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In this paper, we present a high-quality chromosomal-level genome of B. edeni and conduct comparative genomic analyses to address long-standing taxonomic confusion and elucidate speciation of balaenopterids. Our phylogenomic analysis and demographic reconstruction reveal that B. edeni is a distinct sister to Bryde's whale (Balaenoptera brydei), sharing a common ancestor that diverged approximately 7.84 million years ago during the late Miocene. Their genetic divergence exceeds typical intraspecific variation in whales, supporting the reinstatement of B. brydei as a valid species. Chromosomal syntenic analyses suggest that macro-fragment inversions contributed to speciation in balaenopterid whales and uncover unexpected large-scale complex genome rearrangements in Bryde's whale, offering novel insights into cetacean genome evolution. Functional enrichment analysis of inverted regions between B. edeni and Balaenoptera musculus indicates their predominant association with metabolism and biosynthesis, as well as responses to various substances, stress, and stimuli. These genomic resources for B. edeni not only lay a critical foundation for comparative genetic and evolutionary research of cetaceans but also advance our understanding of the taxonomy and evolutionary dynamics of the Bryde's whale complex, with broader implications for baleen whale conservation and biodiversity.<\/jats:p>","DOI":"10.1093\/molbev\/msaf234","type":"journal-article","created":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T01:02:33Z","timestamp":1758330153000},"source":"Crossref","is-referenced-by-count":8,"title":["Chromosome-Level Genome Assembly of Eden's Whale Clarifies the Taxonomy and Speciation of Bryde's Whale Complex"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0724-4326","authenticated-orcid":false,"given":"Yi-Tao","family":"Lin","sequence":"first","affiliation":[{"name":"Department of Biology, Hong Kong Baptist University , Hong Kong SAR 999077 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-8609-4075","authenticated-orcid":false,"given":"Fan","family":"Hui","sequence":"additional","affiliation":[{"name":"Department of Biology, Hong Kong Baptist University , Hong Kong SAR 999077 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1423-3975","authenticated-orcid":false,"given":"Wentao","family":"Han","sequence":"additional","affiliation":[{"name":"Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) , Guangzhou 511458 ,","place":["China"]},{"name":"Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China , Qingdao 266100 ,","place":["China"]},{"name":"Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Laoshan Laboratory , Qingdao 266100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2023-2867","authenticated-orcid":false,"given":"Yi-Xuan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biology, Hong Kong Baptist University , Hong Kong SAR 999077 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-4799-4388","authenticated-orcid":false,"given":"Bonnie Yuen Wai","family":"Heung","sequence":"additional","affiliation":[{"name":"Department of Biology, Hong Kong Baptist University , Hong Kong SAR 999077 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5219-3826","authenticated-orcid":false,"given":"Chun Ming","family":"How","sequence":"additional","affiliation":[{"name":"Department of Biology, Hong Kong Baptist University , Hong Kong SAR 999077 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9571-9864","authenticated-orcid":false,"given":"Shi","family":"Wang","sequence":"additional","affiliation":[{"name":"Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) , Guangzhou 511458 ,","place":["China"]},{"name":"Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China , Qingdao 266100 ,","place":["China"]},{"name":"Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Laoshan Laboratory , Qingdao 266100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1541-9627","authenticated-orcid":false,"given":"Jian-Wen","family":"Qiu","sequence":"additional","affiliation":[{"name":"Department of Biology, Hong Kong Baptist University , Hong Kong SAR 999077 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,9,18]]},"reference":[{"key":"2025101300113782800_msaf234-B1","doi-asserted-by":"publisher","DOI":"10.5962\/bhl.title.50434","volume-title":"Anatomical and zoological researches: comprising an account of the zoological results of the two expeditions to western Yunnan in 1868 and 1875; 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