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Premise of research. Earlier molecular systematic studies revealed that the genus Ligusticum is polyphyletic, with its members allied with representatives of several other genera in five clades of Apiaceae subfamily Apioideae. These studies included only a small sampling of Ligusticum species and its putative allies, including those from the Hengduan Mountains of southwestern China, a major distribution center for the genus. The proper circumscription of the genus, the placement and phylogenetic relationships among those species hitherto accommodated in Ligusticum , and the relationships among the Chinese endemic species have been elusive. Methodology. Internal transcribed spacer (ITS) sequences were obtained from 103 accessions of Ligusticum and its putative allies, representing the most comprehensive sampling of Ligusticum to date (46 species). These data, along with published ITS sequences from selected Apioideae (for a total of 2911 accessions), were subjected to a maximum likelihood analysis. Pivotal results. Besides the five clades to which Ligusticum has been referred previously (Acronema clade, Conioselinum chinense clade, Pyramidoptereae, Selineae, and Sinodielsia clade), two members allied with the East-Asia (Physospermopsis) clade. Most Chinese endemic Ligusticum species (plus members of other polyphyletic genera, such as Cortiella , Ligusticopsis , and Oreocome) fell within the Chinese Ligusticum clade of tribe Selineae. All North American species of Ligusticum except L. scoticum (the generic type) occur within the North American Ligusticum clade (the previously recognized Conioselinum chinense clade). Excluding the monotypic Paraligusticum and Rupiphila , many Eurasian genera putatively allied with Ligusticum s.lat. (such as Cnidium , Hymenidium , Ligusticopsis , Pachypleurum , Selinum , and Tilingia) are polyphyletic, and none ally with Ligusticum s.s. Conclusions. Ligusticum s.s., placed in the Acronema clade, is reduced to comprise only two species: L. scoticum (with subspecies scoticum and hultenii) and L. holopetalum. Relationships among those other species traditionally accommodated in Ligusticum , especially those of the Chinese Ligusticum clade, are far more complex than previously realized and will require further study utilizing the framework phylogeny presented herein before their taxonomy can be revised to reflect evolutionary relationships. [ABSTRACT FROM AUTHOR]

Large-scale loach (Paramisgurnus dabryanus) is a commercially important species in East Asia; however, the cultured population that exhibited degradation of germplasm resource cannot meet the market needs, and the genome resources for P. dabryanus are still lacking. In this study, the first high-density genetic map of P. dabryanus was constructed using 15,830 SNP markers based on high-throughput sequencing with an improved SLAF-seq strategy. The quantitative trait locus (QTL) mapping for sex, growth, and morphology traits was performed for the first time. The genetic map spanned 4,657.64 cM in length with an average inter-marker distance of 0.30 cM. QTL mapping and association analysis identified eight QTLs of growth traits, nine QTLs of morphology traits, and five QTLs of sex-related traits, respectively. Interestingly, the most significant QTLs for almost all the traits were concentrated on the same linkage group LG11. Seven candidate markers and 12 potentially key genes, which were associated with sex determination and growth, were identified within the overlapped QTL regions on LG11. Further, the first genome survey analysis of P. dabryanus was performed which represents the first step toward fully decoding the P. dabryanus genome. The genome scaffolds were anchored to the high-density linkage map, spanning 960.27 Mb of P. dabryanus reference genome. The collinearity analysis revealed a high level of collinearity between the genetic map and the reference genome of P. dabryanus. Moreover, a certain degree of homology was observed between large-scale loach and zebrafish using comparative genomic analysis. The constructed high-density genetic map was an important basis for QTL fine mapping, genome assembly, and genome comparison. The present study will provide a valuable resource for future marker-assisted breeding, and further genetic and genomic researches in P. dabryanus. [ABSTRACT FROM AUTHOR]