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[交流] 无意间发现两篇论文中许多句子十分相似，会是巧合吗已有55人参与

这两天阅读文献时，无意间发现两篇论文中许多句子十分相似，有些几乎一模一样，这会是巧合吗？现将两篇论文中相似句子整理如下。字母A代表论文Genome-Wide Analysis of the Dof Transcription Factor Gene Family Reveals Soybean-Specific Duplicable and Functional Characteristics，于2013年发表在PLOS ONE。字母B代表论文Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa，于2010年发表在BMC Plant Biology。

Introduction/Background (3 places)
1.
A
Therefore,  the identification and functional characterization of TFs is essential for the reconstruction of transcriptional regulatory networks [3].In  plants,  ~60  families  of  TFs  have  been  identified  based  on
bioinformatics  analysis  and  manual  inspection  [4,5].  The Arabidopsis genome  codes  for  at  least  1533  TFs,  which account for about 5.9% of its estimated total number of genes[1].  As  for  soybean  (Glycine  max),  ~12.2%  of  the  46,430 predicted  protein-coding  loci  have  been  identified  to  encode
5,671 putative TFs [6].

B
Thus, the identification and functional characterization of TFs is essential for the reconstruction of transcriptional regulatory networks[3]. In plants, totally more than 50 different families of TFs have been identified based on bioinformatics analysis so far [1,3]. The Arabidopsis genome encodes at least 1550 TFs, accounting for about 6.2% of its estimated total number of gene [4]. As for Populus,about6.4%of
its genome was found to encode more than 2900 TFs [3,5].

2.
A
Although  quite  a  few  Dof  TFs  have  been  functionally characterized  in  the  model  plant  Arabidopsis and  others,  the functions of most members of the Dof family remain unknown. Especially  in  soybean,  the  typical  legume  species,  there  are only  very  limited  reports  on  the  functional  characterization  of Dof TFs.

B
Although quite a few NAC TFs have been functionally characterized in model plantsArabidopsisand rice, the functions of majority of NAC members remain unknown. Especially inPopulus, the typical model tree
species, there are only very limited reports on the functional characterization of NAC TFs.

3.
A
In  the  present study,  a  genome-wide  identification  of  Dof  domain  TFs  in soybean was performed and revealed an expanded Dof family with 78 members. Detailed  analysis  of  the  sequence  phylogeny,  genome organization,  gene  structure,  conserved  motifs,  duplication status, expression profiling, and cis-elements was performed. It is  noteworthy  that

B
In the present study, we further performed a genome-wide identification of NAC domain TFs in Populus and revealed an expanded NAC family with totally 163 members. Detailed analysis including sequence phylogeny, genome organization, gene structure, conserved motifs and expression profiling was performed. It is noteworthy that

Materials and Methods (4 places)
1.
A
All  non-redundant hits with expected values <1E-5 were collected and compared with  the  Dof  family  in  PlantTFDB  (http://planttfdb.cbi.edu.cn/) [5]  and  LegumeTFDB  (http://legumetfdb.psc.riken.jp/)  [36].  As for  the  incorrectly-predicted  genes,  manual  re-annotation  was performed  using  the  on-line  web  server  GENSCAN  (http://genes.mit.edu/GENSCAN.html)  [37]  and/or  RT-PCR  cloning. The re-annotated sequences were further manually analyzed to confirm the presence of the Dof domain using the InterProScan program (http://www.ebi.ac.uk/Tools/InterProScan/) [38].

B
All non-redundant hits with expected values less than 1.0 were collected and then compared with the NAC family in PlnTFDB http://plntfdb.bio.uni-potsdam.de/v3.0/[3] and DPTF http://dptf.cbi.pku.edu.cn/[58]. As for the incorrectly predicted genes, manual reannotation was performed using online web server FGENESH http://linux1.softberry.com/berry.phtml[59]. The reannotated sequences were further manually analyzed to confirm the presence of NAM domain using InterProScan program http://www.ebi.ac.uk/Tools/InterProScan/[60].

2.
A
Unrooted  phylogenetic  trees  were  constructed with  MEGA  4.0  using  the  Neighbor-Joining  (NJ)  method  and the  bootstrap  test  carried  out  with  1000  iterations  [41].  The pairwise gap deletion mode was used to ensure that the more divergent C-terminal domains could contribute to the topology
of the NJ tree.

B
The unrooted phylogenetic trees were constructed with MEGA 4.0 using the NeighborJoining (NJ), Minimal Evolution (ME) and Maximum Parsimony (MP) methods and the bootstrap test carried out with 1000 iterations [91]. Pairwise gap deletion mode was used to ensure that the more divergent C-terminal domains could contribute to the topology of the NJ tree.

3.
A
The Gene Structure Display Server program [42] was used to  illustrate  the  exon/intron  organization  for  individual  Dof genes  by  comparison  of  the  coding  sequences  with  their corresponding  genomic  DNA  sequences  from  Phytozome(http://www.phytozome.net/gmax).

