Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae)

Abstract

The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp—typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16–24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.

The complete plastome sequences of invasive weed Parthenium hysterophorus: genome organization, evolutionary significance, structural features, and comparative analysis

“…The utilization of plastome genomes in phylogenetic studies and molecular evolutionary systematics has yielded immense value by offering a profound comprehension of intricate evolutionary connections within the realm of angiosperms. This avenue of research has provided researchers with a comprehensive understanding of the complex relationships that exist among various species of flowering plants 34 , 68 – 71 . Consequently, in this study, we utilized 72 shared protein-coding genes from 75 representatives of 11 genera to establish the phylogenetic position of P. hysterophorus within the tribe Heliantheae.…”

The complete chloroplast genome sequence of Zygophyllum brachypterum (Zygophyllaceae) reveals its distinctive characteristics and evolutionary implication

“…qatarensis OM809718 (Ahmad et al. 2023 ), Tetraena simplex NC_067950 (Ahmad et al. 2023 ), Guaiacum angustifolium NC_043796 (Gonçalves et al.…”

“… 2023 ), Tetraena simplex NC_067950 (Ahmad et al. 2023 ), Guaiacum angustifolium NC_043796 (Gonçalves et al. 2019b ), Larrea tridentata MK726018 (Gonçalves et al.…”