{"refrec":{"BRefID":409304,"RR":"<b>Liao, J.; Li, J.-Y.; Li, Y.-Y.; Zhang, S.-Y.; Yang, Y.-F.; Guo, Y.-S.; Wang, Z.-D.</b> (2025). In-depth analysis of the first complete mitochondrial genome of the rare shrimp <i>Alpheus euphrosyne</i>, with comparative phylogenetic genomics insights into the <i>Alpheus</i> species. <i>Molecular biology reports 52(1)</i>: 1-13. <a href=\"https://dx.doi.org/10.1007/s11033-025-10651-8\" target=\"_blank\">https://dx.doi.org/10.1007/s11033-025-10651-8</a>","BEntID":407109,"PublicFlag":1,"CheckedFlag":0,"wosflag":1,"vabbflag":0,"RefStringPartII":". <i>Molecular biology reports 52(1)</i>: 1-13. <a href=\"https://dx.doi.org/10.1007/s11033-025-10651-8\" target=\"_blank\">https://dx.doi.org/10.1007/s11033-025-10651-8</a>","DocTypID":8,"DocType":"Journal article","MarineFlag":0,"FreshFlag":0,"BrackishFlag":0,"TerrestrialFlag":0,"Authorstring":"Liao, J.; Li, J.-Y.; Li, Y.-Y.; Zhang, S.-Y.; Yang, Y.-F.; Guo, Y.-S.; Wang, Z.-D.","OrigTitleTranslFlag":0,"Authorstringtrunc":"Liao, J. <i>et al.</i>","Englishabstract":"<h3>Background</h3>Mitochondrial genomes, with their maternal inheritance, rapid evolution, and compact organization, are ideal for phylogenetic analysis.<h3>Aim</h3>This study presents the first comprehensive mitochondrial genome analysis of the rare shrimp <i>Alpheus euphrosyne</i>, a species known for its unique morphological traits and ecological niche.<h3>Methods and results</h3>By sequencing and annotating its entire mitochondrial genome, we provide a detailed genetic blueprint that informs future studies on its evolutionary trajectory, population genetics, and conservation status. Additionally, we conducted phylogenetic genomics studies across multiple <i>Alpheus</i> species to reconstruct the evolutionary history of the genus, identify key evolutionary innovations, and elucidate species relationships. Our findings reveal that the mitochondrial genome of <i>A. euphrosyne</i> is 15,866&nbsp;bp long, encoding 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 1 control region. The complete mitochondrial DNA exhibits a positive AT-Skew of 0.048 and a negative CG-Skew of −&nbsp;0.262. It is noteworthy that among the 22 tRNA genes, <i>trnS1</i> forms two approximately circular structures in the middle and lacks a Dihydrouracil arm, while the remaining 21 exhibit a normal clover-leaf structure.&nbsp;The gene order of the mitochondrial genomes is highly conserved across the 9 <i>Alpheus</i> species, with the exception of <i>A. lobidens</i>, which has an additional <i>trnQ</i> inserted between <i>nad4L</i> and <i>trnT</i> genes.<h3>Conclusions</h3>In this study, through in-depth analysis of the mitochondrial genome of <i>A. euphrosyne</i> and combined with phylogenetic analysis methods, nine <i>Alpheus</i> species were divided into two major clades, and it was explicitly revealed that <i>A. euphrosyne</i> has the closest genetic relationship with <i>A. randalli</i>. This achievement provides a new scientific basis for the study of species evolution mechanisms and genus-level taxonomic understanding within the <i>Alpheus</i> genus.","AbstractOtherLang":null,"BibLvlCode":"AS","StandardTitle":"In-depth analysis of the first complete mitochondrial genome of the rare shrimp <i>Alpheus euphrosyne</i>, with comparative phylogenetic genomics insights into the <i>Alpheus</i> species","OrigTitleLangCode":"en","OrigTitleLangCodeExtended":"eng","OrigTitleLangID":15,"DateLastModified":{"date":"2025-07-09 01:35:19.579688","timezone_type":1,"timezone":"+02:00"},"UserAccessRight":null,"UserAccID":null,"AuthorKeywords":null,"OtherDescriptors":null,"Notes":null,"AnaPub":2025,"MonPub":null,"DateUpdate":"2025-07-02","DateCreate":"2025-07-02","SecASFANote":null,"ConfID":null,"PeerRev":1,"VlizCoreFlag":1,"WoScode":null,"VABBcode":null,"OpenAcc":0,"DOI":"10.1007/s11033-025-10651-8"},"refs":null,"anarec":{"AnaID":409304,"PubliDate":2025,"Pagination":"1-13","XtraPublOfAnaID":null,"ISBN":null,"Volume":"52","Issue":"1","BRefMon":null,"BRefMonRR":null,"BRefXtra":null,"BRefXtraRR":null,"SerBRefID":177286,"SerRR":"Molecular biology reports. 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