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重新评估变形虫中巨型基因组的证据。

Re-evaluating evidence for giant genomes in amoebae.

作者信息

Barzilay Daniel, Alcino João P B, Ribeiro Giulia M, Sousa Alfredo L P, Lahr Daniel J G

机构信息

Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil.

Lund University, Department of Bioinformatics, Sölvegatan, Lund, Sweden.

出版信息

Genet Mol Biol. 2024 Dec 20;47Suppl 1(Suppl 1):e20240092. doi: 10.1590/1678-4685-GMB-2024-0092. eCollection 2024.

Abstract

Here we reassess available evidence for the long-held misconception of amoebae possessing exceptionally large genomes. Traditionally, estimates relied on inaccurate methods like DNA weight measurements, leading to inflated sizes. These methods failed to account for contaminating DNA from prey, endosymbionts, and intrinsic genomic features like ribosomal operon amplification. Modern sequencing techniques unveil a different picture. Fully sequenced amoebozoa genomes range from 14.4 to 52.37 mega basepairs, well within the typical single-celled eukaryote expectation. While the whole genome of the historically relevant Amoeba proteus has not yet been fully sequenced, we provide here a statistical analysis using protein-coding genes from transcriptomic data, suggesting that the genome size is consistent with this range, far smaller than previously claimed. The misconception likely originated in the early 21st century and perpetuated through popular science materials. We conclude that there is no longer reason to reaffirm that amoeba genomes are giant.

摘要

在此,我们重新评估了长期以来关于变形虫拥有异常大基因组这一误解的现有证据。传统上,估计依赖于如DNA重量测量等不准确的方法,导致基因组大小被高估。这些方法未能考虑到来自猎物、内共生体的污染DNA以及核糖体操纵子扩增等内在基因组特征。现代测序技术揭示了不同的情况。已完全测序的变形虫基因组范围为1440万至5237万个碱基对,完全在典型单细胞真核生物的预期范围内。虽然具有历史意义的大变形虫的全基因组尚未完全测序,但我们在此使用转录组数据中的蛋白质编码基因进行了统计分析,表明其基因组大小与此范围一致,远小于先前声称的大小。这种误解可能起源于21世纪初,并通过科普材料得以延续。我们得出结论,不再有理由重申变形虫基因组是巨大的。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6bb6/11773323/5c000bd85869/1415-4757-GMB-47-s1-e20240092-gf1.jpg

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