Genetic variation and diversity in 199 Melilotus accessions based on a combination of 5 DNA sequences
Authors: Jiyu Zhang
Fan Wu
Xianfeng Yi
Zhuanzhuan Yan
Hongxiang Zhang
Yufei Zhang
Rong Bai
Wenli Guo
Blaise Pascal Muvunyi
Qi Yan
Journal: PLoS ONE (2018)
Discipline: Multidisciplinary
Keywords: Melilotus; genetic diversity; chloroplast loci; nuclear region; phylogenetic trees
Affiliations: State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture; College of Pastoral Agriculture Science and Technology, Lanzhou University; Lanzhou, China., Guangxi Institute of Animal Sciences, Nanning, China.

Abstract:  Melilotus is an important genus of legume plants and an herbage with excellent nitrogen fixation; it can tolerate extreme environmental conditions and possesses important medicinal value. However, there is limited genetic information about the genus; thus, we analysed four chloroplast loci (rbcL, matK, psbA-trnH and trnL-F) and one nuclear region (ITS) to determine the genetic diversity of 199 accessions from 18 Melilotus species. The rbcL and matK sequences were highly conserved, whereas the trnL-F and ITS sequences contained variable and parsimony-informative sites. In our analyses of the single and combined regions, we calculated the pairwise distance, haplotype and nucleotide diversity and gaps and then constructed phylogenetic trees to assess the genetic diversity, and our results revealed significant variations among the different accessions. The genetic distance values were between zero and nine, and based on the combined regions, the highest frequency value was approximately four. Melilotus showed high haplotype and nucleotide diversity, particularly in the ITS sequences, with values of 0.86 and 0.0087, respectively. The single ITS sequence, psbA-trnH, and the combined matK+rbcL+trnL-F (MRT) and matK+rbcL+psbA-trnH+trnL-F+ITS (MRPTI) regions showed interspecific variation in the gap analysis. Phylogenetic trees calculated using ITS, psbA-trnH and MRPTI sequences indicated distinct genetic relationship in 18 species, and these species could be divided into two groups. By determining the genetic diversity of plants, we can evaluate the genetic relationships among species and accessions, providing a basis for preserving and utilizing the genetic resources of Melilotus. 

Retracted: Yes

PubPeer comments:
 2020 retraction. https: journals.plos.org plosone article?id=10.1371 journal.pone.0230311 Following publication of this article [1], concerns were raised about the contribution of this study in the context of previously published works. An assessment carried out in consultation with members of the Editorial Board found overlap in the research question, approach, and datasets with articles previously published by some of the same authors [2, 3]. [2] was cited, but the relationship to this work was not clearly discussed. The previous work [2] investigated the phylogenetic relationships among Melilotus species by analysing DNA sequence data from four of the same loci: rbcL, matK, trnL-F and ITS. The current study [1] uses sequence data from one additional region, psbA-trnH, and analyzes a larger dataset (the majority of additional accessions were from the National Gene Bank of Forage Germplasm (NGBFG, China)). The dataset for this study [1] reused some of the raw sequencing data used in [2] and [3]. The authors have stated that the emphasis of the articles differs, with [2] focusing on interspecific phylogenic relationships within genus Melilotus, and [3] focusing on constructing the standard barcode sequence for each species, while the current study [1] focuses on the genetic variation and diversity of Melilotus accessions collected in China. The Data Availability statement for this article [1] states that all relevant data are within the paper and its Supporting Information files. However, the full raw sequencing data generated during this study were not deposited in an appropriate public repository at the time of publication. The available sequencing data have since been deposited at Genbank with the following accession numbers: 166 ITS sequences (MK918643u2014MK918756, MK918758u2014MK918771, MK918773u2014MK918810); 164 matK sequences (MN532828u2014MN532973, MN532975u2014MN532982, MN532984u2014MN532993); 165 rbcL sequences (MN532693u2014MN532708, MN532710u2014MN532717, MN532719u2014MN532728, MN533354u2014MN533485); 164 trnH-psbA sequences (MN533090u2014MN533103, MN533105u2014MN533112, MN533114u2014MN533123, MN533222u2014MN533353); and 117 trnL-F sequences (MN533486u2014MN533501, MN533503u2014MN533510, MN533512u2014MN533521, MN533622u2014MN533688, MN533690u2014MN533705). Eight germplasm accessions were omitted from the published S1 Table in error: PI549124, PI549125, PI549126, and PI549127 belonging to M. albus; ZM-2483 belonging to M. dentatus; and PI595329, PI595335 and PI595338 belonging to M. officinalis. In light of the concerns about the overlap in the research question, approach, and datasets with previously published work, the PLOS ONE Editors retract this article. HZ, FW, WG, RB, ZY, BPM, QY, YZ, XY and JZ did not agree with retraction. References 1.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 pmid:29534094 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.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 ,