Genome-wide Data Reveal Bi-direction and Asymmetrical Hybridization Origin of a Fern Species

Overview

Journal Front Plant Sci

Date 2024 Jul 23

PMID 39040506

Authors

Jun-Jie Luo

Hui Shang

Zhi-Qing Xue

Ying Wang

Xi-Ling Dai

Hui Shen

Yue-Hong Yan

Affiliations

Soon will be listed here.

Abstract

Introduction: Natural hybridization is common and plays a crucial role in driving biodiversity in nature. Despite its significance, the understanding of hybridization in ferns remains inadequate. Therefore, it is imperative to study fern hybridization to gain a more comprehensive understanding of fern biodiversity. Our study delves into the role of hybridization in shaping fern species, employing as a case study to investigate its origins of hybridization.

Methods: We performed double digest Genotyping-by-sequencing (dd-GBS) on M. matthewii and its potential parent species, identifying nuclear and chloroplast SNPs. Initially, nuclear SNPs were employed to construct the three cluster analysis: phylogenetic tree, principal component analysis, and population structure analysis. Subsequently, to confirm whether the observed genetic mixture pattern resulted from hybridization, we utilized two methods: ABBA-BABA statistical values in the D-suite program and gene frequency covariance in the Treemix software to detect gene flow. Finally, we employed chloroplast SNPs to construct a phylogenetic tree, tracing the maternal origin.

Results And Discussion: The analysis of the nuclear SNP cluster revealed that M. matthewii possesses a genetic composition that is a combination of and . Furthermore, the analysis provided strong evidence of significant gene flow signatures from the parental species to the hybrid, as indicated by the two gene flow analyses. The samples of cluster separately with or on the chloroplast systematic tree. However, the parentage ratio significantly differs from 1:1, suggesting that is a bidirectional and asymmetrical hybrid offspring of and .

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