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Microsynteny related to miR167 families in a) Arabidopsis; c) Populus; e) grape; g) rice and reconstruction of the miRNA167 families evolution in b) Arabidopsis; d) Populus; f) grape; h) rice. a, c, e, g: The genomic fragment is represented by a series of triangles that represent a gene in a family and its flanking genes. The genes in the same fragment show the same color except the gene in a family which is shaded by black triangle. The triangle also indicates gene's orientation on strands. The homologous genes on two fragments are connected by a gray line. b, d, f, h: These evolution relationship were generated to demonstrate the order of duplication events for the miR167 families in respective species. Black vertical line indicates tandem duplication. The orthologous miRNAs are classified into four orthologous groups designated as A, B, C and D, each of which is represented by the same color. Group D miRNAs are most ancient and the colinearity found between the group D and other groups are not significant, therefore, the group D is represented by a dashed line. In rice, miR167s out of the group D are designated as group A/B/C.

Microsynteny related to miR167 families in a) Arabidopsis; c) Populus; e) grape; g) rice and reconstruction of the miRNA167 families evolution in b) Arabidopsis; d) Populus; f) grape; h) rice. a, c, e, g: The genomic fragment is represented by a series of triangles that represent a gene in a family and its flanking genes. The genes in the same fragment show the same color except the gene in a family which is shaded by black triangle. The triangle also indicates gene's orientation on strands. The homologous genes on two fragments are connected by a gray line. b, d, f, h: These evolution relationship were generated to demonstrate the order of duplication events for the miR167 families in respective species. Black vertical line indicates tandem duplication. The orthologous miRNAs are classified into four orthologous groups designated as A, B, C and D, each of which is represented by the same color. Group D miRNAs are most ancient and the colinearity found between the group D and other groups are not significant, therefore, the group D is represented by a dashed line. In rice, miR167s out of the group D are designated as group A/B/C.

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The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in...

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... are four miR167 genes in Arabidopsis. miR167a and miR167b have con- served neighboring regions; with less conserved colinear genes surrounding miR167a and miR167c and no con- served colinear genes between miR167b and miR167c ( Figure 4a). MicroSyn did not detect microsynteny between miR167d and other family members. ...
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... did not detect microsynteny between miR167d and other family members. Based on the predicted syntenic relationships, Arabidopsis miR167a and miR167b appear to have evolved from a single duplication event, while miR167c existed prior to this duplication event and miR167d is an ancient gene that has no detected linkage with other miR167 genes (Figure 4b). Eight miR167 genes were identified in Populus. ...
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... miR167 genes were identified in Populus. The tandemly duplicated miR167a and miR167b share sub- stantial colinear region with the tandemly duplicated miR167c and miR167d (Figure 4c). miR167f and miR167g share conserved synteny and microsynteny was detected between miR167e and miR167h. ...
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... and miR167g share conserved synteny and microsynteny was detected between miR167e and miR167h. According to the extent of conservation within this gene family, miR167f/miR167g and miR167a/miR167b/miR167c/ miR167d arose from a duplication event, and the com- mon ancestor of miR167f/miR167g and miR167a/ miR167b/miR167c/miR167d, might be evolved from duplication after the ancestor of miR167e/miR167h appeared (Figure 4d). ...
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... grape, there are five members in the miR167 family. The microsynteny between the miR167c and miR167e is extensive, followed by the miR167b and miR167e and then miR167b and miR167c (Figure 4e). Interestingly, the region around miR167a lacks detectable colinear relationship to all other miR167 genes in grape. ...
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... the region around miR167a lacks detectable colinear relationship to all other miR167 genes in grape. The predicted syntenic relationships suggest that miR167c/ miR167d and miR167e arose from a recent duplication event, and that the miR167b and the ancestor of miR167c/miR167d and miR167e evolved from an ancient duplication (Figure 4f). The region of miR167a lacks significant colinear relations to all other miR167 genes; therefore, miR167a is placed close to miR167b as an outlier (Figure 4f). ...
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... predicted syntenic relationships suggest that miR167c/ miR167d and miR167e arose from a recent duplication event, and that the miR167b and the ancestor of miR167c/miR167d and miR167e evolved from an ancient duplication (Figure 4f). The region of miR167a lacks significant colinear relations to all other miR167 genes; therefore, miR167a is placed close to miR167b as an outlier (Figure 4f). ...
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... miR167a and miR167h are tandem genes located on chromosome 12. Microsynteny was detected between 1) miR167c and miR167d, 2) miR167f and miR167g and 3) miR167e and miR167i (Figure 4g). These gene pairs all ...
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... miR167j, no conserved regions were observed. In rice, three pairs (miR167c/miR167d, miR167f/miR167g and miR167e/ miR167i) appear to have evolved from a recent duplica- tion event as these gene pairs all have a conservative region with miR167a (Figure 4h). Relationship and evolution of miR167s in eudicots To clarify the relationship of miR167s across eudicots, the microsynteny of miR167 genes across Arabidopsis, Populus and grape was then examined. ...
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... and evolution of miR167s in eudicots To clarify the relationship of miR167s across eudicots, the microsynteny of miR167 genes across Arabidopsis, Populus and grape was then examined. Four orthologous groups were predicted and are designated as A, B, C and D (Figure 4; Figure 5). miR167a in Arabidopsis, miR167f and miR167g in Populus, and miR167e in grape have a conserved colinearity, and are classified into the group "A". ...
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... in Arabidop- sis, miR167e/miR167h in Populus, and miR167b in grape are grouped as group "C". miR167d in Arabidop- sis, and miR167a in grape are grouped as group "D" (Figure 4). It is thought that miRNA families evolved from a pro- cess of genome-wide duplication, tandem duplication and segmental duplication accompanied by post-duplica- tion diversification, similar to the evolution process of protein-coding gene families [10]. ...
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... verify reliability of the phylogenetic trees representing phylogenetic predictions, the discre- pancy in the two obtained phylogenetic trees and the branches with low bootstrap values (< 60%) were selected for searching their microsyntenies by MicroSyn. Initially, the phylogenetic analysis indicated that XTH gene family from Populus consists of four subfamilies of more closely related sequences, named here subfamily I (20 genes), II (3 genes), III (5 genes), IV (5 genes), and V (3 genes) ( Figure 6, Additional file 1: Supplemental Fig. S4). In subfamily I, POPTR_0011s02980 has a bootstrap value 46 and 34 in NJ and ML trees, respectively, but POPTR_0011s02980 has a significant microsynteny with POPTR_0002s06130 in subfamily I; the bootstrap value between POPTR_0013s00710 and POPTR_0005s00900 is 39, and the microsynteny between them was detected (8e-31) (Additional file 1: Supplemental Table S1). ...
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... S3 -Microsynteny related to miR167 families between grape and rice. Figure S4 - Phylogenetic tree of 39 XTH genes from Populus. Table S1 -Microsynteny of XTH genes in Populus. ...

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... Transcription factors, also known as trans-acting factors [29], exist in the form of a gene superfamily and play a critical regulatory role in the growth and development of plants and their response to the external environment. Thus far, the research on the identification and analysis of transcription factor families from the whole genome is increasing, which has become one of the focuses of genomics research [30], aiming to provide a reference for further study. The WRKY family is one of the ten transcription factor families in higher plants, and WRKY is famous for its highly conserved sequence (WRKYGQK), which is essential for WRKY transcription factor recognition and binding to the W-box element at the target gene promoter [3,7,31]. ...
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