Data from: Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploid Arabidopsis kamchatica

Allopolyploidization combines parental genomes and often confers broader species distribution. However, little is known about parentally transmitted gene expression underlying quantitative traits following allopolyploidization because of the complexity of polyploid genomes. The allopolyploid species Arabidopsis kamchatica is a natural hybrid of the zinc hyperaccumulator A. halleri and of the nonaccumulator A. lyrata. We found that A. kamchatica retained the ability to hyperaccumulate zinc from A. halleri and grows in soils with both low and high metal content. Hyperaccumulation of zinc by A. kamchatica was reduced to about half of A. halleri, but is 10-fold greater than A. lyrata. Homeologs derived from A. halleri had significantly higher levels of expression of genes such as HEAVY METAL ATPASE4 (HMA4), METAL TRANSPORTER PROTEIN1 and other metal ion transporters than those derived from A. lyrata, which suggests cis-regulatory differences. A. kamchatica has on average half the expression of these genes compared with A. halleri due to fixed heterozygosity inherent in allopolyploids. Zinc treatment significantly changed the ratios of expression of 1% of homeologous pairs, including genes putatively involved in metal homeostasis. Resequencing data showed a significant reduction in genetic diversity over a large genomic region (290 kb) surrounding the HMA4 locus derived from the A. halleri parent compared with the syntenic A. lyrata-derived region, which suggests different evolutionary histories. We also estimated that three A. halleri-derived HMA4 copies are present in A. kamchatica. Our findings support a transcriptomic model in which environment-related transcriptional patterns of both parents are conserved but attenuated in the allopolyploids.

异源多倍化（allopolyploidization）可整合双亲基因组，通常能赋予物种更广泛的分布范围。然而，由于多倍体基因组的复杂性，学界对异源多倍化后数量性状背后的亲本传递型基因表达模式仍知之甚少。堪察加拟南芥（Arabidopsis kamchatica）是锌超富集植物拟南芥A. halleri与非富集植物拟南芥A. lyrata的天然杂交异源多倍体物种。研究发现，堪察加拟南芥保留了源自A. halleri的锌超富集能力，可在金属含量高低各异的土壤中生长；其锌超富集能力降至A. halleri的约一半，但仍比A. lyrata高出10倍。源自A. halleri的部分同源基因（homeologs），其编码的重金属ATP酶4（HEAVY METAL ATPASE4, HMA4）、金属转运蛋白1（METAL TRANSPORTER PROTEIN1, MTP1）及其他金属离子转运蛋白的表达水平，显著高于源自A. lyrata的对应部分同源基因，这提示二者存在顺式调控差异。受异源多倍体固有的固定杂合性影响，堪察加拟南芥上述基因的平均表达量仅为A. halleri的一半。锌处理显著改变了1%的部分同源基因对的表达比例，其中包含推测参与金属稳态（metal homeostasis）的基因。重测序数据显示，相较于同线性（syntenic）的A. lyrata来源基因组区域，A. halleri亲本来源的HMA4位点周围的大片基因组区域（290 kb）内遗传多样性显著降低，这表明二者具有不同的进化历史。研究还估算出，堪察加拟南芥中存在3个源自A. halleri的HMA4拷贝。本研究结果支持如下转录组学模型：异源多倍体保留了双亲的环境相关转录模式，但该模式在多倍体中被弱化。