Assembly and annotation of eleven Salix (shrub willow) genomes

The shrub willows (Salix section Vetrix) are an emerging bioenergy crop in North America and Eurasia. However, genomics resources in this section are still quite limited, with only a few reference genomes available, despite many species in use in breeding programs. Here we present de novo assemblies and annotations of eleven shrub willow genomes from six species. Copy number variation of candidate sex determination genes within each genome was characterized and revealed remarkable differences in putative master regulator gene duplication and deletion. We also analyzed copy number and expression of candidate genes involved in floral secondary metabolism and identified substantial variation across genotypes, which can be used for parental selection in breeding programs. Lastly, we report on a genotype that produces only female descendants and identified gene presence/absence variation in the mitochondrial genome that may be responsible for this unusual inheritance., DNA Sequencing
Fresh young leaf tissue for all 11 Salix genotypes was collected and ground in liquid nitrogen. DNA extraction was performed using a modified CTAB based protocol. For long read sequencing, 1 μg of DNA was used as input to Oxford Nanopore’s genomic DNA by ligation sequencing kit (SQK-LSK109) and the subsequent library was sequenced on a R.9.4.1 flow cell. Short read sequencing of the same samples was performed on the Illumina HiSeq X Ten platform.
RNA Sequencing
RNA was extracted from eight tissues (root, xylem, internode, node, young leaf, mature leaf, petiole, and young stem) for all 11 genotypes, as well as fasciated shoot tissue from 04-BN-051. Strand-specific RNA-Seq libraries were prepared by BGI and sequenced on the DNB-Seq platform, which generated paired-end 150 bp reads. The same RNA preps from mature leaves and roots were also sequenced on the Oxford Nanopore MinION platform, with the exception of ‘Jorr’, which failed quality control. The SQK-PCB109 PCR-based cD..., Data include fasta files of genome assemblies, gff3 annotation files, and text files with genome annotation info. All files can be opened in any text editor in principle, but fasta files are large may be too large to open on smaller memory machines or may take considerable time to load and should be viewed in a command line. Assemblies and annotations can be loaded into IGV to view the assembly and annotation in browser form. , , #  Assembly and Annotation of Eleven Salix (shrub willow) genomes

Full assemblies and annotations of eleven shrub willow (Salix) genomes. Assemblies were performed using long read Oxford nanopore and short read illumina data and scaffolded with HiC. Annotation was performed using LoReAn software and illumina short read and Oxford Nanopore long read RNA-Seq from eight tissues from each genotype. Raw sequencing reads are available on NCBI SRA.

## Description of the Data and file structure

The prefixes for each of the eleven genomes are as follows:
94006, a Salix purpurea female
94001, a Salix purpurea male
P63, a Salix suchowensis male
P294, a Salix suchowensis female
P295, a Salix suchowensis female
P336, a Salix integra female
SH3, a Salix koriyanagi female
04-FF-016, a Salix koriyanagi male
07-MBG-5027, a Salix viminalis female
Jorr, a Salix viminalis male
04-BN-051, a Salix udensis male

Each genome contains five files, as described below:
*_hap.FINAL.fasta ; This is the assem...