High levels of gene flow and genetic diversity in Irish populations of Salix caprea L. inferred from chloroplast and nuclear SSR markers

Population Variation and Phylogeography of Cherry Blossom (Prunus conradinae) in China

Prunus conradinae (subgenus Cerasus, Rosaceae) is a significant germplasm resource of wild cherry blossom in China. To ensure the comprehensiveness of this study, we used a large sample size (12 populations comprising 244 individuals) which involved the fresh leaves of P. conradinae in Eastern, Central, and Southwestern China. We combined morphological and molecular evidence (three chloroplast DNA (cpDNA) sequences and one nuclear DNA (nr DNA) sequence) to examine the population of P. conradinae variation and differentiation. Our results revealed that Central, East, and Southwest China are important regions for the conservation of P. conradinae to ensure adequate germplasm resources in the future. We also found support for a new variant, P. conradinae var. rubrum. We observed high genetic diversity within P. conradinae (haplotype diversity [Hd] = 0.830; ribotype diversity [Rd] = 0.798), with novel genetic variation and a distinct genealogical structure among populations. There was genetic variation among populations and phylogeographic structure among populations and three geographical groups (Central, East, and Southwest China). The genetic differentiation coefficient was the lowest in the Southwest region and the gene exchange was obvious, while the differentiation was obvious in Central China. In the three geographic groups, we identified two distinct lineages: an East China lineage (Central China and East China) and a Southwest China lineage ((Central China and Southwest China) and East China). These two lineages originated approximately 4.38 million years ago (Mya) in the early Pliocene due to geographic isolation. P. conradinae expanded from Central China to East China at 3.32 Mya (95% HPD: 1.12-5.17 Mya) in the Pliocene. The population of P. conradinae spread from East China to Southwest China, and the differentiation time was 2.17 Mya (95% (HPD: 0.47-4.54 Mya), suggesting that the population of P. conradinae differentiated first in Central and East China. The population of P. conradinae experienced differentiation from Central China to Southwest China around 1.10 Mya (95% HPD: 0.11-2.85 Mya) during the early Pleistocene of the Quaternary period. The southeastern region of East China, near Mount Wuyi, likely serves as a refuge for P. conradinae. This study establishes a theoretical foundation for the classification, identification, conservation, and exploitation of germplasm resources of P. conradinae.

Comparative analysis of the organelle genomes of Aconitum carmichaelii revealed structural and sequence differences and phylogenetic relationships

In this study, we conducted an assembly and analysis of the organelle genomes of Aconitum carmichaelii. Our investigation encompassed the examination of organelle genome structures, gene transfer events, and the environmental selection pressures affecting A. carmichaelii. The results revealed distinct evolutionary patterns in the organelle genomes of A. carmichaelii. Especially, the plastome exhibited a more conserved structure but a higher nucleotide substitution rate (NSR), while the mitogenome displayed a more complex structure with a slower NSR. Through homology analysis, we identified several instances of unidirectional protein-coding genes (PCGs) transferring from the plastome to the mitogenome. However, we did not observe any events which genes moved from the mitogenome to the plastome. Additionally, we observed multiple transposable element (TE) fragments in the organelle genomes, with both organelles showing different preferences for the type of nuclear TE insertion. Divergence time estimation suggested that rapid differentiation occurred in Aconitum species approximately 7.96 million years ago (Mya). This divergence might be associated with the reduction in CO2 levels and the significant uplift of the Qinghai-Tibet Plateau (QTP) during the late Miocene. Selection pressure analysis indicated that the dN/dS values of both organelles were less than 1, suggested that organelle PCGs were subject to purification selection. However, we did not detect any positively selected genes (PSGs) in Subg. Aconitum and Subg. Lycoctonum. This observation further supports the idea that stronger negative selection pressure on organelle genes in Aconitum results in a more conserved amino acid sequence. In conclusion, this study contributes to a deeper understanding of organelle evolution in Aconitum species and provides a foundation for future research on the genetic mechanisms underlying the structure and function of the Aconitum plastome and mitogenome.

Molecular characterisation of Pinus sylvestris (L.) in Ireland at the western limit of the species distribution

BACKGROUND

Scots pine (Pinus sylvestris L.) underwent significant population declines across much of northwest Europe during the mid-to-late Holocene and was thought to have become extirpated in Ireland from about 400 AD. However, most extant populations are plantations reintroduced from Scotland. Others are naturalised therefrom and one in Western Ireland is a putative relict. In this paper, Scots pine in Ireland are genetically described for the first time.

