{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T13:30:49Z","timestamp":1772717449856,"version":"3.50.1"},"reference-count":82,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,9,30]],"date-time":"2021-09-30T00:00:00Z","timestamp":1632960000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:p>Spiny head croaker (<jats:italic>Collichthys lucidus<\/jats:italic>), belonging to the family Sciaenidae, is a small economic fish with a main distribution in the coastal waters of Northwestern Pacific. Here, we constructed a nonredundant chromosome-level genome assembly of spiny head croaker and also made genome-wide investigations on genome evolution and gene families related to otolith development. A primary genome assembly of 811.23\u00a0Mb, with a contig N50 of 74.92\u00a0kb, was generated by a combination of 49.12-Gb Illumina clean reads and 35.24\u00a0Gb of PacBio long reads. Contigs of this draft assembly were further anchored into chromosomes by integration with additional 185.33-Gb Hi-C data, resulting in a high-quality chromosome-level genome assembly of 817.24\u00a0Mb, with an improved scaffold N50 of 26.58\u00a0Mb. Based on our phylogenetic analysis, we observed that <jats:italic>C. lucidus<\/jats:italic> is much closer to <jats:italic>Larimichthys crocea<\/jats:italic> than <jats:italic>Miichthys miiuy<\/jats:italic>. We also predicted that many gene families were significantly expanded (<jats:italic>p<\/jats:italic>-value &amp;lt;0.05) in spiny head croaker; among them, some are associated with \u201ccalcium signaling pathway\u201d and potential \u201cinner ear functions.\u201d In addition, we identified some otolith-related genes (such as otol1a that encodes Otolin-1a) with critical deletions or mutations, suggesting possible molecular mechanisms for well-developed otoliths in the family Sciaenidae.<\/jats:p>","DOI":"10.3389\/fgene.2021.730255","type":"journal-article","created":{"date-parts":[[2021,9,30]],"date-time":"2021-09-30T18:29:51Z","timestamp":1633026591000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae"],"prefix":"10.3389","volume":"12","author":[{"given":"Wu","family":"Gan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenxi","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinran","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chao","family":"Bian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiong","family":"Shi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinxin","family":"You","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Song","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2021,9,30]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1002\/0471142905.hg0720s76","article-title":"Predicting Functional Effect of Human Missense Mutations Using PolyPhen\u20102","volume":"76","author":"Adzhubei","year":"2013","journal-title":"Curr. 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