High-quality genome assembly and comparative genomic profiling of yellowhorn (Xanthoceras sorbifolia) revealed environmental adaptation footprints and seed oil contents variations

Wang, Juan; Hu, Haifei; Liang, Xin; Qamar, Muhammad Tahir ul; Zhang, Yunxiang; Zhao, Jianguo; Ren, Hongqian; Yan, Xingrong; Ding, Baopeng; Guo, Jing

doi:10.3389/fpls.2023.1147946

Cited by 5 publications

(1 citation statement)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In contrast, comparative genomics approaches allow the identification of genomic footprints of adaptation, 3 such as protein family expansions. 4 Gene duplication is a major driver of molecular evolution, 5 , 6 and in plants, whole-genome duplication events are frequent (reviewed in Ref. 7 ), but tandem and transposon-mediated duplications also play a role (reviewed in Ref.…”

Section: Introductionmentioning

confidence: 99%

A2TEA: Identifying trait-specific evolutionary adaptations

et al. 2023

View full text Add to dashboard Cite

Background: Plants differ in their ability to cope with external stresses (e.g., drought tolerance). Genome duplications are an important mechanism to enable plant adaptation. This leads to characteristic footprints in the genome, such as protein family expansion. We explore genetic diversity and uncover evolutionary adaptation to stresses by exploiting genome comparisons between stress tolerant and sensitive species and RNA-Seq data sets from stress experiments. Expanded gene families that are stress-responsive based on differential expression analysis could hint at species or clade-specific adaptation, making these gene families exciting candidates for follow-up tolerance studies and crop improvement. Software: Integration of such cross-species omics data is a challenging task, requiring various steps of transformation and filtering. Ultimately, visualization is crucial for quality control and interpretation. To address this, we developed A2TEA: Automated Assessment of Trait-specific Evolutionary Adaptations, a Snakemake workflow for detecting adaptation footprints in silico. It functions as a one-stop processing pipeline, integrating protein family, phylogeny, expression, and protein function analyses. The pipeline is accompanied by an R Shiny web application that allows exploring, highlighting, and exporting the results interactively. This allows the user to formulate hypotheses regarding the genomic adaptations of one or a subset of the investigated species to a given stress. Conclusions: While our research focus is on crops, the pipeline is entirely independent of the underlying species and can be used with any set of species. We demonstrate pipeline efficiency on real-world datasets and discuss the implementation and limits of our analysis workflow as well as planned extensions to its current state. The A2TEA workflow and web application are publicly available at: https://github.com/tgstoecker/A2TEA.Workflow and https://github.com/tgstoecker/A2TEA.WebApp, respectively.

show abstract

Section: Introductionmentioning

confidence: 99%

A2TEA: Identifying trait-specific evolutionary adaptations

et al. 2023

View full text Add to dashboard Cite

show abstract

Genome-wide identification of XsDGAT family and their expression patterns in yellowhorn ( Xanthoceras sorbifolium )

Liu,

Wang,

Zhang

et al. 2024

Biotechnology & Biotechnological Equipment

View full text Add to dashboard Cite

Pan-genome of pear provides insights into the fruit quality traits differentiation between Asian and European pears

Ding,

Hu,

Liu

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

The pear (Pyrus spp.) is a remarkable fruit, well known for its diverse flavors, textures, culinary versatility, and global horticultural importance. However, the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored. Here, wede novoassembled and annotated the genomes of the maternal (PsbM) and paternal (PsbF) lines of the hybrid ‘Yuluxiang’ pear and constructed the first pear pangenome of 1.15Gb by combining these two genomes with five previously published pear genomes. Using the constructed pangenome, we identified 21,224 gene PAVs and 1,158,812 SNPs in the non-reference genome that were absent in the PsbM reference genome. Compared with SNP markers, we found that PAV-based analysis provides additional insights into the pear population structure. In addition, we also revealed that some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations. Moreover, our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the genePsbMGH3.1potentially enhances sepal shedding in ‘Xuehuali’ which is vital for pear quality. This research helps further capture the genetic diversity of pear populations and provides valuable genomic resources for accelerating pear breeding.

show abstract

High-quality genome assembly and comparative genomic profiling of yellowhorn (Xanthoceras sorbifolia) revealed environmental adaptation footprints and seed oil contents variations

Cited by 5 publications

References 51 publications

A2TEA: Identifying trait-specific evolutionary adaptations

A2TEA: Identifying trait-specific evolutionary adaptations

Genome-wide identification of XsDGAT family and their expression patterns in yellowhorn ( Xanthoceras sorbifolium )

Pan-genome of pear provides insights into the fruit quality traits differentiation between Asian and European pears

Contact Info

Product

Resources

About