Thinking about recording the journey of paper reading, I find it might be fun to write down some *stupid thoughts* and *immature opinions* in a serial that I call ‘WhatToReadTody’. This may sound like a paper review/recommandation, but it is not, at least not at present, although I hope it could be in future (and I will continue writing).
- /Charing the genomic landscape of seed-free plants/ Nature Plants, 2021. The paper reviews several current available seed-free plant genomes, but provides few insights with respect to Bioinformatics or Genome Evolution. I just quickly browsed a few sections and figures though. A few points that in my mind:
- Seed-free plants do not have many WGDs. At first, it was thought due to the presence of mature sex chromosomes, but later the genome of a moss (Ceratodon purpureus) with ancient sex chromosome system also shows evidence of ancient WGD. Many animal genomes already provide evidence against this hypothesis and polyploidizations might not be too rare in animals.
- There are still some collinearity between seed-free plants and seed plants.
- /New prospects in the detection and comparative analysis of hybridisation in the tree of life/ American Journal of Botany, 2014. Basically, I only checked Figure 1 and integrating gene order (collinearity) and gene trees may hint hybridisation histories of different species. I thought this was first shown in mammals (if not mouses?), which I read in the book /Tree thinking/.
- /The effects of Arabidopsis genome duplication on chromatin organisation and transcriptional regulation/ Nucleic Acids Research, 2018. This study generated Hi-C data and ChIP-Seq data for diploid and novel tetraploid Arabidopsis (col0). They found more inter-chromosome interactions in tetraploids and differences of histon methylations between diploids and tetraploids. Differential expressed genes were analysed without spike-ins, although it is still difficult to tell if the spike-in system is required (theoretically yes, I think).
- /Altered chromatin architecture and gene expression during polyploidization and domestication of soybean/ The Plant Cell, 2021. I came across this paper by checking papers cited the previous one. HiC and various eipgenomic data for soybean, wild soybean and common beans are produced in this study. Genes retained after the latest WGD in the soybean genome have long-range chromosome interactions, higher gene expression, higher chromatin accessibility, but lower DNA methylation. It might be interesting to further classified WGD retained genes to figure out if chromatin architecture is correlated with duplicate fates.