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作者更正:近8000个宏基因组组装基因组的恢复极大地扩展了生命之树。

Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

作者信息

Parks Donovan H, Rinke Christian, Chuvochina Maria, Chaumeil Pierre-Alain, Woodcroft Ben J, Evans Paul N, Hugenholtz Philip, Tyson Gene W

机构信息

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.

出版信息

Nat Microbiol. 2018 Feb;3(2):253. doi: 10.1038/s41564-017-0083-5.

Abstract

In the original version of this Article, the authors stated that the archaeal phylum Parvarchaeota was previously represented by only two single-cell genomes (ARMAN-4_'5-way FS' and ARMAN-5_'5-way FS'). However, these are in fact unpublished, low-quality metagenome-assembled genomes (MAGs) obtained from Richmond Mine, California. In addition, the authors overlooked two higher-quality published Parvarchaeota MAGs from the same habitat, ARMAN-4 (ADCE00000000) and ARMAN-5 (ADHF00000000) (B. J. Baker et al., Proc. Natl Acad. Sci. USA 107, 8806-8811; 2010). The ARMAN-4 and ARMAN-5 MAGs are estimated to be 68.0% and 76.7% complete with 3.3% and 5.6% contamination, respectively, based on the archaeal-specific marker sets of CheckM. The 11 Parvarchaeota genomes identified in our study were obtained from different Richmond Mine metagenomes, but are highly similar to the ARMAN-4 (ANI of ~99.7%) and ARMAN-5 (ANI of ~99.6%) MAGs. The highest-quality uncultivated bacteria and archaea (UBA) MAGs with similarity to ARMAN-4 and ARMAN-5 are 82.5% and 83.3% complete with 0.9% and 1.9% contamination, respectively. The Parvarchaeota represents only 0.23% of the archaeal genome tree and addition of the ARMAN-4 and ARMAN-5 MAGs do not change the conclusions of this Article, but do impact the phylogenetic gain for this phylum. This has now been corrected in all versions of the Article. An updated version of Fig. 5 has also been used to replace the previous version, with the row for Parvarchaeota removed, and Supplementary Table 15 and Supplementary Table 17 have both been replaced to reflect the availability of the two additional Parvarchaeota genomes. In addition, the Methods incorrectly stated that all metagenomes identified as being from studies where MAGs had previously been recovered were excluded from consideration. Metagenomes from studies where MAGs had previously been recovered were retained if the UBA MAGs provided appreciable improvements in genome quality or phylogenetic diversity. All versions of the Article have been updated to indicate the retention of such metagenomes.

摘要

在本文的原始版本中,作者称古菌门微小古菌门(Parvarchaeota)此前仅由两个单细胞基因组(ARMAN-4_“5-way FS”和ARMAN-5_“5-way FS”)代表。然而,实际上这些是从未发表过的、从加利福尼亚州里士满矿获得的低质量宏基因组组装基因组(MAGs)。此外,作者忽略了来自同一栖息地的两个质量更高的已发表的微小古菌门MAGs,即ARMAN-4(ADCE00000000)和ARMAN-5(ADHF00000000)(B. J. 贝克等人,《美国国家科学院院刊》107,8806 - 8811;2010年)。根据CheckM的古菌特异性标记集估计,ARMAN-4和ARMAN-5 MAGs的完整性分别为68.0%和76.7%,污染率分别为3.3%和5.6%。我们研究中鉴定出的11个微小古菌门基因组是从里士满矿的不同宏基因组中获得的,但与ARMAN-4(ANI约为99.7%)和ARMAN-5(ANI约为99.6%)MAGs高度相似。与ARMAN-4和ARMAN-5相似的质量最高的未培养细菌和古菌(UBA)MAGs的完整性分别为82.5%和83.3%,污染率分别为0.9%和1.9%。微小古菌门仅占古菌基因组树的0.23%,添加ARMAN-4和ARMAN-5 MAGs不会改变本文的结论,但会影响该门的系统发育增益。本文的所有版本现已对此进行了修正。还使用了更新后的图5版本来替换之前的版本,删除了微小古菌门那一行,并替换了补充表15和补充表17,以反映另外两个微小古菌门基因组的可用性。此外,方法部分错误地指出,所有被鉴定为来自此前已回收MAGs的研究的宏基因组都被排除在考虑之外。如果UBA MAGs在基因组质量或系统发育多样性方面有显著改善,那么来自此前已回收MAGs的研究的宏基因组会被保留。本文的所有版本都已更新,以表明保留了此类宏基因组。

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