biostudies-literatureUnknown65(9)Szczesniak MWCANTATAdb 3.0 is an updated database of plant long non-coding RNAs (lncRNAs), containing 571,688 lncRNAs identified across 108 species, including 100 Magnoliopsida (flowering plants), a significant expansion from the previous version. A notable feature is the inclusion of 112,980 lncRNAs that are expressed specifically in certain plant organs or embryos, indicating their potential role in development and organ-specific processes. In addition, CANTATAdb 3.0 includes 74,886 pairs of evolutionarily conserved lncRNAs found across 47 species and inferred from genome-genome alignments as well as conserved lncRNAs obtained using a similarity search approach in 5,479 species pairs, which would further aid in the selection of lncRNAs for functional studies. Interestingly, we find that conserved lncPlant & cell physiology1486-1493https://www.ebi.ac.uk/biostudies/studies/S-EPMC11447640biostudies-literatureCANTATAdb 3.0: An Updated Repository of Plant Long Non-Coding RNAs.PMC11447640Szczesniak MWWanowska EfalseCANTATAdb 3.0: An Updated Repository of Plant Long Non-Coding RNAs.CANTATAdb 3.0 is an updated database of plant long non-coding RNAs (lncRNAs), containing 571,688 lncRNAs identified across 108 species, including 100 Magnoliopsida (flowering plants), a significant expansion from the previous version. A notable feature is the inclusion of 112,980 lncRNAs that are expressed specifically in certain plant organs or embryos, indicating their potential role in development and organ-specific processes. In addition, CANTATAdb 3.0 includes 74,886 pairs of evolutionarily conserved lncRNAs found across 47 species and inferred from genome-genome alignments as well as conserved lncRNAs obtained using a similarity search approach in 5,479 species pairs, which would further aid in the selection of lncRNAs for functional studies. Interestingly, we find that conserved lnc2024-01-01T00:00:00Z2024 Oct2025-04-04T01:14:39.58Z2025-04-04T01:14:39.58ZS-EPMC114476403901802710.1093/pcp/pcae081