B
Gene structure display server (GSDS) program [92] was used to illustrate exon/intron organization for individual NAC genes by comparison of the cDNAs with their corresponding genomic DNA sequences from Phytozome http://www.phytozome.net/poplar.
4.
A
Structural  motif  annotation  was  performed  using  the  SMART (http://smart.embl-heidelberg.de)  [49]  and  Pfam  (http://pfam.sanger.ac.uk) databases [50].

B
Structural motif annotation was performed using the SMART http://smart.embl-heidelberg.de[95] and Pfam http://pfam.sanger.ac.uk databases [96].

Results and Discussion (15 places)
1.
A
The  identified  GmDof genes  encode  peptides ranging from 147 to 555 amino-acids in length with an average of  335.

B
The identified NAC genes in Populus encode proteins ranging from 117 to 718 amino acids (aa) in length with an average of 342 aa.

2.
A
The  detailed  information  of  the  Dof  family  genes  in soybean, including accession numbers and similarities to their Arabidopsis orthologs,  as  well  as  nucleotide  and  protein sequences, are listed in Table 1 and Additional Table S1. The Dof  gene  family  in  soybean  is  largest  compared  with  the estimates  for  other  plant  species,  which  range  from  ~36  in Arabidopsis  [13], ~30 in rice [8], ~28 in sorghum [11] and ~27 in  Brachypodium  distachyon  [54]. The member of  Dofgenes in soybean  is roughly  2.4-fold  that  in  Arabidopsis,  which  is consistent with the ratio of 1.4-1.6 putative  Populus  homologs for  each  Arabidopsis gene,  based  on  comparative  genomics studies [9].

B
The detailed information of NAC family genes inPopulus, including accession numbers and similarities to their Arabidopsis orthologs as well as nucleotide and protein sequences was listed in Table 1 and Additional file 1. The NAC gene family inPopulusis by far the largest one compared to the estimates for other plant species, which range from ~105 inArabidopsis[6], ~140 in rice[7] and ~101 in soybean [8]. The member of NAC genes in Populusis roughly 1.58 fold than that of Arabidopsis, which is in consistency with the ratio of 1.4~1.6 putative Populus homologs for each Arabidopsis gene based on comparative genomics studies [5].

3.
A
To  examine  the  phylogenetic  relationships  among the Dof domain proteins in soybean, an unrooted tree was constructed from alignments of the full-length amino-acid sequences of all GmDof proteins (Figure 2A).

B
To examine the phylogenetic relationship among the NAC domain proteins inPopulus, Arabidopsisand rice, an unrooted tree was constructed from alignments of the full-length NAC protein sequences (Figure 1).

4.
A
It  is  well  known  that  gene  structural  diversity  is  a  possible mechanism for the evolution of multigene families. In order to gain further insight into the structural diversity of Dof genes, we compared  the  exon/intron  organization  in  the  coding sequences  of  individual  Dof  genes  in  soybean.  A  detailed illustration of the exon/intron structures is shown in Figure 2B.

B
It is well known that gene structural diversity is a possible mechanism for the evolution of multigene families. In order to gain further insights into the structural diversity of NAC genes, we compared the exon/intron organization in the coding sequences of individual NAC genes in Populus. A detailed illustration of the exon/intron structures was shown in Figure 3B.

5.
A
In contrast,  the  gene  structure  appeared  to  be  more  variable  in subgroups I, V and VI, which had the largest numbers of exon/intron structural variants with striking distinctions.

B
In contrast, the gene structure appeared to be more variable in subfamilies II and V, which had the largest number of exon/intron structure variants with striking distinctions.

6.
A
Substantial clustering of  Dof genes was evident on several chromosomes, especially  on  those  with  high  densities  of  the  genes.

B
Substantial clustering of Populus NAC genes was evident on several LGs, especially on those with high densities of NAC genes.

7
A
Previous studies revealed that the soybean genome has undergone  at  least  two  rounds  of  genome-wide  duplication followed by multiple segmental duplication, tandem duplication, and  transposition  events  such  as  retroposition  and  replicative transposition  [58].

B
Previous studies revealed that Populus genome had undergone at least three rounds of genome-wide duplications followed by multiple segmental duplication, tandem duplication, and transposition events such as retroposition and replicative transposition [5,68].

8.
A
The distributions of Dof genes relative to the  corresponding  duplicate  genomic  blocks  are  illustrated  in Figure  3.  Within  the  duplicated  blocks  associated  with  a duplication event, 22 out of 38 putative paralogous pairs were preferentially-retained  duplicates  that  were  located  in  a segmental  duplication  of  a  long  fragment  (>1  Mb),

B
The distributions of NAC genes relative to the corresponding duplicate genomic blocks were illustrated in Figure 2. Within the 36 identified duplicated blocks associated with the recent salicoid duplication event, about 73% (87 of 120) of Populus NACs were preferentially retained duplicates that locate in both duplicated regions of 28 block pairs,

9.
A
In  general,  the Dof members demonstrated an interspersed distribution in most subfamilies,
indicating that the expansion of  Dof genes occurred before the divergence  of  soybean,  Arabidopsis,  and  rice.

