Comparative genomics of widespread and narrow-range white-bellied rats in the Niviventer niviventer species complex sheds light on invasive rodent success

Widespread species that inhabit diverse environments possess large population sizes and exhibit a high capacity for environmental adaptation,thus enabling range expansion.In contrast,narrow-range species are confined to restricted geographical areas and are ecologically adapted to narrow environmental conditions,thus limiting their ability to expand into novel environments.However,the genomic mechanisms underlying the differentiation between closely related species with varying distribution ranges remain poorly understood.The Niviventer niviventer species complex(NNSC),consisting of highly abundant wild rats in Southeast Asia and China,offers an excellent opportunity to investigate these questions due to the presence of both widespread and narrow-range species that are phylogenetically closely related.In the present study,we combined ecological niche modeling with phylogenetic analysis,which suggested that sister species cannot be both widespread and dominant within the same geographical region.Moreover,by assessing heterozygosity,linkage disequilibrium decay,and Tajima's D analysis,we found that widespread species exhibited higher genetic diversity than narrow-range species.In addition,by exploring the“genomic islands of speciation”,we identified 13 genes in highly divergent regions that were shared by the two widespread species,distinguishing them from their narrow-range counterparts.Functional annotation analysis indicated that these genes are involved in nervous system development and regulation.The adaptive evolution of these genes likely played an important role in the speciation of these widespread species.

The genome of okra (Abelmoschus esculentus) provides insights into its genome evolution and high nutrient content

Okra(Abelmoschus esculentus)is an important vegetable crop with high nutritional value.However,the mechanism underlying its high nutrient content remains poorly understood.Here,we present a chromosome-scale genome of okra with a size of 1.19 Gb.Comparative genomics analysis revealed the phylogenetic status of A.esculentus,as well as whole-genome duplication(WGD)events that have occurred widely across the Malvaceae species.We found that okra has experienced three additional WGDs compared with the diploid cotton Gossypium raimondii,resulting in a large chromosome number(2n=130).After three WGDs,okra has undergone extensive genomic deletions and retained substantial numbers of genes related to secondary metabolite biosynthesis and environmental adaptation,resulting in significant differences between okra and G.raimondii in the gene families related to cellulose synthesis.Combining transcriptomic and metabolomic analysis,we revealed the relationship between gene expression and metabolite content change across different okra developmental stages.Furthermore,the sinapic acid/S-lignin biosynthesis-related gene families have experienced remarkable expansion in okra,and the expression of key enzymes involved in the sinapic acid/S-lignin biosynthesis pathway vary greatly across developmental periods,which partially explains the differences in metabolite content across the different stages.Our study gains insights into the comprehensive evolutionary history of Malvaceae species and the genetic basis that underlies the nutrient content changes in okra,which will facilitate the functional study and genetic improvement of okra varieties.

Effects of simulated gut pH environment on bacterial composition and pheromone production of Dendroctonus valens

Bark beetles are an economically and ecologically important insect group,with aggregation behavior and thus host colonization success depends on pheromone-mediated communication.For some species,such as the major invasive forest pest in China,red turpentine beetle(Dendroctonus valens),gut microbiota participates in pheromone production by converting tree monoterpenes into pheromone products.However,how variation in gut microenvironment,such as pH,affects the gut microbial composition,and consequently pheromone production,is unknown.In this study,we fed wild caught D.valens with 3 different pH media(main host diet with natural pH of 4.7;a mildly acidic diet with pH 6 mimicking the beetle gut pH;and highly acidic diet with pH 4),and measured their effects on the gut pH,bacterial community and production of the main aggregation and anti-aggregation pheromone(verbenone).We further tested the verbenone production capacity of 2 gut bacterial isolates in different pH environments(pH 6 and 4).Compared to natural state or main host diet,feeding on less acidic diet(pH 6)diluted the acidity of the gut,whereas feeding on highly acidic diet(pH 4)enhanced it.Both changes in gut pH reduced the abundance of dominant bacterial genera,resulting in decreased verbenone production.Similarly,the highest pheromone conversion rate of the bacterial isolates was observed in pH mimicking the acidity in beetle gut.Taken together,these results indicate that changes in gut pH can affect gut microbiota composition and pheromone production,and may therefore have the potential to affect host colonization behavior.

Avian lower beak is always overlooked:its coordinate role in shaping species-specific beak should not be underestimated

The beak is a key evolutionary innovation in the avian tree of life.Its diversity in morphology shows birds’successful colonization of various ecological niches on the Earth(Pigot et al.2020),and its morphological plasticity can also enable birds to rapidly respond to changes in environments(Grant&Grant 2006).These natures helped birds survive multiple extinction events(Larson et al.2016).Therefore,investigating the morphological evolution of avian beaks and the underlying developmental and molecular mechanisms will help to decipher the evolution of birds and boost the development of the theory of evolutionary biology.