Chromosome-Level Genome Assembly of the Hemiparasitic Taxillus chinensis (DC.) Danser.
Chromosome-Level Genome Assembly of the Hemiparasitic Taxillus chinensis (DC.) Danser.
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半寄生中国红豆杉的染色体水平基因组组装
DOI：
10.1093/gbe/evac060
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发表时间：
2022-05-03
影响因子：
3.3
通讯作者：
Pan, Limei
中科院分区：
文献类型：
--
作者：
Fu, Jine;Wan, Lingyun;Song, Lisha;He, Lili;Jiang, Ni;Long, Hairong;Huo, Juan;Ji, Xiaowen;Hu, Fengyun;Wei, Shugen;Pan, Limei
半寄生丹瑟是一种根寄生药用植物，具有光合作用能力，这是其他寄生植物所失去的。然而，该物种的栽培和医学应用受到该物种的种子的限制，并且尽管已经使用转录组学和蛋白质组学方法研究了这种萌发的分子机制，但是T.中国尚未有报道。因此，本研究的目的是使用纳米孔、短读取和高通量染色体构象捕获测序来构建T.中国人基因组最终的基因组组装长度为521.90 Mb，496.43 Mb（95.12%）可分为9条染色体，重叠群和支架N50值分别为3.80和56.90 Mb。 此外，共预测了33，894个蛋白质编码基因，基因家族聚类确定了11个光系统相关基因家族，从而表明了半寄生植物的特征光合能力。这种染色体水平的T. chinensis为阐明T. chinensis种子和寄生植物光合作用损失的进化。
The hemiparasitic Taxillus chinensis (DC.) Danser is a root-parasitizing medicinal plant with photosynthetic ability, which is lost in other parasitic plants. However, the cultivation and medical application of the species are limited by the recalcitrant seeds of the species, and even though the molecular mechanisms underlying this recalcitrance have been investigated using transcriptomic and proteomic methods, genome resources for T. chinensis have yet to be reported. Accordingly, the aim of the present study was to use nanopore, short-read, and high-throughput chromosome conformation capture sequencing to construct a chromosome-level assembly of the T. chinensis genome. The final genome assembly was 521.90 Mb in length, and 496.43 Mb (95.12%) could be grouped into nine chromosomes with contig and scaffold N50 values of 3.80 and 56.90 Mb, respectively. In addition, a total of 33,894 protein-coding genes were predicted, and gene family clustering identified 11 photosystem-related gene families, thereby indicating photosynthetic ability, which is a characteristic of hemiparasitic plants. This chromosome-level genome assembly of T. chinensis provides a valuable genomic resource for elucidating the genetic basis underlying the recalcitrant characteristics of T. chinensis seeds and the evolution of photosynthesis loss in parasitic plants.
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影响因子：
14.9
作者：
Mistry J;Chuguransky S;Williams L;Qureshi M;Salazar GA;Sonnhammer ELL;Tosatto SCE;Paladin L;Raj S;Richardson LJ;Finn RD;Bateman A
通讯作者：
Bateman A
通过高精度和完整的纠错，高效组装纳米孔读数。
影响因子：
16.6
作者：
Chen Y;Nie F;Xie SQ;Zheng YF;Dai Q;Bray T;Wang YX;Xing JF;Huang ZJ;Wang DP;He LJ;Luo F;Wang JX;Liu YZ;Xiao CL
通讯作者：
Xiao CL
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
5.8
作者：
Johnson, Andrew D.;Handsaker, Robert E.;de Bakker, Paul I. W.
通讯作者：
de Bakker, Paul I. W.
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