Genome Characterization, Comparison and Phylogenetic Analysis of Complete Mitochondrial Genome of Evolvulus alsinoides Reveals Highly Rearranged Gene Order in Solanales.

Pattayampadam Ramakrishnan Shidhi,Sasi Anu,Chandrasekharan Laila Vipin,Kumar Raveendran Deelip,Vadakkemukadiyil Chellappan Biju,Sukumaran Nair Achuthsankar

doi:10.3390/life11080769

Abstract

Mitogenome sequencing provides an understanding of the evolutionary mechanism of mitogenome formation, mechanisms driving plant gene order, genome structure, and migration sequences. Data on the mitochondrial genome for family Convolvulaceae members is lacking. E. alsinoides, also known as shankhpushpi, is an important medicinal plant under the family Convolvulaceae, widely used in the Ayurvedic system of medicine. We identified the mitogenome of E. alsinoides using the Illumina mate-pair sequencing platform, and annotated using bioinformatics approaches in the present study. The mitogenome of E. alsinoides was 344184 bp in length and comprised 46 unique coding genes, including 31 protein-coding genes (PCGs), 12 tRNA genes, and 3 rRNA genes. The secondary structure of tRNAs shows that all the tRNAs can be folded into canonical clover-leaf secondary structures, except three trnW, trnG, and trnC. Measurement of the skewness of the nucleotide composition showed that the AT and GC skew is positive, indicating higher A’s and G’s in the mitogenome of E. alsinoides. The Ka/Ks ratios of 11 protein-coding genes (atp1, ccmC, cob, cox1, rps19, rps12, nad3, nad9, atp9, rpl5, nad4L) were <1, indicating that these genes were under purifying selection. Synteny and gene order analysis were performed to identify homologous genes among the related species. Synteny blocks representing nine genes (nad9, nad2, ccmFc, nad1, nad4, nad5, matR, cox1, nad7) were observed in all the species of Solanales. Gene order comparison showed that a high level of gene rearrangement has occurred among all the species of Solanales. The mitogenome data obtained in the present study could be used as the Convolvulaceae family representative for future studies, as there is no complex taxonomic history associated with this plant.

Highlights

Plastid, mitochondrial, and nuclear genomes constitute the total genome of a plant cell
A total of 328,334,850 raw reads were generated after the sequencing, and 133,876,340 high-quality reads were obtained after quality trimming
After the gap-filling step, the E. alsinoides mitochondrial genome was assembled into a single, circular molecule with a length of 344,184 bp (Figure 1)

Summary

Introduction

Mitochondrial, and nuclear genomes constitute the total genome of a plant cell. Plant mitogenomes are remarkably different from animal mitogenomes [6] It shows a distinctive 200-fold size divergence, ranging from 66kb in V. scurruloideum to 11.3 Mb in S. conica, due to the expansion primarily from repeat sequence, intronic regions, and the incorporation of plastid and nuclear DNA through intracellular gene transfer (IGT) or foreign mtDNA via horizontal gene transfer (HGT) [7,8]. The accumulation of these repeat sequences in vascular plants causes active recombination and serves as a source of rearrangements, leading to the generation of alternative structure, even within a single individual [9]. In Arabidopsis thaliana and Nicotiana tabacum, two organellar DNA polymerases are dual-targeted to both mitochondria and plastids, termed Pol1A and Pol1B [12,13]

Objectives

Methods

Results

Conclusion