The garden asparagus (Asparagus officinalis L.) mitochondrial genome revealed rich sequence variation throughout whole sequencing data

Abstract

Garden asparagus (Asparagus officinalis L.) is a horticultural crop with high nutritional and medical value, considered an ideal plant for sex determination research among many dioecious plants, whose genomic information can support genetic analysis and breeding programs. In this research, the entire mitochondrial genome of A. officinalis was sequenced, annotated and assembled using a mixed Illumina and PacBio data. The garden asparagus circular mitochondrial genome measures 492,062 bp with a GC value of 45.9%. Thirty-six protein-coding genes, 17 tRNA and 6 rRNA genes were annotated, among which 8 protein-coding genes contained 16 introns. In addition, 254 SSRs with 10 complete tandem repeats and 293 non-tandem repeats were identified. It was found that the codons of edited sites located in the amino acids showed a leucine-formation trend, and RNA editing sites mainly caused the mutual transformation of amino acids with the same properties. Furthermore, 72 sequence fragments accounting for 20,240 bp, presentating 4.11% of the whole mitochondrial genome, were observed to migrate from chloroplast to mitochondrial genome of A. officinalis. The phylogenetic analysis showed that the closest genetic relationship between A. officinalis with onion (Allium cepa) inside the Liliaceae family. Our results demonstrated that high percentage of protein-coding genes had evolutionary conservative properties, with Ka/Ks values less than 1. Therefore, this study provides a high-quality garden asparagus mitochondrial genome, useful to promote better understanding of gene exchange between organelle genomes.

Multichromosomal Mitochondrial Genome of Punica granatum: Comparative Evolutionary Analysis and Gene Transformation from chloroplast genomes

“…These repetitive sequences play a crucial role in the assembly of the P. granatum mitogenome [45]. There were a total of 141 SSRs were detected and mononucleotide repeats of A/T were the most frequent, which was consistent with other research ndings [11,25,[46][47]. It provided a large number of reference markers for the evaluation of pomegranate germplasm diversity and species identi cation.…”

Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance

“…With the rapid development of sequencing and assembly technologies in recent years, the number of high-quality organellar genome assemblies has rapidly increased. Currently, 10,123 cpDNA and 585 mtDNA sequences have been obtained from plants [ 34 ]. The structure and genetic composition of cpDNA are highly conserved.…”

Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes

“…These repetitive sequences play a crucial role in the assembly of the P. granatum mitogenome [ 47 ]. Simple sequence repeats are a special kind of presence among tandem repeats, which can better reflect species’ genetic structure and genetic diversity changes [ 48 , 49 ]. There was a total of 141 SSRs were detected and mononucleotide repeats of A/T were the most frequent, which was consistent with other research findings in Momordica charantia [ 11 ] and Calla Lilies [ 28 ].…”