A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event.
A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event.
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DOI：
10.1093/gigascience/giab016
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发表时间：
2021-03-19
期刊：
影响因子：
9.2
通讯作者：
Zhang ZS
中科院分区：
文献类型：
--
作者：
Fan Z;Yuan T;Liu P;Wang LY;Jin JF;Zhang F;Zhang ZS
反足毛蛛Trichonephila antipodiana（Araneidae），俗称蜡染金网蛛，捕食的节肢动物体长从1.2 ~ 2.2 mm到大于自身的昆虫（>20 ~ 50 mm），表明其多食性和较强的食物解毒能力。虽然有报道称蜘蛛中发生了一次古老的全基因组复制事件，但由于缺乏高质量的基因组，这一事件的特征受到限制。我们提出了一个染色体水平的T基于PacBio和Hi-C测序构建的antipodiana基因组。组装的基因组大小为2.29 Gb，支架N50为172.89 Mb。Hi-C scaffolding将98.5%的碱基分配给13条假染色体，BUSCO完整性分析显示该组装包括94.8%的完整节肢动物通用单拷贝直系同源物（n = 1，066）。重复序列占基因组的59.21%。我们预测了19，001个蛋白质编码基因，其中96.78%得到了基于转录组的证据的支持，96.32%与UniProt数据库中的蛋白质记录匹配。基因组还显示出在几个解毒相关的基因家族，包括细胞色素P450单加氧酶，羧基/胆碱酯酶，谷胱甘肽-S-转移酶，和ATP结合盒转运蛋白，反映了可能的基因组基础的多食。对T. antipodiana基因组结构揭示了一个古老的全基因组复制事件，基于2条证据：（i）来自染色体间同线性分析的大规模复制和（ii）Hox基因的复制簇。高质量的T。antipodiana基因组是蜘蛛研究的宝贵资源，并为了解该物种对环境的适应提供了见解。
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.
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影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
64.8
作者：
Aury, Jean-Marc;Jaillon, Olivier;Wincker, Patrick
通讯作者：
Wincker, Patrick
影响因子：
9.3
作者：
Durand NC;Shamim MS;Machol I;Rao SS;Huntley MH;Lander ES;Aiden EL
通讯作者：
Aiden EL
影响因子：
4.4
作者：
Gendreau KL;Haney RA;Schwager EE;Wierschin T;Stanke M;Richards S;Garb JE
通讯作者：
Garb JE
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T