# Satellite DNA in Populus and Molecular Karyotyping of Populus xiaohei and Its Derived Double Haploids

## TL;DR

Researchers identified satellite DNA in poplar species and used it to create molecular karyotypes, revealing chromosomal variations in hybrids and their double haploids.

## Contribution

Development of satDNA probes and molecular karyotyping in Populus to detect chromosomal variations and improve genome assemblies.

## Key findings

- 12 satDNAs were identified and analyzed in three poplar species, revealing copy number and chromosomal distribution patterns.
- Satellite DNA probes enabled fluorescence in situ hybridization and molecular karyotyping of P. xiaohei and its DH lines.
- Comparative analysis uncovered chromosomal variations in DH lines and errors in current poplar genome assemblies.

## Abstract

Karyotype analysis and the investigation of chromosomal variations in Populus are challenging due to its small and morphologically similar chromosomes. Despite its utility in chromosome identification and karyotype evolutionary research, satellite DNA (satDNA) remains underutilized in Populus. In the present study, 12 satDNAs were identified from P. trichocarpa, and the copy numbers and chromosomal distributions of each satDNA were analyzed bioinformatically in the reference genomes of P. trichocarpa, P. simonii, and P. nigra. Ten satDNA probes for fluorescence in situ hybridization (FISH) were successfully developed and validated on chromosomes of P. xiaohei (poplar hybrid P. simonii × P. nigra). By integrating bioinformatic genomic satDNA distribution patterns with experimental FISH signals, we constructed a molecular karyotype of P. xiaohei. Comparative analysis revealed errors in current poplar genome assemblies. Comparative karyotype analysis of P. xiaohei and its doubled haploid (DH) lines revealed chromosomal variations in the DH lines relative to the donor tree. The results demonstrate that the newly developed satDNA probes constitute robust cytogenetic tools for detecting structural variations in Populus, while molecular karyotyping provides new insights into the genetic mechanisms underlying chromosome variations in P. xiaohei and the DH plants derived.