Phylogeographic forces driving evolution of sea‐dispersed plants are often influenced by regional and species characteristics, although not yet deciphered at a large spatial scale for many taxa like the mangrove species Heritiera littoralis . This study aimed to assess geographic distribution of genetic variation of this widespread mangrove in the Indo‐West Pacific region and identify the phylogeographic factors influencing its present‐day distribution. Analysis of five chloroplast DNA fragments’ sequences from 37 populations revealed low genetic diversity at the population level and strong genetic structure of H. littoralis in this region. The estimated divergence times between the major genetic lineages indicated that glacial level changes during the Pleistocene epoch induced strong genetic differentiation across the Indian and Pacific Oceans. In comparison to the strong genetic break imposed by the Sunda Shelf toward splitting the lineages of the Indian and Pacific Oceans, the genetic differentiation between Indo‐Malesia and Australasia was not so prominent. Long‐distance dispersal ability of H. littoralis propagules helped the species to attain transoceanic distribution not only across South East Asia and Australia, but also across the Indian Ocean to East Africa. However, oceanic circulation pattern in the South China Sea was found to act as a barrier creating further intraoceanic genetic differentiation. Overall, phylogeographic analysis in this study revealed that glacial vicariance had profound influence on population differentiation in H. littoralis and caused low genetic diversity except for the refugia populations near the equator which might have persisted through glacial maxima. With increasing loss of suitable habitats due to anthropogenic activities, these findings therefore emphasize the urgent need for conservation actions for all populations throughout the distribution range of H. littoralis .

23Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major cause 24 of nosocomial infections and hospital outbreaks worldwide, remaining a 25 critical clinical concern. Here we characterized and investigated the 26 phylogenetic relationships of 105 CRAB isolates on intensive care unit 27 surfaces from one hospital in China collected over six years. All strains 28 carried bla , bla genes for carbapenem resistance, also had high 29 resistance gene, virulence factor and insertion sequences burdens. 30Whole-genome sequencing revealed all strains belonged to ST2, the 31 global clone CC2. The phylogenetic analysis based on the core genome 32 showed all isolates was dominated by a single lineage of three clusters 33 and eight different clones. Two clones were popular during the collection 34 time. Using chi-square test to identify the epidemiologically meaningful 35 groupings, we found the significant difference in community structure 36 only present in strains from separation time. The haplotype and 37 median-joining network analysis revealed genetic differences among 38 clusters and changes occurred overtime in the dominating cluster. Our 39 results highlighted substantial multidrug-resistant CRAB burden in 40 hospital ICU environment, demonstrated potential clone outbreak in 41 hospital. 42 Keywords: Carbapenem-resistant Acinetobacter baumannii, 43 whole-genome sequencing, clone spread, nosocomial infection. 48 infections throughout the world(51). The extraordinary ability to survive 49 in a harsh environment and to readily acquire antimicrobial resistance 50 determinants have made A. baumannii as a public health threat(18). 51 Carbapenems are known as the frontline treatment for infections 52 multidrug-resistant A. baumannii infections. However, the wide spread 53 carbapenem resistant A. baumannii (CRAB) strains have caused a major 54concern worldwide due to the limited treatment choices (13). In 2017, the 55 World Health Organization has listed CRAB as one of the most critical 56 pathogens and the highest priority in new antibiotic development(56). 57 Carbapenem resistance in A. baumannii is medicated by several 58 coexisting mechanisms but the most prevalent mechanism is associated 59 with carbapenem-hydrolyzing enzymes(9). There exist three different 60 types of ß-lactamases leading to carbapenem resistance, such as ambler 61 class A β-lactamases (bla GES-14, bla TEM , bla SHV, bla CTX-M and bla KPC ), 62 metallo-ß-lactamases (bla IMP-like , bla VIM-like , bla SIM-1 , and bla NDM-1 ) and 63 oxacillinases (bla OXA-23-like , bla OXA-24-like , bla OXA-58-like, bla OXA-143 , 64 bla OXA-235-like, bla OXA-51-like )(15, 52). Major expression of OXA genes might 65 be facilitated by insertion sequence elements (ISs), such as ISAba1, 19). In addition to the resistance, CRAB also carried a wide arsenal 68 of virulence factors predisposing for a worsening course of disease(2, 37). 69 Although virulence determinants in A. baumannii are incompletely 70 understood, the genes related to biofilm formation, outer membrane ...

Rhodomyrtus tomentosa is an important fleshy-fruited tree and a well-known medicinal plant of the Myrtaceae family that is widely cultivated in tropical and subtropical areas of the world. However, studies on the evolution and genomics breeding potential of R. tomentosa were hindered by the lack of a reference genome. Here, we present a chromosome-level gap-free T2T genomic assembly of R. tomentosa using PacBio and ONT long read sequencing. We assembled the R. tomentosa with size of 470.35 Mb and contig N50 of ~43.80 Mb with 11 pseudochromosomes. We annotated a total of 33,382 genes and 239.31 Mb of repetitive sequences in this genome. Phylogenetic analysis elucidated the independent evolution of R. tomentosa start from 14.37MYA and shared a recent WGD event in Myrtaceae. We identified four major compounds of anthocyanins and their synthetic pathways in R. tomentosa. Comparative genomic and gene expression analysis suggested the coloring and high anthocyanin accumulation in R. tomentosa tends to be determined by the activation of anthocyanin synthesis pathway. The positive selection and up-regulation of MYB transcriptome factors was the implicit factors in this process, while the increase of downstream anthocyanin transport-related OMT and GST gene copy numbers were detected in R. tomentosa. Expression analysis and pathway identification enriched the importance of starch degradation, response to stimuli, effect of hormones, and cell wall metabolism during the fleshy fruit development in Myrtaceae. Our genomic assembly provide a foundation for investigating the origins and differentiation of Myrtaceae and accelerate the genetic improvement of R. tomentosa.

Background and Aims Mikania micrantha, a climbing perennial weed of the family Asteraceae, is native to Latin America and is highly invasive in the tropical belt of Asia, Oceania and Australia. This study was framed to investigate the population structure of M. micrantha at a large spatial scale in Asia and to identify how introduction history, evolutionary forces and landscape features influenced the genetic pattern of the species in this region. Methods We assessed the genetic diversity and structure of 1052 individuals from 46 populations for 12 microsatellite loci. The spatial pattern of genetic variation was investigated by estimating the relationship between genetic distance and geographical, climatic and landscape resistances hypothesized to influence gene flow between populations. Key Results We found high genetic diversity of M. micrantha in this region, as compared with the genetic diversity parameters of other invasive species. Spatial and non-spatial clustering algorithms identified the presence of multiple genetic clusters and admixture between populations. Most of the populations showed heterozygote deficiency, primarily due to inbreeding, and the founder populations showed evidence of a genetic bottleneck. Persistent gene flow throughout the invasive range caused low genetic differentiation among populations and provided beneficial genetic variation to the marginal populations in a heterogeneous environment. Environmental suitability was found to buffer the detrimental effects of inbreeding at the leading edge of range expansion. Both linear and non-linear regression models demonstrated a weak relationship between genetic distance and geographical distance, as well as bioclimatic variables and environmental resistance surfaces. Conclusions These findings provide evidence that extensive gene flow and admixture between populations have influenced the current genetic pattern of M. micrantha in this region. High gene flow across the invaded landscape may facilitate adaptation, establishment and long-term persistence of the population, thereby indicating the range expansion ability of the species.

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