{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T04:15:33Z","timestamp":1792210533249,"version":"4.4.0"},"reference-count":104,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,10,21]],"date-time":"2022-10-21T00:00:00Z","timestamp":1666310400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science Foundation Plant Genome Research Program","award":["IOS-1732253"],"award-info":[{"award-number":["IOS-1732253"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The highly diverse Solanaceae family contains several widely studied models and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus Physalis, which occupy a key evolutionary position in the Solanaceae and capture understudied variation in traits such as inflorescence complexity, fruit ripening and metabolites, disease and insect resistance, self-compatibility, and most notable, the striking inflated calyx syndrome (ICS), an evolutionary novelty found across angiosperms where sepals grow exceptionally large to encapsulate fruits in a protective husk. We recently developed transformation and genome editing in Physalis grisea (groundcherry). However, to systematically explore and unlock the potential of this and related Physalis as genetic systems, high-quality genome assemblies are needed. Here, we present chromosome-scale references for P. grisea and its close relative Physalis pruinosa and use these resources to study natural and engineered variations in floral traits. We first rapidly identified a natural structural variant in a bHLH gene that causes petal color variation. Further, and against expectations, we found that CRISPR\u2013Cas9-targeted mutagenesis of 11 MADS-box genes, including purported essential regulators of ICS, had no effect on inflation. In a forward genetics screen, we identified huskless, which lacks ICS due to mutation of an AP2-like gene that causes sepals and petals to merge into a single whorl of mixed identity. These resources and findings elevate Physalis to a new Solanaceae model system and establish a paradigm in the search for factors driving ICS.<\/jats:p>","DOI":"10.1093\/plcell\/koac305","type":"journal-article","created":{"date-parts":[[2022,10,21]],"date-time":"2022-10-21T07:07:54Z","timestamp":1666336074000},"page":"351-368","source":"Crossref","is-referenced-by-count":40,"title":["Establishing\n                    <i>Physalis<\/i>\n                    as a\n                    <i>Solanaceae<\/i>\n                    model system enables genetic reevaluation of the inflated calyx syndrome"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6086-0115","authenticated-orcid":false,"given":"Jia","family":"He","sequence":"first","affiliation":[{"name":"Cold Spring Harbor Laboratory , Cold Spring Harbor, New York 11724, USA"},{"name":"Howard Hughes Medical Institute, Cold Spring Harbor Laboratory , Cold Spring Harbor, New York 11724, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3692-1819","authenticated-orcid":false,"given":"Michael","family":"Alonge","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, Maryland 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8023-4752","authenticated-orcid":false,"given":"Srividya","family":"Ramakrishnan","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, Maryland 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3958-3173","authenticated-orcid":false,"given":"Matthias","family":"Benoit","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratory , Cold Spring Harbor, New York 11724, USA"},{"name":"Howard Hughes Medical Institute, Cold Spring Harbor Laboratory , Cold Spring Harbor, New York 11724, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0325-4404","authenticated-orcid":false,"given":"Sebastian","family":"Soyk","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratory , Cold Spring Harbor, New York 11724, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3147-9635","authenticated-orcid":false,"given":"Nathan T","family":"Reem","sequence":"additional","affiliation":[{"name":"Boyce Thompson Institute , Ithaca, New York 14853, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6089-710X","authenticated-orcid":false,"given":"Anat","family":"Hendelman","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratory , Cold Spring Harbor, New York 11724, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8005-365X","authenticated-orcid":false,"given":"Joyce","family":"Van Eck","sequence":"additional","affiliation":[{"name":"Boyce Thompson Institute , Ithaca, New York 14853, USA"},{"name":"Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University , Ithaca, New York 14853, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4118-4446","authenticated-orcid":false,"given":"Michael C","family":"Schatz","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratory , Cold Spring Harbor, New York 11724, USA"},{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, Maryland 21218, USA"},{"name":"Department of Biology, Johns Hopkins University , Baltimore, Maryland 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7668-9025","authenticated-orcid":false,"given":"Zachary B","family":"Lippman","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratory , Cold Spring Harbor, New York 11724, USA"},{"name":"Howard Hughes Medical Institute, Cold Spring Harbor Laboratory , Cold Spring Harbor, New York 11724, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,10,21]]},"reference":[{"key":"2023010806452942700_koac305-B1","author":"Alonge","year":"2021"},{"key":"2023010806452942700_koac305-B2","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.cell.2020.05.021","article-title":"Major impacts of widespread structural variation on gene expression and crop improvement in 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