A first AFLP-based genetic linkage map for brine shrimp Artemia franciscana and its application in mapping the sex locus

We report on the construction of sex-specific linkage maps, the identification of sex-linked markers and the genome size estimation for the brine shrimp Artemia franciscana. Overall, from the analysis of 433 AFLP markers segregating in a 112 full-sib family we identified 21 male and 22 female linkage groups (2n = 42), covering 1,041 and 1,313 cM respectively. Fifteen putatively homologous linkage groups, including the sex linkage groups, were identified between the female and male linkage map. Eight sex-linked AFLP marker alleles were inherited from the female parent, supporting the hypothesis of a WZ-ZZ sex-determining system. The haploid Artemia genome size was estimated to 0.93 Gb by flow cytometry. The produced Artemia linkage maps provide the basis for further fine mapping and exploring of the sex-determining region and are a possible marker resource for mapping genomic loci underlying phenotypic differences among Artemia species

Development of a groundwater quality index for seawater intrusion in coastal aquifers

Coastal aquifers are increasingly threatened by seawater intrusion due to increased urbanization, groundwater exploitation, and global sea-level rise. Pattern diagrams, which constitute the outcome of several hydro-geochemical processes, have traditionally been used to characterize vulnerability to seawater intrusion. However, the formats of such diagrams do not facilitate the geospatial analysis of groundwater quality, thus limiting the ability of spatio-temporal mapping and monitoring. This raises the need to transform the information from current pattern diagrams into a format that can be readily used under a GIS framework to define vulnerable areas prone to seawater intrusion. In this study, a groundwater quality index specific to seawater intrusion (GQISWI) was developed for the purpose of aggregating data into a comprehensible format that allows spatial analysis. The index was evaluated with data from various coastal regions worldwide and then applied at a pilot karstic aquifer along the eastern coast of the Mediterranean Sea

GIS-based assessment for the development of a groundwater quality index towards sustainable aquifer management

This study aims at developing Groundwater Quality Indices (GQIs) that constitute a reliable tool in defining aquifer vulnerability. For this purpose, water quality sampling campaigns were conducted on 60 groundwater wells during most vulnerable periods of early and late summer to ensure the representativeness of the targeted GQI under worst case conditions. The samples were tested for various water quality indicators, which were then used to develop the GQIs through GIS-based mapping with spatial geostatistical analysis. The results contribute in filling a gap in GQI definition and form a basis for planning effective water quality management towards sustainable exploitation of groundwater resources particularly during summer periods when recharge is limited

GIS-based assessment for the development of a groundwater quality index towards sustainable aquifer management

This study aims at developing Groundwater Quality Indices (GQIs) that constitute a reliable tool in defining aquifer vulnerability. For this purpose, water quality sampling campaigns were conducted on 60 groundwater wells during most vulnerable periods of early and late summer to ensure the representativeness of the targeted GQI under worst case conditions. The samples were tested for various water quality indicators, which were then used to develop the GQIs through GIS-based mapping with spatial geostatistical analysis. The results contribute in filling a gap in GQI definition and form a basis for planning effective water quality management towards sustainable exploitation of groundwater resources particularly during summer periods when recharge is limited

High Satellite Repeat Turnover in Great Apes Studied with Short- And Long-Read Technologies

Satellite repeats are a structural component of centromeres and telomeres, and in some instances, their divergence is known to drive speciation. Due to their highly repetitive nature, satellite sequences have been understudied and underrepresented in genome assemblies. To investigate their turnover in great apes, we studied satellite repeats of unit sizes up to 50 bp in human, chimpanzee, bonobo, gorilla, and Sumatran and Bornean orangutans, using unassembled short and long sequencing reads. The density of satellite repeats, as identified from accurate short reads (Illumina), varied greatly among great ape genomes. These were dominated by a handful of abundant repeated motifs, frequently shared among species, which formed two groups: 1) the (AATGG)n repeat (critical for heat shock response) and its derivatives; and 2) subtelomeric 32-mers involved in telomeric metabolism. Using the densities of abundant repeats, individuals could be classified into species. However, clustering did not reproduce the accepted species phylogeny, suggesting rapid repeat evolution. Several abundant repeats were enriched in males versus females; using Y chromosome assemblies or Fluorescent In Situ Hybridization, we validated their location on the Y. Finally, applying a novel computational tool, we identified many satellite repeats completely embedded within long Oxford Nanopore and Pacific Biosciences reads. Such repeats were up to 59 kb in length and consisted of perfect repeats interspersed with other similar sequences. Our results based on sequencing reads generated with three different technologies provide the first detailed characterization of great ape satellite repeats, and open new avenues for exploring their functions