{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T21:53:29Z","timestamp":1791323609498,"version":"4.3.1"},"reference-count":0,"publisher":"Canadian Science Publishing","license":[{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.nrcresearchpress.com\/page\/about\/CorporateTextAndDataMining"}],"content-domain":{"domain":["cdnsciencepub.com"],"crossmark-restriction":false},"short-container-title":["Genome"],"abstract":"<jats:p>Plant long interspersed nuclear elements (LINEs) are structurally diverse, experience periodic pulses of degeneration, and occur in lower copy numbers than LTR retrotransposons. Consequently, their macroevolutionary dynamics remain poorly understood. Here, we curated a high-stringency reverse transcriptase (RT) database to annotate structurally complete LINEs across 54 plant genomes spanning from Marchantiopsida to Magnoliopsida. The highly selective filtering yielded a refined dataset dominated by L1 and RTE families, whereas I, R2, and Jockey superfamilies were rare and highly degenerate. Full-length elements retained at least essential ORF2 domains (EEP and RT) alongside a 3\u2032 poly(A) tail. However, those of longer length exhibited structural variability, carrying 5\u2032 ORF1 regions, non-essential ORF2 domains (Zf-RVT and RNH), and, in some cases, 3\u2032 (GTT)n motifs before the poly(A) tail. L1 elements were larger and showed greater EEP-RT domain heterogeneity than RTE. Nonetheless, RT-based phylogeny robustly separated these two groups. An alignment-free k-mer-based pipeline (k = 9) validated our manual annotations and successfully resolved degraded domains and interstitial gaps missed by conventional BLAST alignments. Furthermore, genomic abundance showed only a moderate positive correlation with genome size, underscoring lineage-specific TE dynamics. Overall, our findings demonstrate that plant LINE evolution is driven by widespread structural degeneration, where the selective persistence of core catalytic domains (RT and EEP) sustains element survival amidst extensive domain loss across land plants.<\/jats:p>","DOI":"10.1139\/gen-2026-0080","type":"journal-article","created":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T21:33:47Z","timestamp":1791322427000},"update-policy":"https:\/\/doi.org\/10.1139\/csp-crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Insights into plant LINE evolution: Essential domains persist amidst widespread structural degeneration"],"prefix":"10.1139","author":[{"given":"Thamirys Silva","family":"Valentim","sequence":"first","affiliation":[{"name":"Universidade Estadual de Londrina, Biologia Geral, Londrina, PR, Brazil;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucas","family":"Johnen","sequence":"additional","affiliation":[{"name":"Universidade Estadual de Londrina, Biologia Geral, Londrina, PR, Brazil;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juliana Machado","family":"da Silva","sequence":"additional","affiliation":[{"name":"Universidade Estadual de Londrina, Biologia Geral, Londrina, PR, Brazil;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matheus","family":"Pimenta","sequence":"additional","affiliation":[{"name":"UTFPR Corn\u00e9lio Proc\u00f3pio, Bioinform\u00e1tica, Corn\u00e9lio Proc\u00f3pio, PR, Brazil;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guilherme","family":"Borges","sequence":"additional","affiliation":[{"name":"Universidade Estadual de Londrina, Biologia Geral, Londrina, PR, Brazil;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leticia Maria","family":"Parteka","sequence":"additional","affiliation":[{"name":"Universidade Estadual de Londrina, Biologia Geral, Londrina, PR, Brazil;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael","family":"de Assis","sequence":"additional","affiliation":[{"name":"Universidade Estadual de Londrina, Biologia Geral, Londrina, Paran\u00e1, Brazil;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9","family":"Marques","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Plant Breeding Research, Department of Chromosome Biology, Koln, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabricio Martins","family":"Lopes","sequence":"additional","affiliation":[{"name":"UTFPR Corn\u00e9lio Proc\u00f3pio, Bioinform\u00e1tica, Corn\u00e9lio Proc\u00f3pio, PR, Brazil;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Sr.","given":"Andr\u00e9 Laforga","family":"Vanzela","sequence":"additional","affiliation":[{"name":"Universidade Estadual de Londrina, Biologia Geral, Londrina, Paran\u00e0, Brazil, ;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"155","published-online":{"date-parts":[[2026,10,6]]},"container-title":["Genome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdnsciencepub.com\/doi\/pdf\/10.1139\/gen-2026-0080","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T21:33:48Z","timestamp":1791322428000},"score":1,"resource":{"primary":{"URL":"https:\/\/cdnsciencepub.com\/doi\/10.1139\/gen-2026-0080"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,6]]},"references-count":0,"alternative-id":["10.1139\/gen-2026-0080"],"URL":"https:\/\/doi.org\/10.1139\/gen-2026-0080","relation":{},"ISSN":["0831-2796","1480-3321"],"issn-type":[{"value":"0831-2796","type":"print"},{"value":"1480-3321","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,6]]},"assertion":[{"value":"2026-06-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-10-06","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"gen-2026-0080"}}