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A chromosome-level genome assembly of Pyropia haitanensis (Bangiales, Rhodophyta).
Molecular Ecology Resources ( IF 7.7 ) Pub Date : 2019-11-12 , DOI: 10.1111/1755-0998.13102
Min Cao 1, 2 , Kuipeng Xu 1, 2 , Xinzi Yu 1, 2 , Guiqi Bi 1, 2 , Yang Liu 1, 2 , Fanna Kong 1, 2 , Peipei Sun 1, 2 , Xianghai Tang 1, 2 , Guoying Du 1, 2 , Yuan Ge 1, 2 , Dongmei Wang 1, 2 , Yunxiang Mao 1, 2, 3, 4
Affiliation  

Pyropia haitanensis (Bangiales, Rhodophyta), a major economically important marine crop, is also considered as an ideal research model of Rhodophyta to address several major biological questions such as sexual reproduction and adaptation to intertidal abiotic stresses. However, comparative genomic analysis to decipher the underlying molecular mechanisms is hindered by the lack of high-quality genome information. Therefore, we integrated sequencing data from Illumina short-read sequencing, PacBio single-molecule sequencing and BioNano optical genome mapping. The assembled genome was approximately 53.3 Mb with an average GC% of 67.9%. The contig N50 and scaffold N50 were 510.3 kb and 5.8 Mb, respectively. Additionally, 10 superscaffolds representing 80.9% of the total assembly (42.7 Mb) were anchored and orientated to the 5 linkage groups based on markers and genetic distance; this outcome is consistent with the karyotype of five chromosomes (n = 5) based on cytological observation in P. haitanensis. Approximately 9.6% and 14.6% of the genomic region were interspersed repeat and tandem repeat elements, respectively. Based on full-length transcriptome data generated by PacBio, 10,903 protein-coding genes were identified. The construction of a genome-wide phylogenetic tree demonstrated that the divergence time of P. haitanensis and Porphyra umbilicalis was ~204.4 Ma. Interspecies comparison revealed that 493 gene families were expanded and that 449 were contracted in the P. haitanensis genome compared with those in the Po. umbilicalis genome. The genome identified is of great value for further research on the genome evolution of red algae and genetic adaptation to intertidal stresses.

中文翻译:

坛紫菜(Bangiales,红藻门)的染色体水平基因组组装。

坛紫菜(Pyropia haitanensis,Bangiales,红藻门)是一种重要的经济重要海洋作物,也被认为是红藻门的理想研究模型,可解决有性繁殖和适应潮间带非生物胁迫等几个重大生物学问题。然而,由于缺乏高质量的基因组信息,破译潜在分子机制的比较基因组分析受到阻碍。因此,我们整合了来自 Illumina 短读长测序、PacBio 单分子测序和 BioNano 光学基因组图谱的测序数据。组装的基因组约为 53.3 Mb,平均 GC% 为 67.9%。重叠群 N50 和支架 N50 分别为 510.3 kb 和 5.8 Mb。此外,代表总组装量 (42.7 Mb) 80.9% 的 10 个超级支架根据标记和遗传距离锚定并定向到 5 个连锁组;该结果与基于坛紫菜细胞学观察的5条染色体(n = 5)的核型一致。大约 9.6% 和 14.6% 的基因组区域分别是散布的重复元件和串联重复元件。根据 PacBio 生成的全长转录组数据,鉴定出了 10,903 个蛋白质编码基因。全基因组系统发育树的构建表明坛紫菜和脐紫菜的分化时间约为204.4 Ma。种间比较显示,与鄢鱼相比,坛紫菜基因组中有493个基因家族扩增,449个基因家族收缩。脐带基因组。鉴定出的基因组对于进一步研究红藻基因组进化和潮间带胁迫的遗传适应具有重要价值。
更新日期:2019-11-13
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