Gene network analysis is a powerful tool to identify and prioritize candidate genes, especially from data sets where experimental design renders other approaches, such as differential expression analysis, limiting or infeasible. Numerous gene network inference algorithms have been published and are commonly individually applied in transcriptomics studies. It has, however, been shown that every algorithm is biased towards identifying specific types of gene interaction and that an ensemble of inference methods can reconstruct more accurate networks. This approach has been hindered by lack of an implementation to run and combine such combinations of inference algorithms. Here, we present Seidr: a toolkit to perform multiple gene network inferences and combine their results into a unified meta-network. Availability and implementation:Seidr code is open-source, available from GitHub and also compiled in docker and singularity containers. It is implemented in C++ for fast computation and supports massive parallelisation through MPI. Documentation, tutorials and exemplary use are available from https://seidr.readthedocs.io.

In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.

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