Largest genome assembly in Brassicaceae: retrotransposon-driven genome expansion and karyotype evolution in Matthiola incana

文献类型： 外文期刊

第一作者： Chen, Daozong

作者： Chen, Daozong;Chen, Haidong;Wan, Shubei;Lu, Zhanjun;Tan, Chen;Yang, Taihua;Zhang, Xiaohan;Huang, Fan;Liu, Chao;Ge, Xianhong;Yang, Taihua;Lei, Yong;Jiang, Huifang;Liao, Boshou;King, Graham J.;Lysak, Martin A.;Lysak, Martin A.

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关键词： genome assembly; genome obesity; Lineage III; Hesperodae; Cruciferae; retrotransposons

期刊名称：PLANT BIOTECHNOLOGY JOURNAL （ 影响因子：10.5； 五年影响因子：12.4 ）

ISSN： 1467-7644

年卷期： 2025 年 23 卷 9 期

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收录情况： SCI

摘要： 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 (similar to 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.

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