RESULTS

Using two mitochondrial (mtDNA) loci, eight chloroplast (cpSSR) and 18 nuclear (nSSR) loci, the genetic composition and diversity of 19 Irish Scots pine populations is described and compared to other European populations. All trees sampled in Ireland were fixed for mitotype a, which is the most common across northwest Europe. By contrast, cpSSR (HCP = 0.967) and nSSR (He = 0.540) variation was high, and comparable with estimates for other regions across the species range. Differentiation at both sets of loci were similarly low (cpSSR FST = 0.019; nSSR FST = 0.018), but populations from continental Europe were significantly differentiated from all Irish populations based on nSSR variation.

CONCLUSIONS

All Irish Scots pine are likely part of a common Irish-Scottish gene pool which diverged from continental Scots pine following post-glacial recolonisation. A high genetic diversity and an absence of evidence of inbreeding suggests the regional decline of Scots pine did not critically reduce allelic variation. The post-glacial relationship between Irish and Scottish pine is discussed, and a suggestion from recent palaeoecological work that reintroduced Scots pine be managed as a native species is now further supported by genetic data.

New insights into polyploid evolution and dynamic nature of Ludwigia section Isnardia (Onagraceae)

BACKGROUND

While polyploids are common in plants, the evolutionary history and natural dynamics of most polyploid groups are still unclear. Owing to plentiful earlier systematic studies, Ludwigia sect. Isnardia (comprising 22 wetland taxa) is an ideal allopolyploid complex to investigate polyploid evolution and natural dynamics within and among taxa. With a considerable sampling, we concentrated on revisiting earlier phylogenies of Isnardia, reevaluating the earlier estimated age of the most recent common ancestor (TMRCA), exploring the correlation between infraspecific genetic diversity and ploidy levels, and inspecting interspecific gene flows among taxa.

RESULTS

Phylogenetic trees and network concurred with earlier phylogenies and hypothesized genomes by incorporating 192 atpB-rbcL and ITS sequences representing 91% of Isnardia taxa. Moreover, we detected three multi-origin taxa. Our findings on L. repens and L. sphaerocarpa were consistent with earlier studies; L. arcuata was reported as a multi-origin taxon here, and an additional evolutionary scenario of L. sphaerocarpa was uncovered, both for the first time. Furthermore, estimated Isnardia TMRCA ages based on our data (5.9 or 8.9 million years ago) are in accordance with earlier estimates, although younger than fossil dates (Middle Miocene). Surprisingly, infraspecific genetic variations of Isnardia taxa did not increase with ploidy levels as anticipated from many other polyploid groups. In addition, the exuberant, low, and asymmetrical gene flows among Isnardia taxa indicated that the reproductive barriers may be weakened owing to allopolyploidization, which has rarely been reported.

CONCLUSIONS

The present research gives new perceptions of the reticulate evolution and dynamic nature of Isnardia and points to gaps in current knowledge about allopolyploid evolution.

Complete chloroplast genomes of 11 Sabia samples: Genomic features, comparative analysis, and phylogenetic relationship

The genus Sabia is a woody climber belonging to the family Sabiaceae, order Proteales. Several species of this genus have been utilized as medicines for treating diseases, such as rheumatic arthritis, traumatism, hepatitis, etc. However, the lack of molecular data has prevented the accurate identification and refinement of taxonomic relationships in this genus. In this study, chloroplast genomes of 11 samples of the genus Sabia were assembled and analyzed. These chloroplast genomes showed a typical quadripartite structure and ranged in length from 160,956 to 162,209 bp. The structure of the genomes was found to be relatively conserved, with 130 genes annotated, including 85 coding genes, 37 tRNA genes, and eight rRNA genes. A total of 78-98 simple sequence repeats and 52-61 interspersed repeats were detected. Sequence alignment revealed 11 highly variable loci in chloroplast genomes. Among these loci, ndhF-ndhD achieved a remarkably higher resolution than the other regions. In addition, phylogenetic analysis indicated that Sect. Pachydiscus and Sect. Sabia of Sabia did not form two separate monophyletic groups. The divergence time calculated based on the Reltime method indicated that the evolutionary branches of Sabia and Meliosma started to form approximately 85.95 million years ago (Mya), and the species within Sabia began to diverge approximately 7.65 Mya. In conclusion, our study provides a basis for comprehensively exploring the phylogenetic relationships of Sabia. It also provides a methodological basis and data support for establishing a standardized and scientific identification system for this genus.

