Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
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DOI：
10.1093/database/bau061
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发表时间：
2014-06-30
影响因子：
5.8
通讯作者：
Federhen, Scott
中科院分区：
文献类型：
--
作者：
Schoch, Conrad L.;Robbertse, Barbara;Federhen, Scott
DNA系统发育比较表明，基于形态的物种识别往往低估了真菌的多样性。因此，需要准确的DNA序列数据，与正确的分类名称和清晰注释的标本数据联系起来，从来没有像现在这样大。此外，越来越多使用高通量测序的分子生态学和微生物组项目需要快速有效的方法来进行大规模的物种分配。在这篇文章中，我们重点选择和重新注释了一组标记参考序列，这些序列代表了真菌目前接受的每个顺序。特别关注的是核糖体顺子内部转录间隔区序列，来源于模式标本和/或前型培养。重新注释和验证的序列存储在国家生物技术信息中心（NCBI）的一个公共数据库中，即RefSeq Targeted Loci （RTL）数据库，并将在常规序列相似性检索中以nr_前缀的检索号可见。提出了一套标准和协议，以提高新序列的数据质量，并建议如何使用类型和其他参考序列来提高真菌的鉴定。
DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.