Dataset for co-phylogenetic analysis of Cicadas and their symbionts
Data files
Jan 15, 2025 version files 474.56 KB
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Dataset_of_universal_single-copy_orthologs_(USCOs)_of_cicadas.zip
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README.md
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Abstract
Throughout the lengthy process of evolution, various animals have formed symbiotic associations with diverse microbes. Symbiotic associations between insects and microorganisms enable insects to adapt to a variety of ecological niches and exploit diverse food resources. In most cases, the host insects have evolved specialized cells and organs, called bacteriocytes and bacteriomes, in particular of the plant sap-feeding auchenorrhynchan insects of Hemiptera, to accommodate their bacterial symbionts. Recruitment of novel symbiont is a key strategy for hosts to escape dependence on outdated, inefficient symbiont. However, symbiont replacement is a dynamic process, and its occurrence – from emergence to eventual disappearance – is extremely difficult to ascertain. Prior work has indicated that, in many cicada lineages, the obligate symbiont Hodgkinia has been replaced by yeast-like fungal symbionts (YLS), and YLS replacement by another fungus or YLS has also occurred repeatedly. Considerable diversity has been observed in the genome of Hodgkinia among different cicada species, which possibly suggest that Hodgkinia independently infected the ancestors of different cicada lineages on multiple occasions.
In the present work, phylogenetic analyses reveal that Hodgkinia infected the common ancestor of cicadas and has co-diversified with its host cicadas before replaced by YLS. We demonstrate events of Hodgkinia loss in Cicadidae occurred at least seven times and YLS replaced by another Ophiocordyceps fungus or YLS occurred repeatedly at least 18 times. The most extraordinary replacements and supplementation of symbionts in Cicadidae could be closely related to that cicadas live underground usually for many years but aboveground only several days. Most importantly, we present direct evidence that the extremely genome-degraded Hodgkinia established a nested symbiosis with Karelsulcia – immigrated to the cytoplasm of Karelsulcia to seek refuge when being replaced by YLS. This answers the enduring puzzles in the life sciences of how host insects can break away from their dependence on an ancient and potentially inefficient symbiont and what adaptative or nonadaptive evolution may evolve before a symbiont is going to be replaced by another symbiont. The findings offer fresh insights into the endosymbiotic origins of cellular organelles and intensify our curiosity about the origins of life.
README: Dataset for the Co-phylogeny of Cicadas and Their Symbionts
https://doi.org/10.5061/dryad.dbrv15fbj
Description of the data and file structure
The dissected bacteriomes and feet of cicadas were flash-frozen in liquid nitrogen, ground with a pestle in a plastic tube, and mixed with a lysis buffer of the DNeasy Blood and Tissue Kit (QIAGEN). Subsequently, proteinase K was added to the lysate and the DNA extraction proceeded following the manufacturer’s kit protocol. Sequencing libraries were generated using the TruSeq DNA Sample Preparation Kit (Illumina, USA) and the Template Prep Kit (Pacific Biosciences, USA) with an average insert size of approximately 400 bp following the manufacturer’s protocol. The genome sequencing was then performed by Personal Biotechnology Co., Ltd (Shanghai, China) by using the Illumina Novaseq platform. A minimum of 8 Gb of raw reads (paired-end, 150 bp each) was produced from each DNA sample through metagenomic sequencing, or 20 Gb through whole-genome resequencing. Data assembly was proceeding after adapter contamination removing and data filtering by using AdapterRemoval and SOAPec. The filtered reads were assembled by SPAdes and Megahit v1.2.9 to construct contigs. The assembled cicada genome sequences were used to extract universal single-copy orthologs (USCOs) using BUSCO v5.4.7 from the dataset “hemiptera_odb10”. Subsequent phylogenetic analysis was conducted.
Files and variables
File: Dataset_of_universal_single-copy_orthologs_(USCOs)_of_cicadas.zip
Description: 322 USCOs nucleotide sequences (110,724 bp) and 27 USCOs nucleotide sequences (9118 bp).
Access information
Other publicly accessible locations of the data:
- Sequence Read Archive (SRA) database under BioProject PRJNA1146783 and PRJNA1164630.
- doi:10.1093/gbe/evae001 and doi:10.1093/sysbio/syac043