Assessment of Genetic Diversity of the Salangid, Neosalanx taihuensis, Based on the Mitochondrial COI Gene in Different Chinese River Basins

Simple Summary

In the current study, we estimate the genetic diversity of the salangid Neosalanxtaihuensis sampled from 11 populations in the six typical river basins of China. Using the COI gene sequencing technology, the N. taihuensis population’s genetic difference within and between river basins was investigated. Significant levels of genetic subdivision were detected among populations within basins rather than between basins. Population history dynamics showed that N. taihuensis populations experienced a population expansion during the glacial period in the late Pleistocene. These results suggest that different populations should be considered as different management units to achieve effective conservation and management purposes.

Abstract

The salangid Neosalanx taihuensis (Salangidae) is a commercially important economical fish endemic to China and restricted to large freshwater systems with a wide-ranging distribution. This fish species has continuous distribution ranges and a long-introduced aquaculture history in Chinese basins. However, the research on its population genetic differentiation within and between basins is very limited. In this regard, 197 individuals were sampled from 11 populations in the Nenjiang River Basin (A1–A4), Songhua River Basin (B1), Yellow River Basin (C1–C2), Yangtze River Basin (D1), Lanchang River Basin (E1–E2) and Huaihe River Basin (F1). Based on the COI sequence, the N.taihuensis population’s genetic difference within and between river basins was investigated. The haplotypes and their frequency distributions were strongly skewed, with most haplotypes (n = 13) represented only in single samples each and thus restricted to a single population. The most common haplotype (H4, 67/197) was found in all individuals. The analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. The mismatch between the distribution and neutrality tests supported the evidence of a population expansion, which occurred during the late Pleistocene (0.041–0.051 million years ago). Significant levels of genetic subdivision were detected among populations within basins rather than between the six basins. Population history dynamics showed that N. taihuensis experienced an expansion during the glacial period in the late Pleistocene. Therefore, different populations should be considered as different management units to achieve effective conservation and management purposes. These results have great significance for the evaluation and exploitation of the germplasm resources of N. taihuensis.

Comparative Chloroplast Genomics and Phylogenetic Analysis of Zygophyllum (Zygophyllaceae) of China

The genus Zygophyllum comprises over 150 species within the plant family Zygophyllaceae. These species predominantly grow in arid and semiarid areas, and about 20 occur in northwestern China. In this study, we sampled 24 individuals of Zygophyllum representing 15 species and sequenced their complete chloroplast (cp) genomes. For comparison, we also sequenced cp genomes of two species of Peganum from China representing the closely allied family, Nitrariaceae. The 24 cp genomes of Zygophyllum were smaller and ranged in size from 104,221 to 106,286 bp, each containing a large single-copy (LSC) region (79,245-80,439 bp), a small single-copy (SSC) region (16,285-17,146 bp), and a pair of inverted repeat (IR) regions (3,792-4,466 bp). These cp genomes contained 111-112 genes each, including 74-75 protein-coding genes (PCGs), four ribosomal RNA genes, and 33 transfer RNA genes, and all cp genomes showed similar gene order, content, and structure. The cp genomes of Zygophyllum appeared to lose some genes such as ndh genes and rRNA genes, of which four rRNA genes were in the SSC region, not in the IR regions. However, the SC and IR regions had greater similarity within Zygophyllum than between the genus and Peganum. We detected nine highly variable intergenic spacers: matK-trnQ, psaC-rps15, psbZ-trnG, rps7-trnL, rps15-trnN, trnE-trnT, trnL-rpl32, trnQ-psbK, and trnS-trnG. Additionally, we identified 156 simple sequence repeat (cpSSR) markers shared among the genomes of the 24 Zygophyllum samples and seven cpSSRs that were unique to the species of Zygophyllum. These markers may be useful in future studies on genetic diversity and relationships of Zygophyllum and closely related taxa. Using the sequenced cp genomes, we reconstructed a phylogeny that strongly supported the division of Chinese Zygophyllum into herbaceous and shrubby clades. We utilized our phylogenetic results along with prior morphological studies to address several remaining taxonomic questions within Zygophyllum. Specifically, we found that Zygophyllum kaschgaricum is included within Zygophyllum xanthoxylon supporting the present treatment of the former genus Sarcozygium as a subgenus within Zygophyllum. Our results provide a foundation for future research on the genetic resources of Zygophyllum.

