Comparative chloroplast genome analysis of seven extant Citrullus species insight into genetic variation, phylogenetic relationships, and selective pressure

Abstract

Citrullus ecirrhosus, Citrullus rehmii, and Citrullus naudinianus are three important related wild species of watermelon in the genus Citrullus, and their morphological differences are clear, however, their chloroplast genome differences remain unknown. This study is the first to assemble, analyze, and publish the complete chloroplast genomes of C. ecirrhosus, C. rehmii, and C. naudinianus. A comparative analysis was then conducted among the complete chloroplast genomes of seven extant Citrullus species, and the results demonstrated that the average genome sizes of Citrullus is 157,005 bp, a total of 130–133 annotated genes were identified, including 8 rRNA, 37 tRNA and 85–88 protein-encoding genes. Their gene content, order, and genome structure were similar. However, noncoding regions were more divergent than coding regions, and rps16-trnQ was a hypervariable fragment. Thirty-four polymorphic SSRs, 1,271 SNPs and 234 INDELs were identified. Phylogenetic trees revealed a clear phylogenetic relationship of Citrullus species, and the developed molecular markers (SNPs and rps16-trnQ) could be used for taxonomy in Citrullus. Three genes (atpB, clpP1, and rpoC2) were identified to undergo selection and would promote the environmental adaptation of Citrullus.

Effect of Algae on Melon (Cucumis melo subsp. agrestis var. conomon) Growth and Development under Drought-Stress Conditions

“…According to Lakshmi et al [58], the use of algae-based biofertilizers and bio-stimulants offers several benefits, including increased plant growth, productivity, and tolerance to various abiotic stresses. Because algae (Chlorella TLD6B) grow rapidly and increase adaptability under abiotic stress (extreme desert environment) conditions [23]. According to previous reports, algae affect the internal responses of plants, and there are strong relationships between proline and algae, which promotes the biochemical and enzymatic responses of plants with positive effects against abiotic stress conditions [59].…”

“…However, subsequent molecular phylogenetic studies, based on DNA sequences from chloroplast genes (rbcL, matK, rpl20-rps12, trnL, and trnL-F), nuclear ITS, and plastid trnS-trnG regions, indicated that species from closely related genera such as Cucumella, Dicaelospermum, Mukia, Myrmecosicyos, and Oreosyce should be incorporated into the Cucumis genus [21]. Furthermore, an extensive phylogenetic study was conducted on Cucumis, examining the diversity of both nuclear and chloroplastic DNA [22,23]. Therefore, the objective of this study was to identify the most drought-tolerant wild melon genotypes by assessing their development, yield, and molecular parameters under drought-stress conditions.…”

Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution

“…Consistent with previous studies (Azarin et al, 2021;Zhao et al, 2022;Li et al, 2023), Leucine (Leu) was the most frequent amino acid, and cysteine (Cys) was the least common. In Linderniaceae, codons mainly ended with A and U when the RSCU value was greater than 1, and codons primarily ended with G and C when the RSCU value was below 1, which appears to be a common phenomenon in gene expression of land plants (Cui et al, 2019;Chakraborty et al, 2020;Gao et al, 2022;Bai et al, 2023;Zhou et al, 2023). Moreover, the GC content of synonymous third codons positions (GC3s) showed that AT content was more abundant in the protein-coding genes (Supplementary Table 5), which may be correlated with the abundant AT content of plastid genomes.…”