Origin of subgenomes in the circumboreal allopolyploid carnivorous plant Drosera anglica (Droseraceae)

Premise of Study
The parentage of one of the most widespread members of the carnivorous sundew genus Drosera, the enigmatic allopolyploid Drosera anglica, remains uncertain despite over 100 years of morphological, cytological, and more recently, molecular study.
Methods
Using transcriptomic and genomic data from 12 species and 20 populations across Drosera sect. Drosera including four D. anglica populations and a disjunct Idaho population of D. intermedia, we carried out reference-based assembly in HybPiper and phased sequences in HybPhaser. We estimated a species tree and quantified gene tree discordance; we calculated heterozygosity statistics and pairwise divergence between individuals. In addition to genome-wide analyses, we extracted and assembled rbcL and ITS reads from genome and transcriptome datasets to compare to previous Sanger sequencing data. We also generated flow cytometry data to verify the ploidy levels of D. anglica and D. rotundifolia populations.
Key Results
Seq..., , , This repository contains data and analysis files for Mohn, RA, Yang, Y. Origin of subgenomes in the circumboreal allopolyploid carnivorous plant Drosera anglica (Droseraceae).

### Dspat\_6443\_refgenes.fa

The 6443 reference genes from D. spatulata used for input to HybPiper

The genes are labeled with their Drosera spatulata names as published in Palfalvi et al., 2020 Current Biology. [https://doi.org/10.1016/j.cub.2020.04.051](https://doi.org/10.1016/j.cub.2020.04.051)
They are in a fasta format.

The complete list of Drosera spatulata genes were obtained here: [https://www.biozentrum.uni-wuerzburg.de/carnivorom/resources/](https://www.biozentrum.uni-wuerzburg.de/carnivorom/resources/)

### finalAlnPreCleaning

The alignments of recovered genes after phasing of D. anglica subgenomes before trimming with Phyx

This zipped folder contains a separate file for each gene, titled by the D. spatulata name. All samples with that gene are included in the gene alignment file in FASTA format.

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## 研究背景
食肉茅膏菜属（Drosera）分布最广泛的类群之一、神秘的异源多倍体（allopolyploid）长柱茅膏菜（Drosera anglica），尽管已有百余年的形态学、细胞学以及近年的分子生物学研究，但其亲本起源仍不明确。

## 研究方法
本研究针对茅膏菜属茅膏菜组（Drosera sect. Drosera）的12个物种、20个种群（包含4个长柱茅膏菜种群以及一个间断分布于爱达荷州的中间茅膏菜（D. intermedia）种群）的转录组（transcriptomic）与基因组（genomic）数据，采用HybPiper进行基于参考序列的组装，并通过HybPhaser对序列进行分型。我们构建了物种树（species tree）并量化了基因树（gene tree）的冲突程度；同时计算了杂合性（heterozygosity）统计量以及个体间的成对遗传分化。除全基因组分析外，我们还从基因组与转录组数据中提取并组装了rbcL与ITS序列，用于与既往Sanger测序（Sanger sequencing）得到的数据进行比对验证。此外，我们还通过流式细胞术（flow cytometry）获取数据，以验证长柱茅膏菜与圆叶茅膏菜（D. rotundifolia）种群的倍性水平（ploidy levels）。

## 主要结果
本数据集包含Mohn RA与Yang Y发表的《环北分布异源多倍体食肉植物长柱茅膏菜（茅膏菜科）的亚基因组起源》一文所涉及的数据与分析文件。

### Dspat_6443_refgenes.fa
该文件包含取自匙叶茅膏菜（D. spatulata）的6443个参考基因，用于作为HybPiper的输入数据。
这些基因以Palfalvi等于2020年发表于《当代生物学（Current Biology）》的匙叶茅膏菜基因命名规则进行标注，相关文献DOI：[https://doi.org/10.1016/j.cub.2020.04.051](https://doi.org/10.1016/j.cub.2020.04.051)
文件格式为FASTA。
匙叶茅膏菜基因的完整列表可从以下网址获取：[https://www.biozentrum.uni-wuerzburg.de/carnivorom/resources/](https://www.biozentrum.uni-wuerzburg.de/carnivorom/resources/)

### finalAlnPreCleaning
该文件夹包含长柱茅膏菜亚基因组分型后、尚未经Phyx软件进行序列修剪的已获取基因的比对结果。
该压缩文件夹内包含每个基因对应的独立比对文件，文件名以匙叶茅膏菜的基因名称命名；所有携带该基因的样本序列均纳入该FASTA格式的基因比对文件中。
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