Assessing Genotypic and Environmental Effects on Endophyte Communities of Fraxinus (Ash) Using Culture Dependent and Independent DNA Sequencing

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.

Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

Taxonomic and phylogenetic relationships of Christia, Urariopsis, Uraria and related genera within the tribe Desmodieae (Fabaceae: Papilionoideae) have long been controversial. Here, we report the complete chloroplast (cp) genomes of Christia vespertilionis and Urariopsis brevissima and perform comparative and phylogenetic analyses with Uraria lagopodioides and other relatives in the Desmodieae. The cp genomes of C. vespertilionis and U. brevissima are 149,656 and 149,930 bp long, with 128 unique genes (83 protein-coding genes, 37 tRNA genes and 8 rRNA genes), respectively. Comparative analyses revealed 95-129 simple sequence repeats (SSRs) and eleven highly variable regions (trnK-rbcL, rbcL-atpB, ndhJ-trnF, trnL-trnT, psbD-rpoB, accD-cemA, petA-psbL, psbE-petL, rps11-rps19, ndhF-ccsA, and rps15-ycf1) among six Desmodieae species. Phylogenetic analyses clearly resolved two subtribes (Desmodiinae and Lespedezinae) of Desmodieae as monophyletic, and the newly reported C. vespertilionis and U. brevissima clustered in subtribe Desmodiinae. A sister relationship of C. vespertilionis to U. lagopodioides was supported. Evidence was presented to support the treatment of Urariopsis as a distinct genus rather than in synonymy with Uraria. The results provide valuable information for further studies on species delimitation, phylogenetics, population genetics, and the evolutionary process of speciation in the Desmodieae.

Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling

The rose is one of the most important ornamental woody plants because of its extensive use and high economic value. Herein, we sequenced a complete chloroplast genome of the miniature rose variety Rosa 'Margo Koster' and performed comparative analyses with sequences previously published for other species in the Rosaceae family. The chloroplast genome of Rosa 'Margo Koster', with a size of 157,395 bp, has a circular quadripartite structure typical of angiosperm chloroplast genomes and contains a total of 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Conjunction regions in the chloroplast genome of Rosa 'Margo Koster' were verified and manually corrected by Sanger sequencing. Comparative genome analysis showed that the IR contraction and expansion events resulted in rps19 and ycf1 pseudogenes. The phylogenetic analysis within the Rosa genus showed that Rosa 'Margo Koster' is closer to Rosa odorata than to other Rosa species. Additionally, we identified and screened highly divergent sequences and cpSSRs and compared their power to discriminate rose varieties by Sanger sequencing and capillary electrophoresis. The results showed that 15 cpSSRs are polymorphic, but their discriminating power is only moderate among a set of rose varieties. However, more than 150 single nucleotide variations (SNVs) were discovered in the flanking region of cpSSRs, and the results indicated that these SNVs have a higher divergence and stronger power for profiling rose varieties. These findings suggest that nucleotide mutations in the chloroplast genome may be an effective and powerful tool for rose variety discrimination and DNA profiling. These molecular markers in the chloroplast genome sequence of Rosa spp. will facilitate population and phylogenetic studies and other related studies of this species.

Genome-wide analysis of Cushion willow provides insights into alpine plant divergence in a biodiversity hotspot

The Hengduan Mountains (HDM) biodiversity hotspot exhibits exceptional alpine plant diversity. Here, we investigate factors driving intraspecific divergence within a HDM alpine species Salix brachista (Cushion willow), a common component of subnival assemblages. We produce a high-quality genome assembly for this species and characterize its genetic diversity, population structure and pattern of evolution by resequencing individuals collected across its distribution. We detect population divergence that has been shaped by a landscape of isolated sky island-like habitats displaying strong environmental heterogeneity across elevational gradients, combined with population size fluctuations that have occurred since approximately the late Miocene. These factors are likely important drivers of intraspecific divergence within Cushion willow and possibly other alpine plants with a similar distribution. Since intraspecific divergence is often the first step toward speciation, the same factors can be important contributors to the high alpine species diversity in the HDM.

Reproductive and genetic consequences of extreme isolation in Salix herbacea L. at the rear edge of its distribution

BACKGROUND AND AIMS

At the rear edge of the distribution of species, extreme isolation and small population size influence the genetic diversity and differentiation of plant populations. This may be particularly true for Arctic-alpine species in mid-latitude mountains, but exactly how peripherality has shaped their genetic and reproductive characteristics is poorly investigated. The present study, focused on Salix herbacea, aims at providing new insights into the causes behind ongoing demographic dynamics and their consequences for peripheral populations of Arctic-alpine species.

