Potential DNA barcodes for Melilotus species based on five single loci and their combinations
Authors: Daiyu Zhang
Jiyu Zhang
Fan Wu
Yanrong Wang
Kai Luo
Yuqin Meng
Hongyan Di
Wenli Guo
Baochang Feng
Blaise Pascal Muvunyi
Jinxing Ma
Journal: PloS one (2017)
Discipline: Multidisciplinary
Keywords: Melilotus; species identification; barcodes; ITS; rbcL
Affiliations: State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China., National Quality Control & Inspection Centre for Grassland Industry Products, National Animal Husbandry Service, Ministry of Agriculture, Beijing, China., China Agricultural Veterinarian Biology Science and Technology Co. Ltd, Lanzhou, China.

Abstract:  Melilotus, an annual or biennial herb, belongs to the tribe Trifolieae (Leguminosae) and consists of 19 species. As an important green manure crop, diverse Melilotus species have different values as feed and medicine. To identify different Melilotus species, we examined the efficiency of five candidate regions as barcodes, including the internal transcribed spacer (ITS) and two chloroplast loci, rbcL and matK, and two non-coding loci, trnH-psbA and trnL-F. In total, 198 individuals from 98 accessions representing 18 Melilotus species were sequenced for these five potential barcodes. Based on inter-specific divergence, we analysed sequences and confirmed that each candidate barcode was able to identify some of the 18 species. The resolution of a single barcode and its combinations ranged from 33.33% to 88.89%. Analysis of pairwise distances showed that matK+rbcL+trnL-F+trnH-psbA+ITS (MRTPI) had the greatest value and rbcL the least. Barcode gap values and similarity value analyses confirmed these trends. The results indicated that an ITS region, successfully identifying 13 of 18 species, was the most appropriate single barcode and that the combination of all five potential barcodes identified 16 of the 18 species. We conclude that MRTPI is the most effective tool for Melilotus species identification. Taking full advantage of the barcode system, a clear taxonomic relationship can be applied to identify Melilotus species and enhance their practical production. 

Retracted: No

PubPeer comments:
 2020 expression of concern. https: journals.plos.org plosone article?id=10.1371 journal.pone.0230324 The PLOS Data Availability Policy requires that, with rare prior exception, all data underlying the findings described in an article are fully available without restriction. The Data Availability Statement for this article [1] states that all relevant data are within the paper and its Supporting Information files. The full raw sequencing data generated during this study were not deposited in an appropriate public repository at the time of publication. In an update to the Data Availability Statement, the available sequencing data used in the analyses reported in the article are deposited at Genbank. The authors have provided the Genbank accession numbers in a revised S1 Table, included in the Supporting Information. The authors have provided the following additional information regarding the dataset: The sequence data for a number of germplasm accessions could not be deposited because the data are missing or the information is no longer available to match the sequence data to the germplasm accession. The dataset for this study [1] includes some of the accessions from the National Plant Germplasm System (NPGS, USA) that were analysed in a previous study [2]; the raw sequence data for these accessions were reused (specifically, raw sequences of ITS, rbcL and matK of M.suaveolens (PI593408, Ames23793), M. tauricus (Ames18446, PI67510), M. dentatus (PI108656, PI90753), M. wolgicus (PI317665, PI502547), M. spicatus (Ames18402, Ames25647), M. infestus (PI306326, PI306327), M. siculus (PI318508, PI33366), and M. sulcatus (PI198090, PI227595)). To construct the standard barcode sequence, the head and tail of each raw sequence was cut, and the trimmed sequences were used in further analyses. As the reused sequences are therefore not identical to the raw sequences generated in [2], all standard barcode sequences were submitted separately to Genbank. Thus, although the raw sequence data were reused, the Genbank sequence accessions do not overlap with those reported in [2]. For each of the 18 species, two barcode sequences were submitted to Genbank. In total, 670 sequences associated with this article [1] are deposited in Genbank. A further 204 sequences were used in the study to expand the sample sizes and increase accuracy for the analyses in Fig 4. These accession numbers are listed in the revised S1 Table and are deposited in Genbank in association with a different article [3], which has since been retracted [4]. In addition, there is an error in S1 Table of the original article. The germplasm accession PI43597 was omitted from the table. Please see the revised S1 Table here. The PLOS ONE Editors issue this Expression of Concern to alert readers that the underlying sequence data for the article are not available in full, which affects the reproducibility of the reported analyses. References 1.Wu F, Ma J, Meng Y, Zhang D, Pascal Muvunyi B, Luo K, et al. (2017) Potential DNA barcodes for Melilotus species based on five single loci and their combinations. PLoS ONE 12(9): e0182693. https: doi.org 10.1371 journal.pone.0182693. pmid:28910286 2.Di H, Duan Z, Luo K, Zhang D, Wu F, Zhang J, et al. (2015) Interspecific Phylogenic Relationships within Genus Melilotus Based on Nuclear and Chloroplast DNA. PLoS ONE 10(7): e0132596. https: doi.org 10.1371 journal.pone.0132596. pmid:26167689 3.Zhang H, Wu F, Guo W, Bai R, Yan Z, Muvunyi BP, et al. (2018) Genetic variation and diversity in 199 Melilotus accessions based on a combination of 5 DNA sequences. PLoS ONE 13(3): e0194172. https: doi.org 10.1371 journal.pone.0194172 4.The PLOS ONE Editors (2020) Retraction: Genetic variation and diversity in 199 Melilotus accessions based on a combination of 5 DNA sequences. PLoS ONE 15(3): e0230311. https: doi.org 10.1371 journal.pone.0230311 ,