor domains and genes related to neurogenesis and chemosensory communication. Conclusions The total genome size for F. varia is similar to the sequenced genomes of other bees. Using specific prediction methods, we identified a large number of repetitive genome components and long non-coding RNAs, which could provide the molecular basis for gene regulatory plasticity, including worker reproduction. The remarkable reshuffling in gene order in the mitochondrial genome suggests that stingless bees may be a hotspot for mtDNA evolution. Hence, while being just the second stingless bee genome sequenced, we expect that subsequent targeting of a selected set of species from this diverse clade of highly eusocial bees will reveal relevant evolutionary signals and trends related to eusociality in these important pollinators.

【 授权许可】

Unknown