Comparative Chloroplast Genomics of Endangered Euphorbia Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny

Abstract

Euphorbia is one of the largest genera in the Euphorbiaceae family, comprising 2000 species possessing commercial, medicinal, and ornamental importance. However, there are very little data available on their molecular phylogeny and genomics, and uncertainties still exist at a taxonomic level. Herein, we sequence the complete chloroplast (cp) genomes of two species, E. larica and E. smithii, of the genus Euphorbia through next-generation sequencing and perform a comparative analysis with nine related genomes in the family. The results revealed that the cp genomes had similar quadripartite structure, gene content, and genome organization with previously reported genomes from the same family. The size of cp genomes ranged from 162,172 to 162,358 bp with 132 and 133 genes, 8 rRNAs, 39 tRNA in E. smithii and E. larica, respectively. The numbers of protein-coding genes were 85 and 86, with each containing 19 introns. The four-junction regions were studied and results reveal that rps19 was present at JLB (large single copy region and inverted repeat b junction) in E. larica where its complete presence was located in the IRb (inverted repeat b) region in E. smithii. The sequence comparison revealed that highly divergent regions in rpoC1, rpocB, ycf3, clpP, petD, ycf1, and ndhF of the cp genomes might provide better understanding of phylogenetic inferences in the Euphorbiaceae and order Malpighiales. Phylogenetic analyses of this study illustrate sister clades of E. smithii with E. tricullii and these species form a monophyletic clade with E. larica. The current study might help us to understand the genome architecture, genetic diversity among populations, and evolutionary depiction in the genera.

Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship

“…Repetitive sequences in plastid genomes play an essential role in population genetics and biogeography studies [51,52], and these repeats may result from slipped-strand mispairing and improper recombination [53]. In this study, short dispersed repeats (SDRs) analysis found 22 forward, 0 reverse, 0 complement and 20 palindromic repeats in the plastid genome of B. chinense ( Figure 4A), of which 32 were 30-40 bp in length, 7 were 41-50 bp in length, and 3 exceeded 70 bp in length ( Figure 4B).…”

The evolutionary fate of rpl32 and rps16 losses in the Euphorbia schimperi (Euphorbiaceae) plastome

“…Pseudogenization or loss of plastid genes is often accompanied by the transfer of the gene to the nuclear genome or substitution by a nuclear gene that is already targeted to the plastid 27,66 . Plastid gene loss and transfer to the nucleus or substitution by a dual targeted nuclear gene targeted to organelles has been recorded for several genes across multiple angiosperm lineages [4][5][6][7][8][9][10][11][12][13][14][15][16][17] . The focus of this study was to use transcriptome data to bioinformatically identify the fate of two plastid genes, rpl32 and rps16, in Euphorbia schimperi that have either been lost or pseudogenized.…”

“…Most angiosperm plastomes have a highly conserved gene content ranging between 120-130 genes out of the approximately 1000 to 8000 genes that were present in the cyanobacterial ancestor 3 . There are some exceptions in various lineages including losses/transfers of infA in most rosids 4,5 , rpl33 in some legume lineages 6,7 , rpl32 in Salicaceae 8,9,10,11 , Rhizophoraceae 10 , Ranunculaceae 12 , Passi oraceae 13,14 and Euphorbiaceae 15,16,17 , rps16 in various legumes 6,18,19,20,21 , Salicaceae 8,9,22 , Passi oraceae 14 and Euphorbiaceae [15][16][17]23,24,25 , rpl22 in Fabaceae, Fagaceae, Passi oraceae, and Salicaceae 13,14,26,27 and rpl20 in Passi oraceae 14 .…”

“…rpl32 and rps16 have been characterized as being lost in plastomes and either transferred to the nucleus or substituted by a nuclear-encoded mitochondrially-targeted gene in three families of Malpighiales, Rhizophoraceae, Salicaceae and Passi oraceae 10,11,14,22 . The fate of these two missing genes in other families of Malpighiales (Bonnetiaceae , Hypericaceae, Clusiaceae, Podostemaceae, Euphorbiaceae, Malpighiaceae, Chrysobalanaceae, Irvingiaceae, Pyllanthaceae, Erythoxylaceae, Linaceae and Violaceae) has not been characterized [15][16][17][23][24][25]40,41,42,43,44,45,46 . Thus, little is known about the extent of the transfer/substitution of these genes in other families of Malpighiales.…”

“…Only 21 species of Euphorbiaceae have complete plastome sequences available in NCBI (accessed on December 13, 2020) with eleven published and most of these are economically important and have some medicinal activities due to the presence of isoprenoids [15][16][17][23][24][25]46,57,58,59,60,61,62,63,64 . Using next generation sequencing technologies and de novo assembly, the plastome and nuclear transcriptome of Euphorbia schimperi was sequenced.…”