ddRAD Sequencing-Based Scanning of Genetic Variants in Sargassum fusiforme

Abstract

Sargassum fusiforme is a commercially important brown seaweed that has experienced significant population reduction both from heavy exploitation and degradation of the environment. Cultivated breed strains are also in a state of population mixing. These population stressors make it necessary to investigate the population genetics to discover best practices to conserve and breed this seaweed. In this study, the genetic diversity and population structure of S. fusiforme were investigated by the genome-wide SNP data acquired from double digest restriction site-associated DNA sequencing (ddRAD-seq). We found a low genetic diversity and a slight population differentiation within and between wild and cultivated populations, and the effective population size of S. fusiforme had experienced a continuous decline. Tajima’s D analysis showed the population contraction in wild populations may be related to copper pollution which showed a consistent trend with the increase of the sea surface temperature. The potential selection signatures may change the timing or level of gene expression, and further experiments are needed to investigate the effect of the mutation on relevant pathways. These results suggest an urgent need to manage and conserve S. fusiforme resources and biodiversity considering the accelerating change of the environment.

Pan-Transcriptome Analysis of Willow Species from Diverse Geographic Distributions

“…The pantranscriptome showed extensive presence/absence variation, with 69.6% of gene families being variable in willows. This number is similar to the report in a pan-genomic study of 16 sorghum cultivars (64%) [23] but smaller than the pan-transcriptome study of 116 Camellia plants (93%) [53]. As reported in the literature, hybridization and polyploidization are quite common in willow species [9,10], which may cause challenges for pan-genome and pan-transcriptome analysis.…”

The Structure and Function of the Sargassum fusiforme Microbiome under Different Conditions

“…The analysis of GC content and microbial community has shown that compared with the change in the environment, the effect of genetic information is still limited. Our previous study also showed low genetic diversity within and between S. fusiforme populations [38]. The structure of the S. fusiforme microbiome did not change much in the seawater environmental state after 10 days, which supports the difficulty of degradation in the natural state.…”