Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
J Phycol. 2020 Oct;56(5):1339-1348. doi: 10.1111/jpy.13035. Epub 2020 Jun 19.
The determination of the ploidy level of an organism is a prerequisite for studies of evolution, cellular function, and genomic construction. Identification of the ploidy of the economically important red alga Gracilariopsis lemaneiformis has been hindered by its small genome and large number of chromosomes. Therefore, in the current study, PloidyNGS, a tool that calculates the number of reads supporting different alleles at each position along the genome sequence, and fluorescence in situ hybridization coupled with tyramide signal amplification (TSA-FISH) were used to clarify the ploidy of G. lemaneiformis. In addition, flow cytometry (FCM) was used to estimate the ploidy of different somatic cells. The PloidyNGS results showed that most of the alleles in the gametophyte were monomorphic, whereas the TSA-FISH results showed that one hybridization signal was observed in gametophytic nuclei and two in tetrasporophytic nuclei when the nuclei were hybridized by single copy gene probes. These results confirmed that G. lemaneiformis is a haploid in the gametophytic generation and diploid in the sporophytic generation. Moreover, the FCM result suggested that G. lemaneiformis was not an endopolyploid. Based on previous studies, we hypothesize that the nuclear number is important for the cellular differentiation and function of this species. We also suggest that G. lemaneiformis evolved from a paleopolyploid, the genome of which has been diploidized, and that traces of genomic doubling are no longer apparent. Thus, this study provides important evidence for further studies on the evolution and genomes of red algae.
确定生物体的倍性水平是研究进化、细胞功能和基因组结构的前提。由于经济上重要的红藻条斑紫菜基因组小且染色体数量多，因此其倍性鉴定一直受到阻碍。因此，在本研究中，使用了 PloidyNGS 工具，该工具可计算在基因组序列的每个位置上支持不同等位基因的读取数，并结合荧光原位杂交（FISH）和酪胺信号扩增（TSA-FISH）来阐明条斑紫菜的倍性。此外，还使用流式细胞术（FCM）来估计不同体细胞的倍性。PloidyNGS 结果表明，配子体中的大多数等位基因都是单态的，而 TSA-FISH 结果表明，当用单拷贝基因探针杂交时，配子体核中观察到一个杂交信号，而四分孢子体核中观察到两个杂交信号。这些结果证实条斑紫菜在配子体世代是单倍体，在孢子体世代是二倍体。此外，FCM 结果表明条斑紫菜不是内多倍体。基于先前的研究，我们假设核数对于该物种的细胞分化和功能很重要。我们还假设条斑紫菜是从一个古多倍体进化而来的，其基因组已经二倍化，并且基因组加倍的痕迹不再明显。因此，这项研究为进一步研究红藻的进化和基因组提供了重要证据。
