Complete chloroplast genome of the medicinal plant Evolvulus alsinoides: comparative analysis, identification of mutational hotspots and evolutionary dynamics with species of Solanales.

Evolvulus alsinoides, belonging to the family Convolvulaceae, is an important medicinal plant widely used as a nootropic in the Indian traditional medicine system. In the genus Evolvulus, no research on the chloroplast genome has been published. Hence, the present study focuses on annotation, characterization, identification of mutational hotspots, and phylogenetic analysis in the complete chloroplast genome (cp) of E. alsinoides. Genome comparison and evolutionary dynamics were performed with the species of Solanales. The cp genome has 114 genes (80 protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes) that were unique with total genome size of 157,015 bp. The cp genome possesses 69 RNA editing sites and 44 simple sequence repeats (SSRs). Predicted SSRs were randomly selected and validated experimentally. Six divergent hotspots such as trnQ-UUG, trnF-GAA, psaI, clpP, ndhF, and ycf1 were discovered from the cp genome. These microsatellites and divergent hot spot sequences of the Taxa 'Evolvulus' could be employed as molecular markers for species identification and genetic divergence investigations. The LSC area was found to be more conserved than the SSC and IR region in genome comparison. The IR contraction and expansion studies show that nine genes rpl2, rpl23, ycf1, ycf2, ycf1, ndhF, ndhA, matK, and psbK were present in the IR-LSC and IR-SSC boundaries of the cp genome. Fifty-four protein-coding genes in the cp genome were under negative selection pressure, indicating that they were well conserved and were undergoing purifying selection. The phylogenetic analysis reveals that E. alsinoides is closely related to the genus Cressa with some divergence from the genus Ipomoea. This is the first time the chloroplast genome of the genus Evolvulus has been published. The findings of the present study and chloroplast genome data could be a valuable resource for future studies in population genetics, genetic diversity, and evolutionary relationship of the family Convolvulaceae. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01051-w.

Draft Genome Sequence of the Oomycete Globisporangium splendens Strain rgcb-1.

Globisporangium splendens (formerly Pythium splendens) is an oomycete pathogen of many economically important vegetable crops. Here, we present the first draft genome of P. splendens, which comprises 197 scaffolds with a total length of 53.3 Mb and 17,350 predicted protein-coding genes.

High Quality Draft Genome of Arogyapacha (Trichopus zeylanicus), an Important Medicinal Plant Endemic to Western Ghats of India.

Arogyapacha, the local name of Trichopus zeylanicus, is a rare, indigenous medicinal plant of India. This plant is famous for its traditional use as an instant energy stimulant. So far, no genomic resource is available for this important plant and hence its metabolic pathways are poorly understood. Here, we report on a high-quality draft assembly of approximately 713.4 Mb genome of T. zeylanicus, first draft genome from the genus Trichopus The assembly was generated in a hybrid approach using Illumina short-reads and Pacbio longer-reads. The total assembly comprised of 22601 scaffolds with an N50 value of 433.3 Kb. We predicted 34452 protein coding genes in T. zeylanicus genome and found that a significant portion of these predicted genes were associated with various secondary metabolite biosynthetic pathways. Comparative genome analysis revealed extensive gene collinearity between T. zeylanicus and its closely related plant species. The present genome and annotation data provide an essential resource to speed-up the research on secondary metabolism, breeding and molecular evolution of T. zeylanicus.

The Complete Chloroplast Genome of Trichopus zeylanicus, And Phylogenetic Analysis with Dioscoreales.

CORE IDEAS: We presents the first chloroplast genome from the genus Trichopus. Comparative analysis revealed that the IR regions are more conserved than the SC regions. Highly divergent sequence hot spots were identified, which could be used as molecular markers. Phylogenetic analysis gave insight into the evolutionary history of Trichopus zeylanicus. In this study, we determined the complete sequence of the chloroplast genome of an important, rare, and endangered medicinal plant, Trichopus zeylanicus. The analysis of the genome showed that the complete chloroplast genome of Trichopus zeylanicus is 153,497 bp in size, and has a quadripartite structure with a large single copy of 81,091 bp and a small single copy of 17,512 bp separated by inverted repeats of 27,447 bp. Sequence analysis revealed that the chloroplast genome encodes 112 unique genes, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. We also identified 95 simple sequence repeats and 54 long repeats including 34 forward repeats, seven inverted repeats, nine palindromes, three reverse repeats, and one complementary repeat within the chloroplast genome of Trichopus zeylanicus. Whole chloroplast genome comparison with those of other Dioscoreales indicated that the inverted regions are more conserved than large single copy and small single copy regions. In the phylogenetic trees based on complete chloroplast genome and 78 shared chloroplast protein-coding genes in 15 monocot species, including 14 Dioscoreales, Trichopus zeylanicus formed a distinct clade. In summary, the first chloroplast genome from the genus Trichopus reported in this study gave a better insight into the phylogenetic relationships of different genera within the order Dioscoreales. Moreover, the present data will be a valuable chloroplast genomic resource for population genetics.