{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T06:31:20Z","timestamp":1787725880953,"version":"build-2784847793"},"reference-count":81,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"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. Plant Sci."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      As a perennial herb of Poaceae,\n                      <jats:italic>Phalaris arundinacea<\/jats:italic>\n                      plays key roles in grazing, production, and soil and water conservation because of its well-developed rhizomes and seed dispersal. We assembled and annotated the first mitogenome of\n                      <jats:italic>P. arundinacea<\/jats:italic>\n                      to support evolutionary and taxonomic research.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We assembled and annotated the first complete mitochondrial genome of\n                      <jats:italic>P. arundinacea<\/jats:italic>\n                      by integrating Illumina short reads with Nanopore long reads via a hybrid assembly strategy. The genome architecture was comprehensively characterized, encompassing codon usage bias, repetitive sequence organization, and inter-organellar genetic exchange with the chloroplast genome.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results and discussion<\/jats:title>\n                    <jats:p>\n                      Assembly of the\n                      <jats:italic>P. arundinacea<\/jats:italic>\n                      mitogenome revealed two circular structures with a combined length of 526,717 bp. The genome comprised a set of 37 protein-coding genes (PCGs), 27 tRNAs, and 8 rRNAs, with the rRNA genes exhibiting full assembly (100% coverage). The mitochondrial genome contained 154 forward and 164 palindromic repeats, along with 25 tandem repeats and 124 simple sequence repeats (SSRs). Notably, 102 SSRs were distributed on contig1, predominantly in tetrameric form. Furthermore, 376 RNA editing sites were predicted. A total of 104 fragments were integrated into the mitochondrial genome from the chloroplast, amounting to 55,866 bp of transferred sequence. Finally, phylogenetic analysis of 28 plant mitogenomes placed\n                      <jats:italic>P. arundinacea<\/jats:italic>\n                      closest to species within the genus\n                      <jats:italic>Poa<\/jats:italic>\n                      (\n                      <jats:italic>P. chaixii<\/jats:italic>\n                      and\n                      <jats:italic>P. pratensis<\/jats:italic>\n                      ). Comparative analysis of non-synonymous-to-synonymous substitution rate (Ka\/Ks) ratios across divergent species revealed that the mitochondrial genome of\n                      <jats:italic>P. arundinacea<\/jats:italic>\n                      underwent stabilizing evolutionary dynamics, characterized by predominant purifying selection with several lineage-specific variations in selective pressure. Our findings support the close phylogenetic relationship between P. arundinacea and species of the genus Poa and provide a reference mitochondrial genome resource for future comparative studies within Phalaris that incorporate broader taxon sampling. These results support deeper phylogenetic investigations of\n                      <jats:italic>P. arundinacea<\/jats:italic>\n                      and facilitate future work on its germplasm characterization and applied use.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fpls.2026.1926603","type":"journal-article","created":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T06:03:45Z","timestamp":1787724225000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Mitogenome assembly and phylogenetic relationships of Phalaris arundinacea"],"prefix":"10.3389","volume":"17","author":[{"given":"Ze","family":"Teng","sequence":"first","affiliation":[{"name":"Pratacultural College, Gansu Agricultural University","place":["Lanzhou, China"]},{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences","place":["Hohhot, China"]},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunyu","family":"Tian","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences","place":["Hohhot, China"]},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanting","family":"Yang","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences","place":["Hohhot, China"]},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenlong","family":"Gong","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences","place":["Hohhot, China"]},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiyong","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences","place":["Hohhot, China"]},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoming","family":"Bai","sequence":"additional","affiliation":[{"name":"Pratacultural College, Gansu Agricultural University","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zinian","family":"Wu","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences","place":["Hohhot, China"]},{"name":"Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,26]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1002\/csc2.21147","article-title":"Assembly and comparative analysis of the complete mitochondrial genome of poa pratensis","volume":"64","author":"Ai","year":"2024","journal-title":"Crop Sci."},{"key":"B2","doi-asserted-by":"publisher","first-page":"10231","DOI":"10.1073\/pnas.1500012112","article-title":"Why chloroplasts and mitochondria retain their own genomes and genetic systems: Colocation for redox regulation of gene expression","volume":"112","author":"Allen","year":"2015","journal-title":"Proc. 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