Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia

Abstract

Understanding the genetic basis underlying the local adaptation of nonmodel species is a fundamental goal in evolutionary biology. In this study, we explored the genetic mechanisms of the local adaptation of Forsythia suspensa using genome sequence and population genomics data obtained from specific-locus amplified fragment sequencing. We assembled a high-quality reference genome of weeping forsythia (Scaffold N50 = 7.3 Mb) using ultralong Nanopore reads. Then, genome-wide comparative analysis was performed for 15 natural populations of weeping forsythia across its current distribution range. Our results revealed that candidate genes associated with local adaptation are functionally correlated with solar radiation, temperature and water variables across heterogeneous environmental scenarios. In particular, solar radiation during the period of fruit development and seed drying after ripening, cold, and drought significantly contributed to the adaptive differentiation of F. suspensa. Natural selection exerted by environmental factors contributed substantially to the population genetic structure of F. suspensa. Our results supported the hypothesis that adaptive differentiation should be highly pronounced in the genes involved in signal crosstalk between different environmental variables. Our population genomics study of F. suspensa provides insights into the fundamental genetic mechanisms of the local adaptation of plant species to climatic gradients.

Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia

“…However, which pathways and ontologies are associated with heterogeneous drought stress can be detected by identifying candidate SDGs in twenty weeping forsythia populations. A total of 1,269 candidate SDGs involved into drought adaptation were identified by LFMM in previous studies [ 15 ]. Through enrichment analysis of SDGs in natural weeping forsythia populations, the ontologies related to the synthesis of aromatic substances (Table 3 ), such as farnesyl diphosphate metabolic process, sesquiterpene biosynthetic process, germacrene-A synthase activity, and sesquiterpene synthase activity, has undergone sequence differentiation in response to heterogeneous drought stress.…”

“…Although weeping forsythia is a drought-tolerant medicinal crop, long-term drought stress will affect its growth and fruit production. Recently, the genome sequence of weeping forsythia has been published, which provides opportunities for us to explore the genetic mechanisms of local adaptation [ 15 ]. Past studies using population genomics focused on detecting and quantifying adaptive differentiation in gene sequences in response to drought stress among different natural populations [ 15 ].…”

“…Recently, the genome sequence of weeping forsythia has been published, which provides opportunities for us to explore the genetic mechanisms of local adaptation [ 15 ]. Past studies using population genomics focused on detecting and quantifying adaptive differentiation in gene sequences in response to drought stress among different natural populations [ 15 ]. Whether there are differences in gene expression in response to drought stress among the natural populations of weeping forsythia, however, still required verification by common garden experiments.…”

Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases

“…One emerging question is why there are so many TFBS genetic variants. Because the natural selection exerted by environmental factors contributes substantially to the population genetic structure [64], one prominent hypothesis is that TFBS variants arise from natural selection and facilitate human adaptation to the local environment. Several theories suggest that TFBS sequences may be particularly important in evolutionary adaptation.…”

Genomic Adaptive Evolution of Sand Rice (Agriophyllum squarrosum) and Its Implications for Desert Ecosystem Restoration

“…Divergent selection is one of the most important fundamental evolutionary processes for genetic differentiation among populations, and further facilitates reproductive isolation among populations and completes speciation (Thompson, 2016;Bamba et al, 2019;Li J. L. et al, 2020). Numerous studies of plants have found that understanding local population adaptations could not only provide more information on how populations respond to divergent ecological factors but could also provide farreaching implications for species management, conservation, and ability to cope with global climate change (Fady et al, 2016;Lázaro-Nogal et al, 2016;Rellstab et al, 2016;Escalante et al, 2020;Li L.-F. et al, 2020;Moran, 2020). The consequences and mechanisms of balancing selection in plants have seldom been addressed due to the partial or lacking genomic investigation of plant populations (Zou et al, 2017), with the exception of information on biotic interactions such as sex-determining alleles among model plants (Weis et al, 2017).…”