Largest genome assembly in Brassicaceae: retrotransposon-driven genome expansion and karyotype evolution in Matthiola incana
文献类型： 外文期刊
作者： Chen, Daozong 1 ; Yang, Taihua 2 ; Chen, Haidong 1 ; Zhang, Xiaohan 2 ; Huang, Fan 2 ; Wan, Shubei 1 ; Lu, Zhanjun 1 ; Liu, Chao 2 ; Lei, Yong 3 ; Jiang, Huifang 3 ; Liao, Boshou 3 ; King, Graham J. 4 ; Lysak, Martin A. 5 ; Tan, Chen 1 ; Ge, Xianhong 2 ;
作者机构： 1.Gannan Normal Univ, Coll Life Sci, Ganzhou Key Lab Greenhouse Vegetable, Ganzhou, Peoples R China
2.Huazhong Agr Univ, Natl Res Ctr Rapeseed Engn & Technol, Natl Key Lab Crop Genet Improvement, Wuhan, Peoples R China
3.Chinese Acad Agr Sci OCRI CAAS, Minist Agr & Rural Afairs, Key Lab Biol & Genet Improvement Oil Crops, Oil Crops Res Inst, Wuhan, Peoples R China
4.Recombics, Alstonville, NSW 2477, Australia
5.Masaryk Univ, Cent European Inst Technol CEITEC, Fac Sci, Brno, Czech Republic
6.Masaryk Univ, Fac Sci, Dept Expt Bot, Brno, Czech Republic
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
页码：
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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