Instructions:

Synteny conservation, defined as the evolutionary maintenance of gene order and genomic organization across species, serves as the cornerstone of our lncRNA identification pipeline. Through genome-wide analysis of homologous blocks, we have systematically predicted 84,602 conserved syntenic lncRNAs across 19 species, anchored within 234,350 syntenic blocks. For each query lncRNA, our pipeline precisely maps it to syntenic blocks in target genomes and identifies all potential synteny-conserved lncRNAs within these evolutionarily conserved genomic regions.

Methods:

JCVI was used to construct whole-genome syntenic blocks based on protein-coding gene sequence homology between species. And then, we employ two core criteria to screen for synteny-conserved lncRNAs based on each block. LncRNAs were classified as synteny-conserved when meeting dual criteria: (i) at least five (moderate criterion) adjacent homologous protein-coding genes must be syntenic between the two species; and (ii) transcriptional orientation concordance with any neighboring homologous coding gene.

Hierarchical classification system:

Three levels of criteria based on the number of adjacent homologous coding genes:

(i)Lenient (≥3 genes): optimized for lncRNA detection sensitivity, suitable for initial exploration;

(ii)Moderate (≥5 genes): as the main classification criterion, balancing sensitivity and specificity;

(iii)Strict threshold (≥10 genes and in the same transcriptional direction as the most proximal homologous coding gene): dedicated to high-confidence assessment of deeply conserved functional elements.

Help Note:

1. Choose the Query Species; 2. Input LncRNA ID or List; 3. Click "Submit" buttom and show results. Furthermore, clicking on "Example" buttom will display default information.