DOI: 10.5061/dryad.dbrv15fbj
title: Dataset for co-phylogenetic analysis of Cicadas and their symbionts

description: 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 escape dependence on outdated, inefficient symbiont.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 Hodgkinia has been replaced by yeast-like fungal symbionts (YLS),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.
description: # Dataset for the Co-phylogeny of Cicadas and Their Symbionts
 [https://doi.org/10.5061/dryad.dbrv15fbj](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