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.

GI_(FeGSH):A New Genomic Island Might Explain the Differences in Brucella Virulence

An imported dog was confirmed to be positive with canine brucellosis in Sweden in 2010. The whole genome of Brucella canis SVA10 was subjected to phage analysis (WGS-PA) and was assigned to the Asian B. canis cluster. Further analysis indicated that the genome of B. canis SVA10 is smaller compared to genomes of the same species. A 35,781 bp genomic island (GI) was found to be absent in strain SVA10 which was detected by read mapping the paired reads to the genome of B. canis ATCC 23,365T. The lacking genes of genomic island GIFeGSH are mainly coding for iron uptake enzymes and parts of the glutathione pathway. A screening of all available whole genome sequences of Brucella strains confirmed that GIFeGSH is also missing in four more strains of B. canis but present in several strains of B. abortus, B. melitensis, B. suis, B. ovis, B. microti, B. pinnipedialis, and B. ceti. Parts of the GI were present, but scattered in two other B. canis strains. The aim of this study was to find differences in the genomes of Brucella which might explain former described differences in virulence. The analysis was extended to all available Brucella genomes after the detection of a genomic island in strain SVA10.

Genomics of plant speciation

Studies of plants have been instrumental for revealing how new species originate.For several decades,botanical research has complemented and,in some cases,challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form.Now,the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research.Here,we review these recent genome-enabled developments in plant speciation.We discuss complications related to identification of reproductive isolation(RI)loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation,as increasingly revealed by new sequencing technologies.Further,we review how genomics has advanced what we know of some routes to new species formation,like hybridization or whole-genome duplication,while casting doubt on others,like population bottlenecks and genetic drift.While genomics can fast-track identification of genes and mutations that confer RI,we emphasize that follow-up molecular and field experiments remain critical.Nonetheless,genomics has clarified the outsized role of ancient variants rather than new mutations,particularly early during speciation.We conclude by highlighting promising avenues of future study.These include expanding what we know so far about the role of epigenetic and structural changes during speciation,broadening the scope and taxonomic breadth of plant speciation genomics studies,and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.

Analysis of the 3' ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

The purpose of this study was to investigate the characteristics of transfer RNA(tRNA) responsible for the association between tRNA genes and genes of apparently foreign origin(genomic islands) in five high-light adapted Prochlorococcus strains.Both bidirectional best BLASTP(basic local alignment search tool for proteins) search and the conservation of gene order against each other were utilized to identify genomic islands,and 7 genomic islands were found to be immediately adjacent to tRNAs in Prochlorococcus marinus AS9601,11 in P.marinus MIT9515,8 in P.marinus MED4,6 in P.marinus MIT9301,and 6 in P.marinus MIT9312.Monte Carlo simulation showed that tRNA genes are hotspots for the integration of genomic islands in Prochlorococcus strains.The tRNA genes associated with genomic islands showed the following characteristics:(1) the association was biased towards a specific subset of all iso-accepting tRNA genes;(2) the codon usages of genes within genomic islands appear to be unrelated to the codons recognized by associated tRNAs;and,(3) the majority of the 3' ends of associated tRNAs lack CCA ends.These findings contradict previous hypotheses concerning the molecular basis for the frequent use of tRNA as the insertion site for foreign genetic materials.The analysis of a genomic island associated with a tRNA-Asn gene in P.marinus MIT9301 suggests that foreign genetic material is inserted into the host genomes by means of site-specific recombination,with the 3' end of the tRNA as the target,and during the process,a direct repeat of the 3' end sequence of a boundary tRNA(namely,a scar from the process of insertion) is formed elsewhere in the genomic island.Through the analysis of the sequences of these targets,it can be concluded that a region characterized by both high GC content and a palindromic structure is the preferred insertion site.