Expansion and improvement of ChinaMu by MuT-seq and chromosome-level assembly of the Mu-starter genome

文献类型： 外文期刊

第一作者： Liang, Lei

作者： Liang, Lei;Han, Yanbin;Chen, Yicong;Li, Mengfei;Ma, Zeyang;Song, Rentao;Wang, Yuancong;Wu, Yibo;Zhao, Han;Ma, Zeyang;Song, Rentao;Ma, Zeyang;Song, Rentao

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关键词： ChinaMu; Mutator; MuT-seq; PPR gene; Zea mays

期刊名称：JOURNAL OF INTEGRATIVE PLANT BIOLOGY （ 影响因子：11.4； 五年影响因子：10.1 ）

ISSN： 1672-9072

年卷期： 2024 年 66 卷 4 期

页码：

收录情况： SCI

摘要： ChinaMu is the largest sequence-indexed Mutator (Mu) transposon insertional library in maize (Zea mays). In this study, we made significant improvements to the size and quality of the ChinaMu library. We developed a new Mu-tag isolation method Mu-Tn5-seq (MuT-seq). Compared to the previous method used by ChinaMu, MuT-seq recovered 1/3 more germinal insertions, while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental time. Using MuT-seq, we identified 113,879 germinal insertions from 3,168 Mu-active F1 families. We also assembled a high-quality genome for the Mu-active line Mu-starter, which harbors the initial active MuDR element and was used as the pollen donor for the mutation population. Using the Mu-starter genome, we recovered 33,662 (15.6%) additional germinal insertions in 3,244 (7.4%) genes in the Mu-starter line. The Mu-starter genome also improved the assignment of 117,689 (54.5%) germinal insertions. The newly upgraded ChinaMu dataset currently contains 215,889 high-quality germinal insertions. These insertions cover 32,224 pan-genes in the Mu-starter and B73Ref5 genomes, including 23,006 (80.4%) core genes shared by the two genomes. As a test model, we investigated Mu insertions in the pentatricopeptide repeat (PPR) superfamily, discovering insertions for 92% (449/487) of PPR genes in ChinaMu, demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.

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