From tetraploid to diploid, a pangenomic approach to identify genes lost during synthetic diploidization of Eragrostis curvula.
From tetraploid to diploid, a pangenomic approach to identify genes lost during synthetic diploidization of Eragrostis curvula.
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DOI：
10.3389/fpls.2023.1133986
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发表时间：
2023
影响因子：
5.6
通讯作者：
Echenique, Viviana
中科院分区：
文献类型：
--
作者：
Carballo, Jose;Bellido, Andres Martin;Selva, Juan Pablo;Zappacosta, Diego;Gallo, Cristian Andres;Albertini, Emidio;Caccamo, Mario;Echenique, Viviana
在画眉草（通常称为哭泣爱情草）中，兼性无融合生殖四倍体坦噶尼喀 INTA cv 的合成二倍化事件。起源于有性二倍体维多利亚品种。无融合生殖是种子的无性繁殖，其中后代在遗传上与母体植物相同。为了评估与倍性和二倍化过程中发生的繁殖模式相关的基因组变化，采用作图方法获得了第一个 E. curvula 全基因组组装。通过这种方式，提取了坦噶尼喀 INTA 的 gDNA，并在 2x250 Illumina 双端读数中进行测序，并针对维多利亚基因组组装进行映射。未映射的读数用于变体调用，而映射的读数则使用 Masurca 软件进行组装。组装长度为 28,982,419 bp，分布在 18,032 个重叠群中，这些重叠群中注释的可变基因呈现出 3,952 个基因模型。基因的功能注释表明生殖途径存在差异富集。对坦噶尼喀 INTA 和维多利亚的 gDNA 和 cDNA 进行 PCR 扩增，以验证与繁殖和倍性相关的 5 个基因是否存在变异。坦噶尼喀 INTA 基因组的多倍体性质也通过变异调用分析进行了评估，显示单核苷酸多态性 (SNP) 覆盖度和等位基因频率分布以及分段异源四倍体配对行为。这里提出的结果表明，在为抑制无融合生殖途径而进行的二倍化过程中，坦噶尼喀 INTA 中的基因丢失，严重影响了维多利亚品种的育性。
In Eragrostis curvula, commonly known as weeping lovegrass, a synthetic diploidization event of the facultative apomictic tetraploid Tanganyika INTA cv. originated from the sexual diploid Victoria cv. Apomixis is an asexual reproduction by seeds in which the progeny is genetically identical to the maternal plant. To assess the genomic changes related to ploidy and to the reproductive mode occurring during diploidization, a mapping approach was followed to obtain the first E. curvula pangenome assembly. In this way, gDNA of Tanganyika INTA was extracted and sequenced in 2x250 Illumina pair-end reads and mapped against the Victoria genome assembly. The unmapped reads were used for variant calling, while the mapped reads were assembled using Masurca software. The length of the assembly was 28,982,419 bp distributed in 18,032 contigs, and the variable genes annotated in these contigs rendered 3,952 gene models. Functional annotation of the genes showed that the reproductive pathway was differentially enriched. PCR amplification in gDNA and cDNA of Tanganyika INTA and Victoria was conducted to validate the presence/absence variation in five genes related to reproduction and ploidy. The polyploid nature of the Tanganyika INTA genome was also evaluated through the variant calling analysis showing the single nucleotide polymorphism (SNP) coverage and allele frequency distribution with a segmental allotetraploid pairing behavior. The results presented here suggest that the genes were lost in Tanganyika INTA during the diploidization process that was conducted to suppress the apomictic pathway, affecting severely the fertility of Victoria cv.
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影响因子：
4.2
作者：
Dolezel, J;Greilhuber, J;Obermayer, R
通讯作者：
Obermayer, R
影响因子：
2
作者：
Christensen, JR;Borrino, E;Andersen, SB
通讯作者：
Andersen, SB
影响因子：
16.6
作者：
Golicz, Agnieszka A.;Bayer, Philipp E.;Barker, Guy C.;Edger, Patrick P.;Kim, HyeRan;Martinez, Paula A.;Chan, Chon Kit Kenneth;Severn-Ellis, Anita;McCombie, W. Richard;Parkin, Isobel A. P.;Paterson, Andrew H.;Pires, J. Chris;Sharpe, Andrew G.;Tang, Haibao;Teakle, Graham R.;Town, Christopher D.;Batley, Jacqueline;Edwards, David
通讯作者：
Edwards, David
影响因子：
5.6
作者：
通讯作者：
--
DOI：
10.1073/pnas.0705998104
发表时间：
2007-11-20
影响因子：
11.1
作者：
Hartung, Frank;Suer, Stefanie;Puchta, Holger
通讯作者：
Puchta, Holger