B
In general, the NAC members demonstrated an interspersed distribution in majority of subfamilies, indicating that the expansion of NAC genes occurred before the divergence of Populus, Arabidopsis and rice.

10.
A
Inspection  of  the  phylogenetic  tree topology  revealed  several  pairs  of  Dof  proteins  with  a  high degree  of  homology  in  the  terminal  nodes  of  each  subgroup, suggesting that they are putative paralogous pairs (Figure 2A). A  total  of  38  pairs  of  putative  paralogous  Dof  proteins  were identified,  accounting  for  nearly  the  entire  family  (except  for GmDof17.4  and  GmDof05.4),  with  sequence  identity  ranging from  72%  to  97%  (see  Additional  Table  S2  for  details).

B
Inspection of the phylogenetic tree topology revealed several pairs of NAC proteins with a high degree of homology in the terminal nodes of each subfamily, suggesting that they are putative paralogous pairs (homologous genes within a species that diverged by gene duplication) (Figure 1 and Additional file 3). Totally, forty-nine pairs of putative paralogous NAC proteins were identified, accounting for more than 60% of the entire family, with sequence identities ranging from 71% to 97% (see Additional file 5 for details).

11.
A
To  reveal  the  diversification  of  Dof genes  in  soybean, putative motifs were predicted by the program MEME (Multiple Em  for  Motif  Elicitation),  and  a  total  of  30  conserved  motifs were  found  in  all  the  78  Dof  proteins  (Figure  5).

B
To further reveal the diversification of NAC genes in Populus, putative motifs were predicted by the program MEME (Multiple Expectation Maximization for Motif Elicitation), and 20 distinct motifs were identified.

12.
A
As expected,  most  of  the  closely-related  members  in  the phylogenetic  tree  had  common  motif  compositions.

B
As expected, most of the closely related members in the phylogenetic tree had common motif compositions

13.
A
Exon/intron structures of Dof genes from soybean. Exons are represented by green boxes and introns by black lines. The sizes of exons and introns can be estimated using the scale below.

B
Exon/intron structures of NAC genes from Populus. Exons and introns are represented by green boxes and black lines, respectively. The sizes of exons and introns can be estimated using the scale at bottom.

14.
A
The deduced full length  amino-acid  sequences  of  78  soybean,  36  Arabidopsis and  30  rice  Dof genes  were  aligned  by  Clustal  X  1.83  and  the phylogenetic  tree  was  constructed  using  MEGA  4.0  by the  neighbor-joining  method  with  1,000  bootstrap  replicates.  Each  Dof subgroup is indicated by a specific color.

B
The deduced full-length amino acid sequences of 163Populus, 105 Arabidopsis and 140 rice NAC genes were aligned by Clustal X 1.83 and the phylogenetic tree was constructed using MEGA 4.0 by the Neighbor-Joining (NJ) method with 1,000 bootstrap replicates. Each NAC subfamily was indicated in a specific color.

15.
A
The  expression  data were  gene-wise  normalized  and  hierarchically  clustered.  The  relative  expression  level  of  a  particular  gene  in  each  row  was normalized  against  the  mean  value.  The  color  scale  below  represents  expression  values,  green  indicating  low  levels  and  red indicating high levels of transcript abundance.

B
The expression data were gene-wise normalized and hierarchical clustered based on Pearson correlation. The genes marked in the same color indicate duplicated gene pairs. The relative expression level of particular gene in each row is normalized against the maximum value. Color scale at the top of each dendrogram represents log2 expression values, green represents low level and red indicates high level of transcript abundances.

Conclusion (1 place)
1.
A
The  exon/intron  structure  and motif  composition  of  the  Dofs were  highly  conserved  in  each
subfamily,  indicating  their  functional  conservation.  The  Dof genes  were  non-randomly  distributed  within  and  across  19 chromosomes,  and  a  high  proportion  of  GmDofs  were preferentially-retained duplicates located on duplicated blocks.

B
The exon/intron structure and motif compositions of NACs were highly conserved in each subfamily, indicative of their functional conservation. The NAC genes were non-randomly distributed across 19 LGs,
and a high proportion of NACs were preferentially retained duplicates located on the duplicated blocks

Supporting Information/Additional material (1 place)
1.
A
Complete  list  of  soybean  Dof gene  sequences identified in the present study.The list comprises 78 GmDof gene  sequences.  The  amino-acid  sequences  were  deduced from their corresponding coding sequences; the genomic DNA sequences  were  obtained  from  Phytozome.

B
A complete list of NAC gene sequences identified in the present study. The list comprises 163 NAC gene sequences identified. Amino acid sequences are deduced from their corresponding coding sequences and genomic DNA sequences are obtained from Phytozome http://www.phytozome.net/poplar, release 2.0.

更新：
这篇论文已经因为抄袭被撤稿了。

2017.png

[ Last edited by waam12 on 2017-7-27 at 05:41 ]

更新：韩春雨的导师中国农科院作物所博导邱丽娟因学术抄袭被国际期刊撤稿

[ Last edited by waam12 on 2017-8-3 at 12:22 ]

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