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Published (Version of record)CC BY V4.0, Open Access
Published (Version of record)CC BY V4.0, Open
Journal article
Largest genome assembly in Brassicaceae: retrotransposon-driven genome expansion and karyotype evolution in Matthiola incana
Plant biotechnology journal, Vol.First online, pp.1-17
26/06/2025
PMID: 40569825
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Abstract
Matthiola incana, commonly known as stock and gillyflower, is a widely grown ornamental plant whose genome is significantly larger than that of other species in the mustard family. However, the evolutionary history behind such a large genome (~2 Gb) is still unknown. Here, we have succeeded in obtaining a high-quality chromosome-scale genome assembly of M. incana by integrating PacBio HiFi reads, Illumina short reads and Hi-C data. The resulting genome consists of seven pseudochromosomes with a length of 1965 Mb and 38 245 gene models. Phylogenetic analysis indicates that M. incana and other taxa of the supertribe Hesperodae represent an early-diverging lineage in the evolutionary history of the Brassicaceae. Through a comparative analysis, we revisited the ancestral Hesperodae karyotype (AHK, n = 7) and found several differences from the well-established ancestral crucifer karyotype (ACK, n = 8) model, including extensive inter- and intra-chromosomal rearrangements. Our results suggest that the primary reason for genome obesity in M. incana is the massive expansion of long terminal repeat retrotransposons (LTR-RTs), particularly from the Angela, Athila and Retand families. CHG methylation modification is obviously reduced in the regions where the highest density of Copia-type LTR-RTs and the lowest density of Gypsy-type LTR-RTs overlap, corresponding to the putative centromeres. Based on insertion times and methylation profiling, recently inserted LTR-RTs were found to have a significantly different methylation pattern compared to older ones.
Details
- Title
- Largest genome assembly in Brassicaceae: retrotransposon-driven genome expansion and karyotype evolution in Matthiola incana
- Creators
- Daozong Chen - Gannan Normal UniversityTaihua Yang - Huazhong Agricultural UniversityHaidong Chen - Gannan Normal UniversityXiaohan Zhang - Huazhong Agricultural UniversityFan Huang - Huazhong Agricultural UniversityShubei Wan - Gannan Normal UniversityZhanjun Lu - Gannan Normal UniversityChao Liu - Huazhong Agricultural UniversityYong Lei - Oil Crops Research InstituteHuifang Jiang - Oil Crops Research InstituteBoshou Liao - Oil Crops Research InstituteGraham J King - Recombics, Alstonville, 2477, New South Wales, AustraliaMartin A Lysak - Central European Institute of TechnologyChen Tan - Gannan Normal UniversityXianhong Ge - Huazhong Agricultural University
- Publication Details
- Plant biotechnology journal, Vol.First online, pp.1-17
- Publisher
- Wiley
- Grant note
- 25-16142S / Czech Science Foundation 20212BAB215002 / Natural Science Foundation of Jiangxi Province The project TowArds Next GENeration Crops (CZ.02.01.01/00/22_008/0004581) of the ERDF Programme Johannes Amos Comenius 2021YFD1600500 / National Key Research and Development Program of China 2022021302024851 / Wuhan Science and Technology Major Project on Key techniques of biological breeding and Breeding of new varieties 32160454;32260469 / National Natural Science Foundation of China
- Identifiers
- 991013293755602368
- Copyright
- © 2025 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
- Academic Unit
- Office of the Vice Chancellor; Faculty of Science and Engineering; Science
- Language
- English
- Resource Type
- Journal article