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Assembly of Satsuma mandarin mitochondrial genome and identification of cytoplasmic male sterility–specific ORFs in a somatic cybrid of pummelo

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Abstract

Cytoplasmic male sterility (CMS) and seedlessness are highly desirable traits for citrus. However, a high-quality reference mitochondrial genome of citrus is unavailable, and the mechanisms of CMS remain to be elucidated in citrus. We previously generated a male sterile somatic cybrid of pummelo (G1+HBP) by fusing protoplasts from CMS ‘Guoqing No. 1’ Satsuma mandarin (G1) and fertile ‘Hirado Buntan’ pummelo (HBP). Here, we sequenced and assembled the mitochondrial genome of G1, G1+HBP, and HBP into circular molecules of 521.6 kb, 538.4 kb, and 518.3 kb, respectively. Mitochondrial genome of citrus encodes 35–36 proteins, three ribosomal RNAs, and 21 tRNAs. Comparative analysis indicated that nuclear genome and chloroplast genome of the cybrid are from HBP, whereas the mitochondrial genome sequences of the cybrid and G1 have 96.9% synteny, and that the cybrid has an extra recombinant mitochondrial DNA fragment of only 16.8 kb. Compared with the fertile HBP mitochondrial genome, 21 and 20 CMS-specific mitotype-specific sequences (MSSs), and 89 and 70 CMS-specific ORFs were identified in the cybrid and G1 mitochondrial genomes, respectively. Among them, 57 ORFs that co-transcribed with the same mitochondrial genes in the cybrid and G1 were identified as the CMS-specific ORFs. The assembly of mitochondrial genomes and the identification of the CMS-specific ORFs provide basis for determination of the CMS-associated gene and elucidation of CMS mechanisms in citrus.

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Acknowledgments

The authors thank Drs. Yi-Fei Liu and Shuai-Bin Wang from the South China Botanical Garden (CAS), Dr. An-Dan Zhu from the Kunming Institute of Botany, Chinese Academy of Sciences for bioinformatic support, and our colleague Prof. Robert M. Larkin for critical reading of the manuscript.

Data Archiving Statement

The assembled mitochondrial genome sequences can be retrieved from NCBI GenBank using accession numbers It2304200, It2304217, and It2304225. The raw data of Illumina and PacBio Sequel-based sequencing of mitochondrial DNA, total DNA, and lncRNA can be retrieved from the NCBI SRA database using accession numbers SRR10821402 to SRR10821405 (G1), SRR10828042 to SRR10828045 (HBP), and SRR10841900 to SRR10841903 (G1+HBP).

Funding

This research was financially supported by the Ministry of Science and Technology of China (no. 2018YFD1000106), the National Natural Science Foundation of China (nos. 31530065, 31820103011), and the Fundamental Research Funds for Central Universities (nos. 2662018PY007).

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  1. Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China

    Shuai Zhang, Zhao-Ping Yin, Xiao-Meng Wu, Chao-Chao Li, Kai-Dong Xie, Xiu-Xin Deng & Wen-Wu Guo

  2. Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA

    Jude W. Grosser

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  1. Shuai Zhang
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Zhang, S., Yin, ZP., Wu, XM. et al. Assembly of Satsuma mandarin mitochondrial genome and identification of cytoplasmic male sterility–specific ORFs in a somatic cybrid of pummelo. Tree Genetics & Genomes 16, 84 (2020). https://doi.org/10.1007/s11295-020-01480-w

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