For 75 years, the Journal of Systematics and Evolution (JSE) has been a home for work that makes the Tree of Life legible, from the flora of tropical and subtropical Yunnan and the classification of Chinese ferns to the gen-morph species concept, grass family classification, bryophyte families, and the evolutionary history of mid-Cretaceous scorpionflies. In the post-genomic era, JSE has increasingly become a platform for phylogenomics and genome evolution, and its new 75th-anniversary special issue on Genome Evolution across the Tree of Life shows just how far that journey has come.
The special issue, introduced by Taikui Zhang, Yuannian Jiao, Wen-Jun Li, and Huabin Zhao, brings together a broad range of organisms and questions. Angiosperm classification gets a major update with APG V, which draws on large-scale nuclear and plastid phylogenomic data and revises the limits of two major rosid groups and several orders and families. Deep-time paleogenomics, genome assembly and annotation standards, pangenomics, and reticulate evolution all feature prominently—reminders that the genomic era is as much about frameworks and data quality as it is about new sequences.
The biological stories are just as varied. Comparisons of monocentric and holocentric Magnoliales chromosomes shed light on centromere diversification. Metagenomic work from Tengchong hot springs proposes three new bacterial phyla and hints at cross-feeding as a community survival strategy. A broad survey of Acidobacteria genomes sorts 4,317 genomes into seven groups with distinct metabolic and environmental profiles.
In plants, a new paper reveals that serpentine populations of three sympatric species repeatedly colonized extreme soils rather than stemming from a single origin; a telomere-to-telomere genome of Canavalia gladiata coupled with multiomic analyses reveals nutrient-related regulatory networks; a study of Berberis wilsoniae reveals how benzylisoquinoline alkaloid genes have been reshuffled; examination of a haploid-resolved assembly reveals conserved mechanisms of sex determination in Salix; and research on Wikstroemia monnula shows that small-scale duplications, not whole-genome duplication, helped expand cellulose synthase families tied to fiber traits.
Animals are well represented too: examination of the genome of the frog Odorrana margaretae reveals recent transposable-element proliferation; a diverse repertoire of antimicrobial peptides, and expansion of olfactory receptor gene families; and comparative spider genomics probes the repeated evolution of funnel-web building. Conservation genomics, vertebrate lung origins, archaeal survival in extreme environments, and the White Cloud Mountain minnow’s ornamental traits round out a genuinely broad collection.
What ties these contributions together is a shift from single reference genomes to pangenomes, graph-based representations, haplotype-resolved assemblies, and multi-omics integration. For anyone interested in how genomes shape diversification, adaptation, and survival, this special issue is a rich and timely resource.
The issue is available through the JSE website: https://www.jse.ac.cn/EN/volumn/volumn_12951.shtml. Readers are warmly invited to browse the collection and explore the genome evolution stories behind the Tree of Life.
Original Source: https://www.jse.ac.cn/EN/volumn/volumn_12951.shtml
Keywords: Genome evolution; Tree of Life; Phylogenomics; APG V classification; Pangenomics; Genome assembly and annotation; Whole-genome duplication (WGD); Reticulate evolution and hybridization; Metagenomics; Conservation genomics
About the Journal:
Journal of Systematics and Evolution (JSE) is a peer-reviewed, bimonthly, international English-language journal that publishes research related to systematics and evolution of plants, animals, fungi, and microbes (https://www.jse.ac.cn/EN/home). We publish articles, reviews, short communications, and letters to the editor dedicated to the description and understanding of biological diversity across kingdoms. Papers in any of the following and related fields will be considered: phylogenetics and phylogenomics, biogeography (including phylogeography), biosystematics, description of well-documented new taxa, taxonomic revisions and monographs (incorporating data from morphology, molecules, anatomy and ecology), molecular evolution, evolutionary development, evolutionary ecology, population biology, conservation biology, paleobiology, and related methods and theory.
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Journal of Systematics and Evolution