Reference-based assembly of chloroplast genome from leaf transcriptome data of Pterocarpus santalinus

Transcriptome-wide analysis of the differences between MCF7 cells cultured in DMEM or αMEM

MCF7 cells have been used as an experimental model for breast cancer for decades. Typically, a culture medium is designed to supply cells with the nutrients essential for their continuous proliferation. Each medium has a specific nutritional composition. Therefore, cells cultured in different media may exhibit differences in their metabolism. However, only a few studies have investigated the effects of media on cells. In this study, we compared the effects of Dulbecco's modified Eagle medium (DMEM) and minimum essential medium alpha modification (αMEM) on MCF7 cells. The two media differentially affected the morphology, cell cycle, and proliferation of MCF7 cells, but had no effect on cell death. Replacement of DMEM with αMEM led to a decrease in ATP production and an increase in reactive oxygen species production, but did not affect the cell viability. RNA-sequencing and bioinformatic analyses revealed 721 significantly upregulated and 1247 downregulated genes in cells cultured in αMEM for 48 h compared with that in cells cultured in DMEM. The enriched gene ontology terms were related to mitosis and cell proliferation. Kyoto encyclopedia of genes and genomes analysis revealed cell cycle and DNA replication as the top two significant pathways. MCF7 cells were hypoxic when cultured in αMEM. These results show that the culture medium considerably affects cultured cells. Thus, the stability of the culture system in a study is very important to obtain reliable results.

The draft genome reveals early duplication event in Pterocarpus santalinus: an endemic timber species

MAIN CONCLUSION

A 541 Mb draft genome of Pterocarpus santalinus is presented and evidence of whole-genome duplication in the Eocene period with expansion of drought responsive gene families is documented. Pterocarpus santalinus Linn. f., popularly known as Red Sanders, is a deciduous tree, endemic to southern parts of Eastern Ghats in India. The heartwood is highly valued in the international market due to its deep red colour, fragrant heartwood and wavy grained texture. In the present study, a high-quality draft genome of P. santalinus was assembled using short and long reads generated from Illumina and Oxford Nanopore Sequencing platforms, respectively. The haploid genome size was estimated at 541 Mb and the hybrid assembly showed 99.60% genome completeness. A total of 51,713 consensus gene set were predicted with 31,437 annotated genes. The age of the whole-genome duplication event in the species was dated at 30-39 mya with 95% confidence suggesting early genome duplication event during the Eocene period. Concurrently, phylogenomic assessment of seven Papilionoideae members including P. santalinus grouped the species based on the tribal classification and established divergence of the tribe Dalbergieae from tribe Trifolieae at ~ 54.20 mya. A significant expansion of water deprivation/drought responsive gene families documented in the study probably explains the occurrence of the species in dry rocky patches. Additionally, re-sequencing of six diverse genotypes predicted one variant every 27 bases. This report presents the first draft genome in the genus Pterocarpus and the unprecedented genomic information generated is expected to accelerate population divergence studies in the species in relation to its endemic nature, support trait-based breeding programme and aid in development of diagnostic tools for timber forensics.

Genetic Relationship and Evolution Analysis among Malus Mill Plant Populations Based on SCoT Molecular Markers

Malus Mill genotype is highly heterozygous, and many theoretical problems such as genetic relationship and evolution process among germplasm are difficult to be solved by traditional analysis methods. The development of SCoT(start codon targeted polymorphism) molecular markers suitable for apples is of great significance for studying the origin, evolution, genetic relationship and genetic diversity of Malus Mill germplasm resources. In this paper, the genetic relationship and evolution of 15 materials were analyzed by SCoT molecular marker. The results showed that the gene differentiation coefficient values of four Malus Mill plants at the species level were 0.423, 0.439, 0.428 and 0.460, respectively, which indicated that there was obvious genetic differentiation among the populations of these four Malus Mill plants, but there were some differences among the populations of different Malus Mill plants. The gene differentiation coefficient of coextensive populations with different geographical distribution varied from 0.177 to 0.086 (average 0.138), which indicated that the genetic similarity of species in coextensive composite populations was high and there was a close genetic relationship among species. This indicates that SCoT molecular markers can be effectively used in the analysis of intraspecific genetic relationship and identification of intraspecific strains of Malus Mill plants.