Mapping-based genome size estimation

Shakunthala Natarajan

doi:10.1186/s12864-025-11640-8

2025-05-14

Shakunthala Natarajan

Jessica Gehrke

Boas Pucker *

DOI：10.1186/s12864-025-11640-8

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摘要

En 中文

虽然染色体的大小可以在显微镜下测量，但获得基因组的确切大小仍然是一个挑战。生化方法和基于k-mer分布的方法只能进行估算。本文提出了一种基于高连续性组装和读长比对来估算基因组大小的方法。对 *Arabidopsis thaliana* 和 *Beta vulgaris* 数据集的分析展示了不同参数的影响。*Oryza sativa*、*Brachypodium distachyon*、*Solanum lycopersicum*、*Vitis vinifera* 和 *Zea mays* 也被分析，以证明该方法的广泛适用性。此外，MGSE也被用于分析 *Escherichia coli*、*Saccharomyces cerevisiae* 和 *Caenorhabditis elegans* 数据集，以展示其超越植物领域的应用价值。基于比对的基因组大小估算（MGSE）和附加脚本可在GitHub上获取：https://github.com/bpucker/MGSE。MGSE基于短读长或长读长预测基因组大小，要求最低覆盖度为5倍。

Keyword:

Genome size

Short reads

Long reads

Next generation sequencing

Long read sequencing

Read mapping

Nanopore sequencing

期刊

BMC Genomics

IF:

3.7

论文数:

1.9W

被引数:

5.2W

机构

TU Braunschweig

学者数:

论文数: 36

被引数: 9

引用论文

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