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...

柳属黄花柳组（Salix section Vetrix）的灌木柳是北美与欧亚大陆新兴的生物质能源作物。尽管该组内多个物种已应用于育种项目，但目前可获取的参考基因组数量仍十分有限，相关基因组学资源相对匮乏。本研究报道了来自6个物种的11个灌木柳基因组的从头组装（de novo assembly）与注释结果。我们对每个基因组中候选性别决定基因的拷贝数变异（copy number variation）进行了表征，发现潜在主调控基因的复制与缺失存在显著差异。此外，我们还分析了参与花类次生代谢的候选基因的拷贝数与表达模式，鉴定出不同基因型间存在大量可用于育种项目亲本选择的遗传变异。最后，我们报道了一个仅产生雌性后代的基因型，并鉴定出线粒体基因组（mitochondrial genome）上的基因存在/缺失变异，该变异可能是这一特殊遗传现象的成因。

### DNA测序
我们收集了11个柳属基因型的新鲜幼叶组织，经液氮研磨后，采用改良CTAB法提取基因组DNA。对于长读长测序，我们使用1 μg DNA作为起始模板，使用牛津纳米孔（Oxford Nanopore）的连接测序试剂盒（SQK-LSK109）构建文库，并在R.9.4.1流通槽上完成测序。同一批样品的短读长测序则在Illumina HiSeq X Ten平台上进行。

### RNA测序
我们从11个基因型的8种组织（根、木质部、节间、节、幼叶、成熟叶、叶柄与幼茎）中提取RNA，同时还采集了04-BN-051的扁化茎组织。BGI构建了链特异性RNA-seq文库，并在DNB-Seq平台上完成测序，产出了150 bp双端读长序列。此外，我们还使用牛津纳米孔MinION平台对成熟叶与根的同一RNA样品进行了测序，但‘Jorr’样品因质量控制未通过未能获得有效数据。采用基于PCR的cDNA测序试剂盒SQK-PCB109相关数据……

本研究的数据包含基因组组装的fasta文件、gff3注释文件以及基因组注释信息文本文件。原则上所有文件均可通过任意文本编辑器打开，但fasta文件体积较大，在内存较小的设备上可能无法正常打开，或需要较长时间加载，建议通过命令行工具进行查看。组装结果与注释文件可导入IGV以浏览器形式查看组装与注释信息。

# 11个灌木柳（柳属）基因组的组装与注释
11个灌木柳（柳属）基因组的完整组装与注释结果。组装工作基于牛津纳米孔长读长数据与Illumina短读长数据完成，并通过Hi-C技术进行挂载。注释工作使用LoReAn软件完成，同时结合了每个基因型8种组织的Illumina短读长与牛津纳米孔长读长RNA-seq数据。原始测序数据可在NCBI SRA数据库中获取。

### 数据与文件结构说明
11个基因组的前缀标识如下：
94006：紫柳（Salix purpurea）雌性个体
94001：紫柳（Salix purpurea）雄性个体
P63：簸箕柳（Salix suchowensis）雄性个体
P294：簸箕柳（Salix suchowensis）雌性个体
P295：簸箕柳（Salix suchowensis）雌性个体
P336：杞柳（Salix integra）雌性个体
SH3：朝鲜柳（Salix koriyanagi）雌性个体
04-FF-016：朝鲜柳（Salix koriyanagi）雄性个体
07-MBG-5027：欧杞柳（Salix viminalis）雌性个体
Jorr：欧杞柳（Salix viminalis）雄性个体
04-BN-051：龙爪柳（Salix udensis）雄性个体

每个基因组包含5个文件，具体说明如下：
*_hap.FINAL.fasta：该文件为组装完成的基因组序列……