Author:
Ferrari Rafael Rodrigues,Ricardo Paulo Cseri,Dias Felipe Cordeiro,de Souza Araujo Natalia,Soares Dalliane Oliveira,Zhou Qing-Song,Zhu Chao-Dong,Coutinho Luiz Lehmann,Arias Maria Cristina,Batista Thiago Mafra
Abstract
Abstract
Background
The field of bee genomics has considerably advanced in recent years, however, the most diverse group of honey producers on the planet, the stingless bees, are still largely neglected. In fact, only eleven of the ~ 600 described stingless bee species have been sequenced, and only three using a long-read (LR) sequencing technology. Here, we sequenced the nuclear and mitochondrial genomes of the most common, widespread and broadly reared stingless bee in Brazil and other neotropical countries—Tetragonisca angustula (popularly known in Brazil as jataí).
Results
A total of 48.01 Gb of DNA data were generated, including 2.31 Gb of Pacific Bioscience HiFi reads and 45.70 Gb of Illumina short reads (SRs). Our preferred assembly comprised 683 contigs encompassing 284.49 Mb, 62.84 Mb of which (22.09%) corresponded to 445,793 repetitive elements. N50, L50 and complete BUSCOs reached 1.02 Mb, 91 contigs and 97.1%, respectively. We predicted that the genome of T. angustula comprises 17,459 protein-coding genes and 4,108 non-coding RNAs. The mitogenome consisted of 17,410 bp, and all 37 genes were found to be on the positive strand, an unusual feature among bees. A phylogenomic analysis of 26 hymenopteran species revealed that six odorant receptor orthogroups of T. angustula were found to be experiencing rapid evolution, four of them undergoing significant contractions.
Conclusions
Here, we provided the first nuclear and mitochondrial genome assemblies for the ecologically and economically important T. angustula, the fourth stingless bee species to be sequenced with LR technology thus far. We demonstrated that even relatively small amounts of LR data in combination with sufficient SR data can yield high-quality genome assemblies for bees.
Funder
Veracel Celulose - Postdoctoral Fellowship
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – CAPES
Fundação de Amparo à Pesquisa do Estado de São Paulo – FAPESP
Belgian National Fund for Scientific Research
Key Laboratory of the Zoological Systematics and Evolution of the Chinese Academy of Sciences
Conselho Nacional de Desenvolvimento Científico e Tecnológico
Suzano Papel e Celulose
Publisher
Springer Science and Business Media LLC