Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea

Nonindigenous species pose a major threat for coastal and estuarine ecosystems. Risk management requires genetic information to establish appropriate management units and infer introduction and dispersal routes. We investigated one of the most successful marine invaders, the ctenophore Mnemiopsis leidyi, and used genotyping-by-sequencing (GBS) to explore the spatial population structure in its nonindigenous range in the North Sea. We analyzed 140 specimens collected in different environments, including coastal and estuarine areas, and ports along the coast. Single nucleotide polymorphisms (SNPs) were called in approximately 40 k GBS loci. Population structure based on the neutral SNP panel was significant (F-ST .02; p < .01), and a distinct genetic cluster was identified in a port along the Belgian coast (Ostend port; pairwise F-ST .02-.04; p < .01). Remarkably, no population structure was detected between geographically distant regions in the North Sea (the Southern part of the North Sea vs. the Kattegat/Skagerrak region), which indicates substantial gene flow at this geographical scale and recent population expansion of nonindigenous M. leidyi. Additionally, seven specimens collected at one location in the indigenous range (Chesapeake Bay, USA) were highly differentiated from the North Sea populations (pairwise F-ST .36-.39; p < .01). This study demonstrates the utility of GBS to investigate fine-scale population structure of gelatinous zooplankton species and shows high population connectivity among nonindigenous populations of this recently introduced species in the North Sea. OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at: The DNA sequences generated for this study are deposited in the NCBI sequence read archive under SRA accession numbers -, and will be made publically available upon publication of this manuscript

Variability in the structure of rye flour alkali-extractable arabinoxylans

The variability in rye flour alkali-extractable arabinoxylan (AE-AX) structures was examined by extensive fractionation and enzymic degradation studies. AX were isolated from destarched rye water-unextractables by sequential extraction with saturated barium hydroxide solution, water, 1.0 M sodium hydroxide, and water. The isolated AE-AX contained ca. 51% AX with an arabinose to xylose (A/X) ratio of 0.71. Fractionation of the isolated AE-AX by ethanol precipitation yielded a range of AE-AX fractions containing AX molecules with different A/X ratios and substitution patterns. Degradation of these structurally different AE-AX fractions by an Aspergillus aculeatus endoxylanase (XAA) and a Bacillus subtilis endoxylanase (XBS) resulted in AX fragments with various structural features. Further fractionation of the degraded AE-AX fractions by ethanol precipitation showed that a strong correlation exists between the structural features of the AX fragments, that is, average degree of polymerization (DP) of the xylan backbone, A/X ratio, and substitution pattern. Results indicated that the rye flour AE-AX consist of a continuum of structures rather than of two types of AX or two types of regions in the AX molecule.status: publishe

Temporal changes in genetic diversity and forage yield of perennial ryegrass in monoculture and in combination with red clover in swards

Agricultural grasslands are often cultivated as mixtures of grasses and legumes, and an extensive body of literature is available regarding interspecific interactions, and how these relate to yield and agronomic performance. However, knowledge of the impact of intraspecific diversity on grassland functioning is scarce. We investigated these effects during a 4-year field trial established with perennial ryegrass (Lolium perenne) and red clover (Trifolium pratense). We simulated different levels of intraspecific functional diversity by sowing single cultivars or by combining cultivars with contrasting growth habits, in monospecific or bispecific settings (i.e. perennial ryegrass whether or not in combination with red clover). Replicate field plots were established for seven seed compositions. We determined yield parameters and monitored differences in genetic diversity in the ryegrass component among seed compositions, and temporal changes in the genetic composition and genetic diversity at the within plot level. The composition of cultivars of both species affected the yield and species abundance. In general, the presence of clover had a positive effect on the yield. The cultivar composition of the ryegrass component had a significant effect on the yield, both in monoculture, and in combination with clover. For the genetic analyses, we validated empirically that genotyping-by-sequencing of pooled samples (pool-GBS) is a suitable method for accurate measurement of population allele frequencies, and obtained a dataset of 22,324 SNPs with complete data. We present a method to investigate the temporal dynamics of cultivars in seed mixtures grown under field conditions, and show how cultivar abundances vary during subsequent years. We screened the SNP panel for outlier loci, putatively under selection during the cultivation period, but none were detected.status: publishe

Temporal changes in genetic diversity and forage yield of perennial ryegrass in monoculture and in combination with red clover in swards.

Agricultural grasslands are often cultivated as mixtures of grasses and legumes, and an extensive body of literature is available regarding interspecific interactions, and how these relate to yield and agronomic performance. However, knowledge of the impact of intraspecific diversity on grassland functioning is scarce. We investigated these effects during a 4-year field trial established with perennial ryegrass (Lolium perenne) and red clover (Trifolium pratense). We simulated different levels of intraspecific functional diversity by sowing single cultivars or by combining cultivars with contrasting growth habits, in monospecific or bispecific settings (i.e. perennial ryegrass whether or not in combination with red clover). Replicate field plots were established for seven seed compositions. We determined yield parameters and monitored differences in genetic diversity in the ryegrass component among seed compositions, and temporal changes in the genetic composition and genetic diversity at the within plot level. The composition of cultivars of both species affected the yield and species abundance. In general, the presence of clover had a positive effect on the yield. The cultivar composition of the ryegrass component had a significant effect on the yield, both in monoculture, and in combination with clover. For the genetic analyses, we validated empirically that genotyping-by-sequencing of pooled samples (pool-GBS) is a suitable method for accurate measurement of population allele frequencies, and obtained a dataset of 22,324 SNPs with complete data. We present a method to investigate the temporal dynamics of cultivars in seed mixtures grown under field conditions, and show how cultivar abundances vary during subsequent years. We screened the SNP panel for outlier loci, putatively under selection during the cultivation period, but none were detected

Pooling resources: Allele frequency fingerprinting in <em>Lolium perenne</em>

International audienceAllele frequency fingerprinting of heterogeneous plant populations of outbreeding species can be used for variety identification, association mapping, genomic selection or characterization of genetic resources. In the FACCE-JPI GrassLandscape project, we empirically validated a pool-GBS method for Genome-Wide Allele Frequency Fingerprinting (GWAFF). As pool-GBS cannot be targeted to predefined loci such as candidate genes, we integrated it with targeted resequencing using a highly multiplexed amplicon sequencing strategy to measure allele frequencies (pool-HiPlex). A pool-HiPlex assay was designed that amplifies 185 amplicons in 41 L. perenne genes in just two parallel PCRreactions. We validated pool-GBS and pool-HiPlex using pools of 48 individuals, chosen to represent a wide range of genetic diversity in L. perenne, and addressed completeness, reproducibility and accuracy of allele frequencies with >1000 HiPlex SNPs and >150.000 GBS SNPs. We consistently found high correlations between allele frequencies obtained by genotyping individual plants and pool genotyping on leaf tissue pools and DNA extract pools. We also analyzed the error introduced at various steps of the protocol such as weighing, DNA-quantification, pooling, ligation and/or PCRamplification. Applying a minor allele frequency threshold of 5% or 3% effectively removed nonreproducible SNPs in pool-GBS and pool-HiPlex, respectively. Allele frequency spectra could be obtained for single SNPs as well as for haplotypes spanning neighboring SNPs using read-backed phasing. Application of this methodology to a set of 470 natural populations of L. perenne sampled across Europe and the fertile Crescent revealed a geographical pattern of genetic differentiation in this species