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Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago.

Nagano H, Clark LV, Zhao H, Peng J, Yoo JH, Heo K, Yu CY, Anzoua KG, Matsuo T, Sacks EJ, Yamada T - J. Exp. Bot. (2015)

Bottom Line: Sequences of MsiHd1 homologues were compared among 24 wild M. sinensis accessions from Japan, 14 from China, and three from South Korea.MsiMITE1, detected in exon 1 of MsiHd1a, was only observed in Japanese accessions and its revertant alleles derived from retransposition were predominantly in Chinese accessions.These differences in MsiHd1a show that the dependency on functional MsiHd1a alleles is different between accessions from the East Asian mainland and Japan.

View Article: PubMed Central - PubMed

Affiliation: Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.

No MeSH data available.


The structure of MsiMITE1 and a schematic diagram of its insertion and retransposition. (A) A target site before insertion of MsiMITE1. (B) Miniature inverted transposable element (MITE)-like sequences are recognized by terminal inverted repeats (TIRs) and target site duplications (TSDs). (C) Revertant alleles contain a 6bp footprint which encodes two additional amino acids (proline and aspartic acid) at the insertion-retransposition site of MsiMITE1.
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Figure 5: The structure of MsiMITE1 and a schematic diagram of its insertion and retransposition. (A) A target site before insertion of MsiMITE1. (B) Miniature inverted transposable element (MITE)-like sequences are recognized by terminal inverted repeats (TIRs) and target site duplications (TSDs). (C) Revertant alleles contain a 6bp footprint which encodes two additional amino acids (proline and aspartic acid) at the insertion-retransposition site of MsiMITE1.

Mentions: Five novel types of miniature inverted transposable elements (MITEs) with distinctive terminal structures (TIRs: terminal inverted repeats, TSDs: target site duplications) were identified in MsiHd1 alleles and named as MsiMITE1–MsiMITE5 (Fig. 5; see Supplementary Fig. S3 at JXB online). MsiMITE1 and MsiMITE5 were found in MsiHd1a, whereas the other three MITEs were found in MsiHd1b (Table 1; Figs 2, 3). MITEs are known to be preferentially located in the vicinity of genes (Bureau and Wessler, 1994; Feschotte et al., 2002). During the alignment work, if a relatively large insertion gap (<500bp) was found and both ends of the gap had TIRs and TSDs, the insertion sequence was identified as a MITE. MsiMITE1, which was only detected in Japanese accessions, was found to cause loss-of-function of MsiHd1a at the insertion site by forming a stop codon. On the other hand, many accessions from the Asian mainland had revertant alleles derived from retransposition, leaving a footprint of 6bp instead of a full MsiMITE1 sequence (Fig. 5). Revertant alleles were found in most accessions from the Asian mainland but in only one Japanese accession (JM0119-5; although another Japanese accession, JM0058-1, also had a footprint of 6bp, that allele was considered not to be a revertant allele because it had an additional putative loss-of-function mutation; Table 1). Two MITE subfamilies (MsiMITE2 and MsiMITE3) were observed in tandem in the 5’ untranslated region of the MsiHd1b locus (Fig. 2). MsiMITE3, MsiMITE4, and MsiMITE5 were only detected in JM0125-1, JM0058-1, and PMS007, respectively. These three MITEs were also detected in other Poaceae species (see Supplementary Fig. S4 at JXB online), but MsiMITE1 and MsiMITE2 were not (see Supplementary Fig. S3 at JXB online).


Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago.

Nagano H, Clark LV, Zhao H, Peng J, Yoo JH, Heo K, Yu CY, Anzoua KG, Matsuo T, Sacks EJ, Yamada T - J. Exp. Bot. (2015)

The structure of MsiMITE1 and a schematic diagram of its insertion and retransposition. (A) A target site before insertion of MsiMITE1. (B) Miniature inverted transposable element (MITE)-like sequences are recognized by terminal inverted repeats (TIRs) and target site duplications (TSDs). (C) Revertant alleles contain a 6bp footprint which encodes two additional amino acids (proline and aspartic acid) at the insertion-retransposition site of MsiMITE1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4493791&req=5

Figure 5: The structure of MsiMITE1 and a schematic diagram of its insertion and retransposition. (A) A target site before insertion of MsiMITE1. (B) Miniature inverted transposable element (MITE)-like sequences are recognized by terminal inverted repeats (TIRs) and target site duplications (TSDs). (C) Revertant alleles contain a 6bp footprint which encodes two additional amino acids (proline and aspartic acid) at the insertion-retransposition site of MsiMITE1.
Mentions: Five novel types of miniature inverted transposable elements (MITEs) with distinctive terminal structures (TIRs: terminal inverted repeats, TSDs: target site duplications) were identified in MsiHd1 alleles and named as MsiMITE1–MsiMITE5 (Fig. 5; see Supplementary Fig. S3 at JXB online). MsiMITE1 and MsiMITE5 were found in MsiHd1a, whereas the other three MITEs were found in MsiHd1b (Table 1; Figs 2, 3). MITEs are known to be preferentially located in the vicinity of genes (Bureau and Wessler, 1994; Feschotte et al., 2002). During the alignment work, if a relatively large insertion gap (<500bp) was found and both ends of the gap had TIRs and TSDs, the insertion sequence was identified as a MITE. MsiMITE1, which was only detected in Japanese accessions, was found to cause loss-of-function of MsiHd1a at the insertion site by forming a stop codon. On the other hand, many accessions from the Asian mainland had revertant alleles derived from retransposition, leaving a footprint of 6bp instead of a full MsiMITE1 sequence (Fig. 5). Revertant alleles were found in most accessions from the Asian mainland but in only one Japanese accession (JM0119-5; although another Japanese accession, JM0058-1, also had a footprint of 6bp, that allele was considered not to be a revertant allele because it had an additional putative loss-of-function mutation; Table 1). Two MITE subfamilies (MsiMITE2 and MsiMITE3) were observed in tandem in the 5’ untranslated region of the MsiHd1b locus (Fig. 2). MsiMITE3, MsiMITE4, and MsiMITE5 were only detected in JM0125-1, JM0058-1, and PMS007, respectively. These three MITEs were also detected in other Poaceae species (see Supplementary Fig. S4 at JXB online), but MsiMITE1 and MsiMITE2 were not (see Supplementary Fig. S3 at JXB online).

Bottom Line: Sequences of MsiHd1 homologues were compared among 24 wild M. sinensis accessions from Japan, 14 from China, and three from South Korea.MsiMITE1, detected in exon 1 of MsiHd1a, was only observed in Japanese accessions and its revertant alleles derived from retransposition were predominantly in Chinese accessions.These differences in MsiHd1a show that the dependency on functional MsiHd1a alleles is different between accessions from the East Asian mainland and Japan.

View Article: PubMed Central - PubMed

Affiliation: Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.

No MeSH data available.