Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, 38106, Braunschweig, Germany.
New Phytol. 2024 Jan;241(1):471-489. doi: 10.1111/nph.19341. Epub 2023 Oct 28.
In this study, we investigate the genetic mechanisms responsible for the loss of anthocyanins in betalain-pigmented Caryophyllales, considering our hypothesis of multiple transitions to betalain pigmentation. Utilizing transcriptomic and genomic datasets across 357 species and 31 families, we scrutinize 18 flavonoid pathway genes and six regulatory genes spanning four transitions to betalain pigmentation. We examined evidence for hypotheses of wholesale gene loss, modified gene function, altered gene expression, and degeneration of the MBW (MYB-bHLH-WD40) trasnscription factor complex, within betalain-pigmented lineages. Our analyses reveal that most flavonoid synthesis genes remain conserved in betalain-pigmented lineages, with the notable exception of TT19 orthologs, essential for the final step in anthocyanidin synthesis, which appear to have been repeatedly and entirely lost. Additional late-stage flavonoid pathway genes upstream of TT19 also manifest strikingly reduced expression in betalain-pigmented species. Additionally, we find repeated loss and alteration in the MBW transcription complex essential for canonical anthocyanin synthesis. Consequently, the loss and exclusion of anthocyanins in betalain-pigmented species appear to be orchestrated through several mechanisms: loss of a key enzyme, downregulation of synthesis genes, and degeneration of regulatory complexes. These changes have occurred iteratively in Caryophyllales, often coinciding with evolutionary transitions to betalain pigmentation.
在这项研究中,我们调查了负责甜菜色素类黄酮苷类物质丧失的遗传机制,考虑到我们关于多次向甜菜色素类物质演化的假说。利用 357 个物种和 31 个科的转录组和基因组数据集,我们仔细研究了 18 个类黄酮途径基因和 6 个调控基因,这些基因跨越了向甜菜色素类物质演化的四个阶段。我们检查了关于全基因丢失、修饰基因功能、基因表达改变和 MBW(MYB-bHLH-WD40)转录因子复合物退化假说的证据,这些假说存在于甜菜色素类物质谱系中。我们的分析表明,大多数类黄酮合成基因在甜菜色素类物质谱系中保持保守,除了 TT19 同源物的显著例外,TT19 是类黄酮苷合成的最后一步所必需的,它似乎已经被反复和完全丢失。TT19 上游的晚期类黄酮途径基因也表现出在甜菜色素类物质中表达显著降低。此外,我们发现对经典类黄酮合成至关重要的 MBW 转录复合物也出现了重复的丢失和改变。因此,甜菜色素类物质中类黄酮苷的缺失和排除似乎是通过几种机制协调的:关键酶的丢失、合成基因的下调和调控复合物的退化。这些变化在石竹目中反复发生,通常与向甜菜色素类物质演化的进化转变相吻合。