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Previous work revealed that the volume of these air sacs is controlled using a unique mechanochemical system, where alternating bands of resilin and tracheal cuticle produce a composite material which expands and contracts with changing pH. While a simple epithelium enveloping each air sac is known to control the pH of the resilin bands, the molecular mechanisms underpinning its ability to regulate pH, and thus the air sac's volume, are unknown. To reveal these mechanisms, we compared the transcriptome of air sacs from Chaoborus trivitattus larvae with that of tracheal tissue from the aquatic larvae of two other genera within the Chaoboridae: Eucorethra underwoodi, whose larvae possess an unmodified tracheal system which they use to breathe air using a posterior respiratory siphon, and Mochlonyx cinctipes, whose larvae possess a tracheal system with dilated anterior and posterior sac-like regions, but which remains open through a posterior siphon. We found that C. trivitattus air-sac epithelia show strong expression of ion channels related to pH regulation relative to E. underwoodi tracheal tissue, including orthologs of NHA1, Nhe2, Ae2 and pHCl-2, as well the aquaporin Drip. This suggests that the tracheal epithelium of the ancestral chaoborid possesses all functionality required to control pH and deal with the flux of water associated with the swelling and contraction of resilin as part of the ancestral liquid-clearing function of the tracheal epithelium, enabling the evolution of a novel buoyancy control mechanism.<\/jats:p>","DOI":"10.1242\/jeb.251113","type":"journal-article","created":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T09:09:45Z","timestamp":1762506585000},"source":"Crossref","is-referenced-by-count":1,"title":["Molecular mechanisms underpinning buoyancy control in the aquatic larvae of\n                    <i>Chaoborus<\/i>\n                    evolved from tracheal fluid clearing functionality"],"prefix":"10.1242","volume":"228","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9218-2179","authenticated-orcid":false,"given":"Tahnee","family":"Ames","sequence":"first","affiliation":[{"name":"University of British Columbia Department of Zoology , , Vancouver, BC , , V6T 1Z4","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0682-8522","authenticated-orcid":false,"given":"Philip G. D.","family":"Matthews","sequence":"additional","affiliation":[{"name":"University of British Columbia Department of Zoology , , Vancouver, BC , , V6T 1Z4","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8697-699X","authenticated-orcid":false,"given":"Benjamin J.","family":"Matthews","sequence":"additional","affiliation":[{"name":"University of British Columbia Department of Zoology , , Vancouver, BC , , V6T 1Z4","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"237","published-online":{"date-parts":[[2025,12,10]]},"reference":[{"key":"2025121006265933900_JEB251113C1","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s12864-017-3579-8","article-title":"Anopheline salivary protein genes and gene families: an evolutionary overview after the whole genome sequence of sixteen Anopheles species","volume":"18","author":"Arc\u00e0","year":"2017","journal-title":"BMC Genomics"},{"key":"2025121006265933900_JEB251113C2","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1016\/j.jinsphys.2012.01.007","article-title":"Two water-specific aquaporins at the apical and basal plasma membranes of insect epithelia: Molecular basis for water recycling through the cryptonephric rectal complex of lepidopteran larvae","volume":"58","author":"Azuma","year":"2012","journal-title":"J. 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