METHODS

We performed a whole-population, highly detailed sampling of the only two S. herbacea populations in the northern Apennines, comparing their clonal and genetic diversity, sex ratio and spatial genetic structure with a reference population from the Alps. After inspecting ~1800 grid intersections in the three populations, 563 ramets were genotyped at 11 nuclear microsatellite markers (nSSRs). Past demography and mating patterns of Apennine populations were investigated to elucidate the possible causes of altered reproductive dynamics.

KEY RESULTS

Apennine populations, which experienced a Holocene bottleneck and are highly differentiated (FST = 0.15), had lower clonal and genetic diversity compared with the alpine population (RMLG = 1 and HE = 0.71), with the smaller population exhibiting the lowest diversity (RMLG = 0.03 and HE = 0.24). An unbalanced sex ratio was found in the larger (63 F:37 M) and the smaller (99 F:1 M) Apennine population. Both were characterized by the presence of extremely large clones (up to 2500 m2), which, however, did not play a dominant role in local reproductive dynamics.

CONCLUSIONS

Under conditions of extreme isolation and progressive size reduction, S. herbacea has experienced an alteration of genetic characteristics produced by the prevalence of clonal growth over sexual reproduction. However, our results showed that the larger Apennine population has maintained levels of sexual reproduction enough to counteract a dramatic loss of genetic and clonal diversity.

Regional patterns of genetic structure and environmental differentiation in willow populations (Salix humboldtiana Willd.) from Central Mexico

AIM

To infer the geological and climatic factors that have shaped the genetic diversity and structure of a willow species (Salix humboldtiana) in three basins of Central Mexico.

LOCATION

Central Mexico.

METHODS

We collected samples from 11 populations across two hydrological basins (Balsas and Lerma) and one population from another basin (Ameca) within the Mexican Central Plateau (MCP). Individuals were analyzed using sequences of two chloroplast DNA (cpDNA) regions and eight nuclear simple sequence repeats (nSSR). Population genetic diversity and structure were determined from these data. To evaluate whether genetic structure was associated with ecological niche differentiation, we determined whether there is niche equivalence, overlap, or divergence between the Balsas and Lerma basins. Also, we evaluated the relative contributions of geographic distribution and climatic variation on population genetic structuring through redundancy analysis (RDA) and partial RDA.

RESULTS

Both cpDNA and nSSRs data indicated the presence of three highly differentiated genetic groups, mostly geographically congruent with the three main hydrological basins. According to nSSRs, the three genetic groups can be further subdivided into eight subgroups corresponding to different rivers within the main basins. The niche equivalency test showed that the niches of the species in the Balsas and Lerma basins are significantly nonequivalent. The RDA indicated a significant association of genetic variation among populations with climate variables (particularly those related to the precipitation regime), while controlling for geographic distribution.

MAIN CONCLUSIONS

The genetic structure of S. humboldtiana is strongly associated with the historical and current geological configuration of the basins and the rivers within basins. The observed hierarchical genetic differentiation can be due to gene flow limitation resulting from physical barriers to the dispersal of S. humboldtiana, but also to some degree of isolation by environment, as suggested by the significant association between genetic variation among populations and precipitation regime.

Genetic analysis suggests extensive gene flow within and between catchments in a common and ecologically significant dryland river shrub species; Duma florulenta (Polygonaceae)

AIM

The conservation of plant species biodiversity has been identified as a crucial factor for the resilience of dryland ecosystems in the face of climate change and desertification. Duma florulenta (lignum) is a keystone species that facilitates biodiversity in the floodplains and wetlands of Australia's dryland river systems. This paper explores spatial genetic structure of lignum and investigates factors influencing dispersal and gene flow within and among river catchments of the northern Murray-Darling Basin.

LOCATION

Northern Murray-Darling Basin, eastern Australia.

METHODS

A total of 122 individual plants from subpopulations located on rivers in four adjacent catchments were genotyped using 10 microsatellite markers. Microsatellite data were then analyzed using population genetic techniques to evaluate levels of gene flow and genetic structure and identify factors influencing dispersal.

RESULTS

Results suggest high levels of gene flow between lignum subpopulations of the northern Murray-Darling Basin. AMOVA revealed small but significant differences between subpopulations, and STRUCTURE analysis did not detect meaningful structure when sampling information was not provided. However, when sampling information was supplied using the LOCPRIOR model, three genetic clusters were identified. All Lower Balonne subpopulations were assigned to cluster 1 while a number of the other subpopulations showed mixed ancestry. Weak relationships were identified between pairwise genetic distance and geographic as well as river distance, although the R 2 value of the former was only half that of the latter.

