Using RAD‐seq to develop sex‐linked markers in a haplodiplontic alga

For many taxa, including isomorphic haplodiplontic macroalgae, determining sex and ploidy is challenging, thereby limiting the scope of some population demographic and genetic studies. Here, we used double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) to identify sex‐linked molecular markers in the widespread red alga Agarophyton vermiculophyllum. In the ddRAD‐seq library, we included 10 female gametophytes, 10 male gametophytes, and 16 tetrasporophytes from one native and one non‐native site (N = 40 gametophytes and N = 32 tetrasporophytes total). We identified seven putatively female‐linked and 19 putatively male‐linked sequences. Four female‐ and eight male‐linked markers amplified in all three life cycle stages. Using one female‐ and one male‐linked marker that were sex‐specific, we developed a duplex PCR and tested the efficacy of this assay on a subset of thalli sampled at two sites in the non‐native range. We confirmed ploidy based on the visual observation of reproductive structures and previous microsatellite genotyping at 10 polymorphic loci. For 32 vegetative thalli, we were able to assign sex and confirm ploidy in these previously genotyped thalli. These markers will be integral to ongoing studies of A. vermiculophyllum invasion. We discuss the utility of RAD‐seq over other approaches previously used, such as RAPDs (random amplified polymorphic DNA), for future work designing sex‐linked markers in other haplodiplontic macroalgae for which genomes are lacking.     

ROI-Based Compression Strategy of 3D MRI Brain Datasets for Wireless Communications

ObjectivesBecause of the large amount of medical imaging data, the transmission process becomes complicated in telemedicine applications. Thus, in order to adapt the data bit streams to the constraints related to the limitation of the bandwidths a reduction of the size of the data by compression of the images is essential. Despite the improvements in the field of compression, the transmission itself can also introduce errors. For this reason, it is important to develop an adequate strategy which will help reduce this volume of data without having to introduce some distortion and resist the errors introduced by the channel noise during transmission. Thus, in this paper, we propose a ROI-based coding strategy and unequal bit stream protection to meet this dual constraint.Material and methodsThe proposed ROI-based compression strategy with unequal bit stream protection is composed of three parts: the first one allows the extraction of the ROI region, the second one consists of a ROI-based coding and the third one allows an unequal protection of the ROI bit stream.First, the Regions Of Interest (ROI) are extracted by hierarchical segmentation of these regions according to a segmentation method based on the technique of Marker-based-watershed combined with the technique of active contours by level set. The resulting regions are selectively encoded by a 3D coder based on a shape adaptive discrete wavelet transform 3D-BISK, where the compression ratio of each region depends on its relevance in diagnosis. These obtained regions of interest are protected with an error-correcting code of Reed-Solomon type with a code rate that varies according to the relevance of the region by an unequal protection strategy (UEP).ResultsThe performance of the proposed compression scheme is evaluated in several ways. First, tests are performed to study the impact of errors on the different bit streams. In the first place, these tests are carried out in order to study the effect of the variation of the compression rates on the different bit streams. Secondly, different Reed Solomon error-correcting codes of different code rates are tested at different compression rates on a BSC channel. Finally, the performances of this coding strategy are compared with those of SPIHT 3D in the case of transmission on a BSC channel.ConclusionThe obtained results show that the proposed method is quite efficient in transmission time reduction. Therefore, our proposed scheme will reduce the volume of data without having to introduce some distortion and resist the errors introduced by the channel noise in the case of telemedicine.