Signatures of hybridization in Trypanosoma brucei

Genetic exchange among disease-causing micro-organisms can generate progeny that combine different pathogenic traits. Though sexual reproduction has been described in trypanosomes, its impact on the epidemiology of Human African Trypanosomiasis (HAT) remains controversial. However, human infective and non-human infective strains of Trypanosoma brucei circulate in the same transmission cycles in HAT endemic areas in sub-Saharan Africa, providing the opportunity for mating during the developmental cycle in the tsetse fly vector. Here we investigated inheritance among progeny from a laboratory cross of T. brucei and then applied these insights to genomic analysis of field-collected isolates to identify signatures of past genetic exchange. Genomes of two parental and four hybrid progeny clones with a range of DNA contents were assembled and analysed by k-mer and single nucleotide polymorphism (SNP) frequencies to determine heterozygosity and chromosomal inheritance. Variant surface glycopro..., , , , # Signatures of hybridization in *Trypanosoma brucei*

Dataset DOI: [10.5061/dryad.xd2547djb](10.5061/dryad.xd2547djb)

## Description of the data and file structure

Read data for the hybrid clones from the experimental cross is available from the NCBI SRA (Sequence Read Archive [https://www.ncbi.nlm.nih.gov/sra](https://www.ncbi.nlm.nih.gov/sra) Project no. PRJNA795331

All other data have been deposited here. The project contains the folders listed below. Each folder contains a “Readme” file with further details of the contents.

### assembled\_genomes

The genomic SPAdes assembled genomes used to predict ORFs and subsequently VSGs, contigs are of the form:

\>NODE_166886_length_56_cov_1939465.000000

GGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGG

### introgression\_maps

Contains the VCF files used to construct the introgression maps, the script to derive them, and breakdowns of SNP types/density.

### Hybrid\_and\_parent\_maxicircle\_whole\_coding\_region

FASTA file con...

致病微生物间的遗传交换可产生兼具不同致病性状的子代。尽管已在锥虫中报道了有性生殖过程，但其对非洲人类锥虫病（Human African Trypanosomiasis, HAT）流行病学的影响仍存在争议。然而，在撒哈拉以南非洲的HAT流行区，布鲁氏锥虫（Trypanosoma brucei）的人感染株与非人感染株在同一传播循环中循环存在，为其在采采蝇媒介的发育周期内发生交配提供了契机。本研究对布鲁氏锥虫实验室杂交子代的遗传模式进行了分析，并将该分析思路应用于野外分离株的基因组分析，以鉴定既往遗传交换的特征。本研究对两个亲本株以及四个具有不同DNA含量的杂交子代克隆进行了基因组组装，并通过k-mer频率与单核苷酸多态性（single nucleotide polymorphism, SNP）频率分析，以确定其杂合性与染色体遗传模式。变异表面糖蛋白（Variant surface glycoprotein, VSG，原文此处截断）……
# 布鲁氏锥虫的杂交特征

数据集DOI：[10.5061/dryad.xd2547djb](10.5061/dryad.xd2547djb)

## 数据与文件结构说明

本实验杂交获得的杂交克隆的测序读段数据可从NCBI序列读取档案（Sequence Read Archive, SRA，https://www.ncbi.nlm.nih.gov/sra）获取，项目编号为PRJNA795331。其余所有数据均已上传至本数据集。本项目包含以下所列文件夹，每个文件夹均附带一份"Readme"文件，详细说明其内含文件信息。

### assembled_genomes
本文件夹包含用于预测开放阅读框（Open Reading Frame, ORF）及后续变异表面糖蛋白（VSG）的SPAdes组装基因组，序列片段命名格式为：
>NODE_166886_length_56_cov_1939465.000000
GGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGG

### introgression_maps
本文件夹包含用于构建渐渗图谱的VCF（变异检测格式，Variant Call Format）文件、生成这些文件的脚本，以及单核苷酸多态性类型与密度的分类明细。

### Hybrid_and_parent_maxicircle_whole_coding_region
本文件夹包含FASTA格式的[原文此处截断]文件