MAIN CONCLUSIONS

Patterns of genetic variation suggest frequent long-distance overland gene flow largely as a result of the movement of seeds via floodwater. Therefore, maintenance of natural variability in flow regime is key both to maintain conditions favorable to recruitment and to promote dispersal and gene flow across the landscape. However, given future climate change projections persistence may be more reliant on the species ability to endure long periods of drought between flood events.

Genotyping by Sequencing and Plastome Analysis Finds High Genetic Variability and Geographical Structure in Dactylis glomerata L. in Northwest Europe Despite Lack of Ploidy Variation

Large collections of the forage and bioenergy grass Dactylis glomerata were made in northwest (NW) Europe along east to west and north to south clines for genetic resource conservation and to inform breeding programmes of genetic diversity, genepools, and ploidy. Leaves were sampled for genetic analysis and seed and rhizome for ex-situ conservation. Genotyping by sequencing (GBS) was used to assay nuclear DNA diversity and plastome single nucleotide polymorphism (SNP) discovery was undertaken using a long-read PCR and MiSeq approach. Nuclear and plastid SNPs were analysed by principal component analysis (PCA) to compare genotypes. Flow cytometry revealed that all samples were tetraploid, but some genome size variation was recorded. GBS detected an average of approximately 10,000 to 15,000 SNPs per country sampled. The highest average number of private SNPs was recorded in Poland (median ca. 2000). Plastid DNA variation was also high (1466 SNPs, 17 SNPs/kbp). GBS data, and to a lesser extent plastome data, also show that genetic variation is structured geographically in NW Europe with loose clustering matching the country of plant origin. The results reveal extensive genetic diversity and genetic structuring in this versatile allogamous species despite lack of ploidy variation and high levels of human mediated geneflow via planting.

Analysis of the genetic diversity and population structure of Salix psammophila based on phenotypic traits and simple sequence repeat markers

Salix psammophila (desert willow) is a shrub endemic to the Kubuqi Desert and the Mu Us Desert, China, that plays an important role in maintaining local ecosystems and can be used as a biomass feedstock for biofuels and bioenergy. However, the lack of information on phenotypic traits and molecular markers for this species limits the study of genetic diversity and population structure. In this study, nine phenotypic traits were analyzed to assess the morphological diversity and variation. The mean coefficient of variation of 17 populations ranged from 18.35% (branch angle (BA)) to 38.52% (leaf area (LA)). Unweighted pair-group method with arithmetic mean analysis of nine phenotypic traits of S. psammophila showed the same results, with the 17 populations clustering into five groups. We selected 491 genets of the 17 populations to analyze genetic diversity and population structure based on simple sequence repeat (SSR) markers. Analysis of molecular variance (AMOVA) revealed that most of the genetic variance (95%) was within populations, whereas only a small portion (5%) was among populations. Moreover, using the animal model with SSR-based relatedness estimated of S. psammophila, we found relatively moderate heritability values for phenotypic traits, suggesting that most of trait variation were caused by environmental or developmental variation. Principal coordinate and phylogenetic analyses based on SSR data revealed that populations P1, P2, P9, P16, and P17 were separated from the others. The results showed that the marginal populations located in the northeastern and southwestern had lower genetic diversity, which may be related to the direction of wind. These results provide a theoretical basis for germplasm management and genetic improvement of desert willow.

Comparative Analysis of the Complete Chloroplast Genomes of Four Aconitum Medicinal Species

Aconitum (Ranunculaceae) consists of approximately 400 species distributed in the temperate regions of the northern hemisphere. Many species are well-known herbs, mainly used for analgesia and anti-inflammatory purposes. This genus is well represented in China and has gained widespread attention for its toxicity and detoxification properties. In southwestern China, several Aconitum species, called ‘Dula’ in the Yi Nationality, were often used to control the poisonous effects of other Aconitum plants. In this study, the complete chloroplast (cp) genomes of these species were determined for the first time through Illumina paired-end sequencing. Our results indicate that their cp genomes ranged from 151,214 bp (A. episcopale) to 155,769 bp (A. delavayi) in length. A total of 111–112 unique genes were identified, including 85 protein-coding genes, 36–37 tRNA genes and eight ribosomal RNA genes (rRNA). We also analyzed codon usage, IR expansion or contraction and simple sequence repeats in the cp genomes. Eight variable regions were identified and these may potentially be useful as specific DNA barcodes for species identification of Aconitum. Phylogenetic analysis revealed that all five studied species formed a new clade and were resolved with 100% bootstrap support. This study will provide genomic resources and potential plastid markers for DNA barcoding, further taxonomy and germplasm exploration of Aconitum.

Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P. subaequalis, as well as identified the polymorphic chloroplast microsatellites (cpSSRs), nuclear microsatellites (nSSRs) and mutational hotspots of chloroplast. Ten polymorphic cpSSR loci and 12 polymorphic nSSR loci were used to genotype 96 individuals of P. subaequalis from six populations to estimate genetic diversity and population structure. Our results revealed that P. subaequalis exhibited abundant genetic diversity (e.g., cpSSRs: Hcp = 0.862; nSSRs: HT = 0.559) and high genetic differentiation (e.g., cpSSRs: RST = 0.652; nSSRs: RST = 0.331), and characterized by a low pollen-to-seed migration ratio (r ≈ 1.78). These genetic patterns are attributable to its long evolutionary histories and low levels of contemporary inter-population gene flow by pollen and seed. In addition, lack of isolation-by-distance pattern and strong population genetic structuring in both marker systems, suggests that long-term isolation and/or habitat fragmentation as well as genetic drift may have also contributed to the geographic differentiation of P. subaequalis. Therefore, long-term habitat protection is the most important methods to prevent further loss of genetic variation and a decrease in effective population size. Furthermore, both cpSSRs and nSSRs revealed that P. subaequalis populations consisted of three genetic clusters, which should be considered as separated conservation units.

The Complete Chloroplast Genome of Chinese Bayberry (Morella rubra, Myricaceae): Implications for Understanding the Evolution of Fagales

Morella rubra (Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry's domestication are still unresolved. In this study, we report the chloroplast (cp) genome of M. rubra and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three M. rubra individuals were 159,478, 159,568, and 159.586 bp in length, respectively, comprising a pair of inverted repeat (IR) regions (26,014-26,069 bp) separated by a large single-copy (LSC) region (88,683-88,809 bp) and a small single-copy (SSC) region (18,676-18,767 bp). Each cp genome encodes the same 111 unique genes, consisting of 77 different protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes, with 18 duplicated in the IRs. Comparative analysis of chloroplast genomes from four representative Fagales families revealed the loss of infA and the pseudogenization of ycf15 in all analyzed species, and rpl22 has been pseudogenized in M. rubra and Castanea mollissima, but not in Juglans regia or Ostrya rehderiana. The genome size variations are detected mainly due to the length of intergenic spacers rather than gene loss, gene pseudogenization, IR expansion or contraction. The phylogenetic relationships yielded by the complete genome sequences strongly support the placement of Myricaceae as sister to Juglandaceae. Furthermore, seven cpDNA markers (trnH-psbA, psbA-trnK, rps2-rpoC2, ycf4-cemA, petD-rpoA, ndhE-ndhG, and ndhA intron) with relatively high levels of variation and variable cpSSR loci were identified within M. rubra, which will be useful in future research characterizing the population genetics of M. rubra and investigating the origin of domesticated Chinese bayberry.

De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila

Salix psammophila, a sandy shrub known as desert willow, is regarded as a potential biomass feedstock and plays an important role in maintaining local ecosystems. However, a lack of genomic data and efficient molecular markers limit the study of its population evolution and genetic breeding. In this study, chromosome counts, flow cytometry and SSR analyses indicated that S. psammophila is tetraploid. A total of 6,346 EST-SSRs were detected based on 71,458 de novo assembled unigenes from transcriptome data. Twenty-seven EST-SSR markers were developed to evaluate the genetic diversity and population structure of S. psammophila from eight natural populations in Northern China. High levels of genetic diversity (mean 10.63 alleles per locus; mean HE 0.689) were dectected in S. psammophila. The weak population structure and little genetic differentiation (pairwise FST = 0.006-0.016) were found among Population 1-Population 7 (Pop1-Pop7; Inner Mongolia and Shaanxi), but Pop8 (Ningxia) was clearly separated from Pop1-Pop7 and moderate differentiation (pairwise FST = 0.045-0.055) was detected between them, which may be influenced by local habitat conditions. Molecular variance analyses indicated that most of the genetic variation (94.27%) existed within populations. These results provide valuable genetic informations for natural resource conservation and breeding programme optimisation of S. psammophila.

