3 publications mentioning bdi-MIR395d

Open access articles that are associated with the species Brachypodium distachyon and mention the gene name MIR395d. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

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Click here for file Multiple sequence alignment of miR395 genes in Brachypodium and their homologs in rice.

The genome organization of miR395 family in Brachypodium was quite different from that in rice.

Because miR395 only has one member in lower plant Physcomitrella, miR395d may be the ancient form of this family that is kept unchanged in Brachypodium, possibly under some kind of positive selection.

MiR395 belongs to conserved miRNAs that have been found across different plant species.

Although up to now, all the miR395 gene family members in other eudicotyledonous and monocotyledonous plant genomes are clustered, the Brachypodium miR395d was not clustered with other paralogs (Figure 3).

According to the miRBase, the miR395 family has multiple clustered members in both eudicotyledonous and monocotyledonous plants.

Multiple sequence alignment of miR395 genes in Brachypodium and their homologs in rice.

These precursors exhibit different levels of sequence similarity to one another, implying that the duplication events happened at different time points during the evolution history of the miR395 family.

For miR395, its size in Brachypodium was approximately half of that in rice (Figure 3, Table 4).

It is interesting to note that miR395d in Brachypodium is not clustered with other family members (Figure 3) although the members of this family always form clusters in other plant species [49].

The location of miR395 genes are roughly in proportion to their real physical locations.

According to the detected miRNA and miRNA* sequences as well as results of BLASTn search based on sequences similarity, 14 precursors with reasonable minimum free energy value were identified for miR395 in the draft Brachypodium genome (Figure 3).

On the basis of size and sequence similarity, two types of miR395 precursors exist in Brachypodium.

For all the miR395 precursors, the mature miRNAs are all located on the 3' arms.

Asterisks denote miR395 genes whose miRNA* have been detected in our study.

Small and big solid vertical bars represent type A and type B miR395 genes, respectively.

Thus, an alternative explanation is that the unclustered miR395d may result from the loss of miR395 genes happened after duplication events during the evolution of this family.

is a figure showing multiple sequence alignment of Brachypodium miR395 genes as well as their homologs in rice, performed with the ClustalW 1.83 program.

Open vertical bars represent sequences showing similarity to miR395 genes, but containing no mature miR395 sequence.

In Brachypodium, the miR395 family is encoded by 14 genome loci and two clusters are formed (Figure 3), suggesting that duplication evens in Brachypodium are not as active as that in rice.

No miR395- precursor-like sequence was detected in its surrounding region.

Type A includes miR395a~c and miR395f~n, and type B includes miR395d and miR395e.

Both miR395 and miR395* could be detected in the NC library, although their reads were not high.

If this is the case, the loss of miR395 genes probably occurred after the divergence of Ehrhartoideae (rice) and Pooideae (Brachypodium), because there is no unclustered miR395 gene in rice.

Figure 3Genomic organization of the miR395 family in Brachypodium.

Among the conserved Brachypodium miRNA families, miR395 is distinguished because its members are clustered in several plant genomes.

Interestingly, for almost all the conserved miRNA families (except miR395) with multiple members, their family sizes in Brachypodium are much smaller than those in rice and Populus, and most of them have sizes similar to those in Arabidopsis (Table 4).

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In this context, the presence of lncRNAs with miRNA target mimic pairing could potentially compete with the RISC-complex, sequestering the entire miR395 cluster.

Moreover, miR395, which is involved in the regulatory network of sulfate assimilation [58], was found in our Bd1-1 data set associated through a TM mechanism with the two lncRNAs: TCONS_54981.1 and TCONS_11459.1 (Fig.   7b).

We also found TMs related to large miRNA families such as miR156, miR395, miR399 and miR5174.

Moreover, the polycistronic miR395 family, involved in the sulfate assimilation [58], was found in our Bd1-1 data set associated through a TM mechanism with two lncRNAs.

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miRNA Name Species of target was identified Experimentally conformed target miR167 ath/osa Auxin response factors miR395 ath/osa ATP sulphurylase miR160 ath/osa Auxin response factors ath-Arabidopsis thaliana; osa-Oryza sativa.

Chr1 Chr2 Chr3 Chr4 Chr5 miR1127 * miR1128 * * * * * miR1133 * miR1135 * miR1139 * * * miR1439 * * * * * miR167 * miR395 * * miR5049 * * * * * miR5175 * * * miR5180 * * * miR5203 * * * * Bold miRNAs gave the best results that they were syntenic to Bd4.