Transcriptome sequencing and microsatellite marker discovery in Ailanthus altissima (Mill.) Swingle (Simaroubaceae).

Ailanthus altissima Swingle, is a tree species native to East Asia and has a great potential in decorative, bioenergy and industrial applications in many countries. To date, despite its commercial importance, the genomic and genetic resources available for this species are still insufficient. In this study, we characterized the transcriptome of A. altissima and developed thirteen EST-SSRs (expressed sequence tag-simple sequence repeats) based on Illumina paired-end RNA sequencing (RNA-seq). Besides, we developed ten polymorphic chloroplast microsatellite (cpSSR) markers using the available chloroplast genome of A. altissima. The transcriptome data produced 87,797 unigenes, of which 64,891 (73.91%) unigenes were successfully annotated in at least one protein database. For cpSSR markers the number of detected alleles (N) per marker varied from three at cpSSR12 to twelve at cpSSR8, the unbiased haploid diversity indices (uh) varied from 0.111 to 0.485, and haploid diversity indices (h) ranged from 0.101 to 0.444 with an average unbiased haploid diversity index (uh) of 0.274. Overall, a total of 65 different cpSSR alleles were identified at the ten loci among 165 individuals of A. altissima. The allele number per locus for EST-SSRs varied from 2.143 to 9.357, and the values of observed and expected heterozygosity ranged from 0.312 to 1.000 and 0.505 to 0.826, respectively. The molecular markers developed in this study will facilitate future genetic diversity, population structure, long distance-gene transfer and pollen-based gene flow analyses of A. altissima populations from its known distribution ranges in China focusing on planted and natural forest stands.

The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill.) (Sapindales: Simaroubaceae), an Important Pantropical Tree.

Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence. The tree of heaven chloroplast genome was found to be a circular molecule 160,815 base pairs (bp) in size and possess a quadripartite structure. The A. altissima chloroplast genome contains 113 unique genes of which 79 and 30 are protein coding and transfer RNA (tRNA) genes respectively and also 4 ribosomal RNA genes (rRNA) with overall GC content of 37.6%. Microsatellite marker detection identified A/T mononucleotides as majority SSRs in all the seven analyzed genomes. Repeat analyses of seven Sapindales revealed a total of 49 repeats in A. altissima, Rhus chinensis, Dodonaea viscosa, Leitneria floridana, while Azadirachta indica, Boswellia sacra, and Citrus aurantiifolia had a total of 48 repeats. The phylogenetic analysis using protein coding genes revealed that A. altissima is a sister to Leitneria floridana and also suggested that Simaroubaceae is a sister to Rutaceae family. The genome information reported here could be further applied for evolution and invasion, population genetics, and molecular studies in this plant species and family.

Exploring the genetic diversity and population structure of Ailanthus altissima using chloroplast and nuclear microsatellite DNA markers across its native range.

Understanding how anthropogenic disturbances affect the genetics of tree species is crucial; however, how tree populations in the wild can tolerate these activities remains unexplored. Given the ongoing and intensifying anthropogenic disturbances, we conducted a study using Ailanthus altissima to gain new insights into the effects of these pressures on genetic variability in undisturbed and disturbed forests. We analyzed the genetic diversity and population structure of A. altissima using nuclear (EST-SSR) and chloroplast (cpSSR) microsatellite markers. The genetic diversity across the 34 studied populations based on EST-SSRs was found to be moderate to high (nH E = 0.547-0.772) with a mean nH E of 0.680. Bayesian clustering, principal coordinate analysis (PCoA), and discriminant analysis of principal component (DAPC) consistently divided the populations into three distinct groups based on EST-SSRs. Allelic combinations of 92 different chloroplast size variants from 10 cpSSR loci resulted in a total of 292 chloroplast haplotypes. The mean haplotype diversity was relatively high (cpH E = 0.941), and the mean haplotype richness was 2.690, averaged across the 34 populations of A. altissima. Values of F ST in A. altissima from chloroplast and nuclear markers were 0.509 and 0.126, respectively. Modeling results showed evidence for population range contraction during the Last Glacial Maximum with subsequent population expansion in the Holocene and the future. Although genetic variation did not differ substantially across disturbed and undisturbed sites, there were small trends indicating higher genetic diversity and population bottlenecks in disturbed forests. As a result, disrupted ecosystems might display surprising genetic patterns that are difficult to predict and should not be overlooked.

[Distribution Characteristics of Microplastic Surface Bacterial Communities Under Flooded and Non-flooded Conditions in Nanjishan Wetland of Poyang Lake].

Plastic particles smaller than 5 mm in size are known as microplastics which are widespread in the environment and can cause several negative effects. Moreover, only a few studies have focused on the relationship between microplastics and microbes in the natural wetland ecosystem. In this study, microplastics were collected from sediment, water, and sediment flooded and non-flooded conditions in the lake wetland of Poyang Lake as the study area. The structural distribution of bacterial community on sediment, water, and microplastics were analyzed using 16S high-throughput sequencing. The results of the α-diversity analysis showed that the bacterial abundance and diversity on the surface of microplastics were significantly different from those in the environment and were lower than those in the surrounding environment in both flooded and non-flooded conditions. The results of the principal co-ordinates analysis indicated that the bacterial community on the surface of microplastics was more influenced by the sediment in non-flooded conditions and by the water in flooded conditions. The structure of the bacterial community on the microplastic surface also showed significant differences from the surrounding environment, with the sediment mainly consisting of several other bacterial genera with <1% abundance, whereas the bacterial community on the microplastics had clearly dominant species. The relative abundance of Proteobacteria on the microplastic surfaces increased significantly in the non-flooded condition compared to that in the water and sediment samples, whereas the relative abundance of Bacteroidota on the microplastic surface increased in the flooded condition. The genus Flavobacterium, Massilia, and Pseudomonas were the most abundant in the non-flooded state, and the genus Flavobacterium was the most abundant in the flooded state. In this study, Pseudomonas spp. was the focus of future research on plastic biodegradation. This study can further improve the understanding of microplastic pollution in wetland ecosystems and provide a theoretical basis for lake environmental management.

The complete chloroplast genome of Myriophyllum spicatum reveals a 4-kb inversion and new insights regarding plastome evolution in Haloragaceae.

Myriophyllum, among the most species-rich genera of aquatic angiosperms with ca. 68 species, is an extensively distributed hydrophyte lineage in the cosmopolitan family Haloragaceae. The chloroplast (cp) genome is useful in the study of genetic evolution, phylogenetic analysis, and molecular dating of controversial taxa. Here, we sequenced and assembled the whole chloroplast genome of Myriophyllum spicatum L. and compared it to other species in the order Saxifragales. The complete chloroplast genome sequence of M. spicatum is 158,858 bp long and displays a quadripartite structure with two inverted repeats (IR) separating the large single copy (LSC) region from the small single copy (SSC) region. Based on sequence identification and the phylogenetic analysis, a 4-kb phylogenetically informative inversion between trnE-trnC in Myriophyllum was determined, and we have placed this inversion on a lineage specific to Myriophyllum and its close relatives. The divergence time estimation suggested that the trnE-trnC inversion possibly occurred between the upper Cretaceous (72.54 MYA) and middle Eocene (47.28 MYA) before the divergence of Myriophyllum from its most recent common ancestor. The unique 4-kb inversion might be caused by an occurrence of nonrandom recombination associated with climate changes around the K-Pg boundary, making it interesting for future evolutionary investigations.

The hornwort genome and early land plant evolution.

Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.