Genetic Diversity and Population Structure in Vicia faba L. Landraces and Wild Related Species Assessed by Nuclear SSRs

Faba bean (Vicia faba L.) is a facultative cross-pollinating legume crop with a great importance for food and feed due to its high protein content as well as the important role in soil fertility and nitrogen fixation. In this work we evaluated genetic diversity and population structure of faba bean accessions from the Western Mediterranean basin and wild related species. For that purpose we screened 53 V. faba, 2 V. johannis and 7 V. narbonensis accessions from Portugal, Spain and Morocco with 28 faba bean Single Sequence Repeats (SSR). SSR genotyping showed that the number of alleles detected per locus for the polymorphic markers ranged between 2 and 10, with Polymorphic Information Content (PIC) values between 0.662 and 0.071, and heterozygosity (H_O) between 0–0.467. Heterozygosity and inbreeding coefficient levels indicate a higher level of inbreeding in wild related species than in cultivated Vicia. The analysis of molecular variance (AMOVA) showed a superior genetic diversity within accessions than between accessions even from distant regions. These results are in accordance to population structure analysis showing that individuals from the same accession can be genetically more similar to individuals from far away accessions, than from individuals from the same accession. In all three levels of analysis (whole panel of cultivated and wild accessions, cultivated faba bean accessions and Portuguese accessions) no population structure was observed based on geography or climatic factors. Differences between V. narbonensis and V. johannis are undetectable although these wild taxa are clearly distinct from V. faba accessions. Thus, a limited gene flow occurred between cultivated accessions and wild relatives. Contrastingly, the lack of population structure seems to indicate a high degree of gene flow between V. faba accessions, possibly explained by the partially allogamous habit in association with frequent seed exchange/introduction.

Male and Female Subpopulations of Salix viminalis Present High Genetic Diversity and High Long-Term Migration Rates between Them

Dioecy distributed in 157 flowering plant families and 959 flowering plant genera. Morphological and physiological differences between male and female plants have been studied extensively, but studies of sex-specific genetic diversity are relatively scarce in dioecious plants. In this study, 20 SSR loci were employed to examine the genetic variance of male subpopulations and female subpopulations in Salix viminalis. The results showed that all of the markers were polymorphic (Na = 14.15, He = 0.7566) and workable to reveal the genetic diversity of S. viminalis. No statistically significant difference was detected between male and female subpopulations, but the average genetic diversity of male subpopulations (Na = 7.12, He = 0.7071) and female subpopulations (Na = 7.31, He = 0.7226) were high. Under unfavorable environments (West Liao basin), the genetic diversity between male and female subpopulations was still not significantly different, but the genetic diversity of sexual subpopulations were lower. The differentiation of the ten subpopulations in S. viminalis was moderate (FST = 0.0858), which was conformed by AMOVA that most of genetic variance (94%) existed within subpopulations. Pairwise FST indicated no differentiation between sexual subpopulations, which was accompanied by high long-term migrate between them (M = 0.73~1.26). However, little recent migration was found between sexual subpopulations. Therefore, artificial crossing or/and transplantation by cutting propagation should be carried out so as to increase the migration during the process of ex situ conservation.

The use of Hardy-Weinberg Equilibrium in clonal plant systems

Traditionally population genetics precludes the use of the same genetic individual more than once in Hardy-Weinberg (HW) based calculations due to the model's explicit assumptions. However, when applied to clonal plant populations this can be difficult to do, and in some circumstances, it may be ecologically informative to use the ramet as the data unit. In fact, ecologists have varied the definition of the individual from a strict adherence to a single data point per genotype to a more inclusive approach of one data point per ramet. With the advent of molecular tools, the list of facultatively clonal plants and the recognition of their ecological relevance grows. There is an important risk of misinterpretation when HW calculations are applied to a clonal plant not recognized as clonal, as well as when the definition of the individual for those calculations is not clearly stated in a known clonal species. Focusing on heterozygosity values, we investigate cases that demonstrate the extreme range of potential modeling outcomes and describe the different contexts where a particular definition could better meet ecological modeling goals. We emphasize that the HW model can be ecologically relevant when applied to clonal plants, but caution is necessary in how it is used, reported, and interpreted. We propose that in known clonal plants, both genotype (GHet) and ramet (RHet) based calculations are reported to define the full range of potential values and better facilitate cross-study comparisons.