干旱区生态环境知识资源中心(Arid): Assembly and comparative analysis of the first complete mitochondrial genome of Setaria italica

Arid

DOI	10.1007/s00425-024-04386-2
	Assembly and comparative analysis of the first complete mitochondrial genome of Setaria italica
	Zhang, Jiewei; Liu, Guiming; Wei, Jianhua
通讯作者	Zhang, JW ; Liu, GM ; Wei, JH
来源期刊	PLANTA
ISSN	0032-0935
EISSN	1432-2048
出版年	2024
卷号	260 期号:1
英文摘要	The foxtail millet (Setaria italica) holds significant agricultural importance, particularly in arid and semi-arid regions. It plays a pivotal role in diversifying dietary patterns and shaping planting strategies. Although the chloroplast genome of S. italica has been elucidated in recent studies, the complete mitochondrial genome remains largely unexplored. In this study, we employed PacBio HiFi sequencing platforms to sequence and assemble the complete mitochondrial genome. The mitochondrial genome spans a total length of 446,614 base pairs and harbors a comprehensive set of genetic elements, including 33 unique protein-coding genes (PCGs), encompassing 24 unique mitochondrial core genes and 9 variable genes, along with 20 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. Our analysis of mitochondrial PCGs revealed a pronounced codon usage preference. For instance, the termination codon exhibits a marked preference for UAA, while alanine (Ala) exhibits a preference for GCU, and glutamine (Gln) favors CAA. Notably, the maximum Relative Synonymous Codon Usage (RSCU) values for cysteine (Cys) and phenylalanine (Phe) are both below 1.2, indicating a lack of strong codon usage preference for these amino acids. Phylogenetic analyses consistently place S. italica in close evolutionary proximity to Chrysopogon zizanioides, relative to other Panicoideae plants. Collinearity analysis showed that a total of 39 fragments were identified to display homology with both the mitochondrial and chloroplast genomes. A total of 417 potential RNA-editing sites were discovered across the 33 mitochondrial PCGs. Notably, all these editing events involved the conversion of cytosine (C) to uracil (U). Through the employment of PCR validation coupled with Sanger sequencing for the anticipated editing sites of these codons, RNA-editing events were conclusively identified at two specific loci: nad4L-2 and atp6-1030. The results of this study provide a pivotal foundation for advanced genomic breeding research in foxtail millet. Furthermore, they impart essential insights that will be instrumental for forthcoming investigations into the evolutionary and molecular dynamics of Panicoideae species.
英文关键词	Comparative genomics Foxtail millet Mitochondrial genome Phylogeny Setaria italica
类型	Article
语种	英语
收录类别	SCI-E
WOS记录号	WOS:001244501900001
WOS关键词	HORIZONTAL TRANSFER ; DNA ; CHLOROPLAST ; SEQUENCE ; GENES ; RECOMBINATION ; REPLICATION ; EVOLUTION ; ALIGNMENT ; CONTAINS
WOS类目	Plant Sciences
WOS研究方向	Plant Sciences
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/405123
推荐引用方式 GB/T 7714	Zhang, Jiewei,Liu, Guiming,Wei, Jianhua. Assembly and comparative analysis of the first complete mitochondrial genome of Setaria italica[J],2024,260(1).
APA	Zhang, Jiewei,Liu, Guiming,&Wei, Jianhua.(2024).Assembly and comparative analysis of the first complete mitochondrial genome of Setaria italica.PLANTA,260(1).
MLA	Zhang, Jiewei,et al."Assembly and comparative analysis of the first complete mitochondrial genome of Setaria italica".PLANTA 260.1(2024).