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Whole-genome sequencing and assembly reveals crucial genomic adaptations to the environment during plant evolutionary paths

Understanding the phenomenon of adaptation is crucial for deepening the knowledge in a variety of disciplines. For example, clinical data on pathogens (such as antibiotic resistance) or improvement of agricultural species through the addition of genes that improve resistance to pathogens and environmental stresses.

Case study 1: Wild legume species help finding the genes responsible for adaptation to drought.

The research on crucial agricultural species is particularly important nowadays. With the increased risks of new pathogens such as fungus and the need to increase the nutritional value of crops, scientists refer to genomic data of the relevant wild species, that developed resistance to many unfavorable conditions. Wang et al focused their research on Medicago ruthenica, which is one of the legume species, however, it grows on infertile soils and survives low temperatures and droughts. It is a close relative of one of the most crucial legume crop alfalfa. Several Novogene researchers authored this study, assisting in sequencing and data analysis. The authors used to root and leaf samples of M. ruthenica for transcriptome libraries construction. The used enriched mRNA from root samples was used to make RNA-seq libraries, which were sequenced using the Illumina HiSeq PE150 platform [1]. The leaf samples were used for resequencing. The genomic DNA was isolated, Illumina library was constructed and sequenced [1]. After the data clean-up to obtain high-quality results only, the sequencing data had been processed including protein sequence alignment, building protein association networks, and specific gene functionality identification. In general, the authors combined several sequencing approaches, including Illumina, PacBio, 10xGenomics, and Hi-C [1]. The final constructed high-quality reference genome included detailed information on transcription factors, gene families, SNP variations, etc. The authors identified FHY3/FAR1 family as well as many other individual genes to be responsible for drought resistance.

Case study 2: The adaptations of wheat genome to domestication process.

A similar study was done on the wheat species genome, however, the authors looked at how the adaptation of crops throughout the process of domestication affected the genome. The genera Triticum and Aegilopis, which comprise the genetic donors of bread wheat, became the object of study of Zhou et al [2]. The challenge that bread wheat is facing currently is the detrimental effects of climate change. To prevent the deterioration of one of the most important crops in the world, the authors studied wheat adaptation, using novel sequencing methods. The study included 414 wheat accessions from 71 countries [2]. The accessions were sequenced on either a HiSeq 2500 or NovaSeq 6000 Illumina platform [2]. There were two sequencing depths: the average of 10x and the average of 3.8x, and the used pair-end reads were 150-base-pair ones. The sequencing data were processed to obtain only high-quality reads. To identify the genetic adaptations, the authors performed phylogenetic analysis, enrichment of genes, identification of wheat orthologs to rice, maize, and barley. The study showed the dramatic introgression in the wheat genome. The genetic diversity of wheat is low, and increasing it is fundamental for wheat expansion. Additionally, the study showed the convergent adaptation of wheat to breeding selection. The enriched genes are responsible for metabolic processes, cell wall function, and environmental stresses.

Case study 3: Discovering the evolution of seed plants and adaptation to the environment using the data from the very first sequencing and reconstruction of gnetophyte genome.

Modern sequencing methods also enable us to look with mode detail into the evolution. One example is the study of gnetophytes to elucidate the evolution of seed plants. Gnetophytes have an unclear phylogenetic position in plant evolution due to possessing special traits such as similarity to angiosperms. Probably, the gnetophytes can be related to conifers or seed plants, and the authors study the latter. During the evolution, the early seed plants had to undergo several adaptations to the environment, and the genomic data reflect sit. The authors assembled >4Gb of the sequence, including over 27,000 protein-coding genes. The authors sequenced the genomes of Gnetum montanum, Welwitschia mirabilis, and Ephedra squisetina. After the DNA extraction, the libraries containing paired-end libraries with short inserts were prepared and mate-paired libraries were constructed by Cre-Lox recombination. The sequencing was performed on the Illumina HiSeq 2000 and Illumina HiSeq 2500 systems. The RNA-sequencing was also done with libraries constructed using the NEB Next Ultra RNA Library Prep Kit and sequenced using Illumina 2000 platform. The authors used the SOAPdenovo assembly approach with the following assembly quality assessment. The genome was annotated, checked for pseudogenes, and phylogenetic reconstruction. The authors found that the Gnetum montanum genome has remarkable differences as compared to other gymnosperms. There are some evident genetic adaptations to warm environments. Specific functional protein domains and genes, responsible for adaptive morphologic changes were identified. All genome sequencing, assembly, and annotation were done by Novogene.

These studies highlight the usage of novel sequencing and genome reconstruction method in resolving issues related to agriculture. The vast bioinformatics methods allow scientists to look at specific gene functionalities on adaptation to the environment. The data of the mentioned case studied can be used to improve the tolerance of crops to various environmental stresses, strengthening their physiological responses to pathogens and climate change.

  1. Wang T, Ren L, Li C, et al. The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress [J]. BMC Biol, 2021. doi: 10.1186/s12915-021-01033-0
  2. Zhou Y, Zhao X, Li Y, et al. Triticum population sequencing provides insights into wheat adaptation [J]. Nature Genetics, 2020. doi: 10.1038/s41588-020-00722-w
  3. Wan T, Liu Z, Li L, et al. A genome for gnetophytes and early evolution of seed plants [J]. Nature Plants, 2018. doi: 10.1038/s41477-017-0097-2