Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA.
Department of Evolution, Ecology, and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA.
Genes (Basel). 2021 Nov 9;12(11):1777. doi: 10.3390/genes12111777.
The de novo birth of functional genes from non-coding DNA as an important contributor to new gene formation is increasingly supported by evidence from diverse eukaryotic lineages. However, many uncertainties remain, including how the incipient de novo genes would continue to evolve and the molecular mechanisms underlying their evolutionary trajectory. Here we address these questions by investigating evolutionary history of the de novo antifreeze glycoprotein (AFGP) gene and gene family in gadid (codfish) lineages. We examined AFGP phenotype on a phylogenetic framework encompassing a broad sampling of gadids from freezing and non-freezing habitats. In three select species representing different AFGP-bearing clades, we analyzed all AFGP gene family members and the broader scale genomic regions in detail. Codon usage analyses suggest that motif duplication produced the intragenic AFGP tripeptide coding repeats, and rapid sequence divergence post-duplication stabilized the recombination-prone long repetitive coding region. Genomic loci analyses support originated once from a single ancestral genomic origin, and shed light on how the de novo gene proliferated into a gene family. Results also show the processes of gene duplication and gene loss are distinctive in separate clades, and both genotype and phenotype are commensurate with differential local selective pressures.
从头产生的功能性基因来自非编码 DNA，这是新基因形成的一个重要贡献，越来越多的证据支持这一观点，这些证据来自不同的真核生物谱系。然而，仍有许多不确定性，包括初生的从头基因将如何继续进化以及它们进化轨迹的分子机制。在这里，我们通过研究 Gadid（鳕鱼）谱系中从头抗冻蛋白（AFGP）基因和基因家族的进化历史来解决这些问题。我们在一个包含广泛的冷冻和非冷冻栖息地 Gadid 样本的系统发育框架上检查了 AFGP 表型。在代表不同 AFGP 携带类群的三个选定物种中，我们详细分析了所有 AFGP 基因家族成员和更广泛的基因组区域。密码子使用分析表明，基序重复产生了内含子 AFGP 三肽编码重复，重复后快速的序列分歧稳定了易发生重组的长重复编码区。基因组位点分析支持 AFGP 基因最初从单个祖先基因组起源，这揭示了从头基因如何增殖为基因家族。结果还表明，基因复制和基因丢失的过程在不同的类群中是独特的，基因型和表型与不同的局部选择压力相一致。
