Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing 400715, China.
Department of Entomology, College of Plant Protection, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, Jiangsu 210095, China.
Gigascience. 2021 Mar 19;10(3). doi: 10.1093/gigascience/giab016.
The spider Trichonephila antipodiana (Araneidae), commonly known as the batik golden web spider, preys on arthropods with body sizes ranging from ∼2 mm in length to insects larger than itself (>20‒50 mm), indicating its polyphagy and strong dietary detoxification abilities. Although it has been reported that an ancient whole-genome duplication event occurred in spiders, lack of a high-quality genome has limited characterization of this event.
We present a chromosome-level T. antipodiana genome constructed on the basis of PacBio and Hi-C sequencing. The assembled genome is 2.29 Gb in size with a scaffold N50 of 172.89 Mb. Hi-C scaffolding assigned 98.5% of the bases to 13 pseudo-chromosomes, and BUSCO completeness analysis revealed that the assembly included 94.8% of the complete arthropod universal single-copy orthologs (n = 1,066). Repetitive elements account for 59.21% of the genome. We predicted 19,001 protein-coding genes, of which 96.78% were supported by transcriptome-based evidence and 96.32% matched protein records in the UniProt database. The genome also shows substantial expansions in several detoxification-associated gene families, including cytochrome P450 mono-oxygenases, carboxyl/cholinesterases, glutathione-S-transferases, and ATP-binding cassette transporters, reflecting the possible genomic basis of polyphagy. Further analysis of the T. antipodiana genome architecture reveals an ancient whole-genome duplication event, based on 2 lines of evidence: (i) large-scale duplications from inter-chromosome synteny analysis and (ii) duplicated clusters of Hox genes.
The high-quality T. antipodiana genome represents a valuable resource for spider research and provides insights into this species' adaptation to the environment.
蜘蛛 Trichonephila antipodiana（Araneidae），通常被称为蜡染金蛛，捕食的节肢动物体长从约 2 毫米到比自身大的昆虫（>20-50 毫米）不等，表明其杂食性和强大的膳食解毒能力。尽管已经报道蜘蛛中发生了一次古老的全基因组复制事件，但缺乏高质量的基因组限制了对该事件的特征描述。
我们提出了一个基于 PacBio 和 Hi-C 测序构建的 Trichonephila antipodiana 染色体水平基因组。组装的基因组大小为 2.29 Gb，支架 N50 为 172.89 Mb。Hi-C 支架将 98.5%的碱基分配到 13 条假染色体上，BUSCO 完整性分析表明，组装包括 94.8%的完整节肢动物通用单拷贝直系同源物（n = 1,066）。重复元件占基因组的 59.21%。我们预测了 19,001 个蛋白质编码基因，其中 96.78%得到了转录组证据的支持，96.32%与 UniProt 数据库中的蛋白质记录匹配。该基因组在几个解毒相关基因家族中也显示出大量扩张，包括细胞色素 P450 单加氧酶、羧酸酯酶/胆碱酯酶、谷胱甘肽 S-转移酶和 ATP 结合盒转运蛋白，反映了其可能的多食性的基因组基础。对 Trichonephila antipodiana 基因组结构的进一步分析表明，基于 2 条证据存在一次古老的全基因组复制事件：（i）从染色体间同线性分析推断出的大规模重复，以及（ii）Hox 基因的重复簇。
高质量的 Trichonephila antipodiana 基因组为蜘蛛研究提供了有价值的资源，并为该物种对环境的适应提供了新的见解。
