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Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.
Nature Microbiology ( IF 28.3 ) Pub Date : 2018-Feb-01 , DOI: 10.1038/s41564-017-0083-5
Donovan H. Parks , Christian Rinke , Maria Chuvochina , Pierre-Alain Chaumeil , Ben J. Woodcroft , Paul N. Evans , Philip Hugenholtz , Gene W. Tyson

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 However, these are in fact unpublished, low-quality metagenome-assembled genomes (MAGs) obtained from Richmond Mine, California.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.

中文翻译:

作者更正:恢复近8000个由基因组组集的基因组,可以极大地扩展生命之树。

在本文的原始版本中,作者指出,古细菌门Parvarchaeota以前仅由两个单细胞基因组(ARMAN-4_'5-way FS'和ARMAN-5_'5-way FS')代表。但是,这些实际上是从未发表的,从加利福尼亚州里士满矿获得的低质量的由基因组组装的基因组(MAG)。此外,作者还忽略了来自同一栖息地的两个更高质量的Parvarchaeota MAG,ARMAN-4(ADCE00000000)和ARMAN-5(ADHF00000000)(BJ Baker等,美国国家科学院学报107,8806- 8811; 2010)。根据CheckM的古细菌特异性标记集,估计ARMAN-4和ARMAN-5 MAG的完成度分别为68.0%和76.7%,污染度分别为3.3%和5.6%。在我们的研究中鉴定出的11个Parvarchaeota基因组是从不同的Richmond Mine元基因组中获得的,但是与ARMAN-4(ANI约为99.7%)和ARMAN-5(ANI约为99.6%)MAG非常相似。与ARMAN-4和ARMAN-5相似的最高质量的未培养细菌和古细菌(UBA)MAG分别为82.5%和83.3%,污染程度分别为0.9%和1.9%。Parvarchaeota仅占古细菌基因组树的0.23%,添加ARMAN-4和ARMAN-5 MAG不会改变本文的结论,但会影响该门的系统发育增益。现在,该条款的所有版本中均已对此问题进行了更正。图5的更新版本也已用于替换以前的版本,其中Parvarchaeota的行已删除,并且补充表15和补充表17都已被替换,以反映两个附加Parvarchaeota基因组的可用性。此外,该方法错误地指出,所有被认为来自先前已恢复MAG的研究中的元基因组均被排除在考虑范围之外。如果UBA MAG在基因组质量或系统发育多样性方面有显着改善,则保留先前恢复了MAG的研究中的元基因组。该条款的所有版本均已更新,以指示此类元基因组的保留。
更新日期:2017-12-12
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