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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 gene structure of Miscanthus CO/Hd1 homologues, MsiHd1. Two types of homologues, MsiHd1a and MsiHd1b, were detected. MsiHd1b is a putative pseudogene, given that its sequences are discriminated unambiguously from MsiHd1a by a common MsiMITE2 insertion and additional indels with deleterious mutations, including one crucial, 1bp insertion that causes a premature stop codon. The positions of the start and stop codon and polyA addition site are shown. Insertional sites of five miniature inverted transposable elements (MITEs) (MsiMITE1–5) are indicated by filled triangles. Miscanthus accessions in which MITE sequences were detected are indicated in parentheses below the names of the MITEs. All PCR products from the genus Miscanthus in this study were amplified by a pair of primers, F14 and R17, depicted as arrowheads above the figure.
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Figure 2: The gene structure of Miscanthus CO/Hd1 homologues, MsiHd1. Two types of homologues, MsiHd1a and MsiHd1b, were detected. MsiHd1b is a putative pseudogene, given that its sequences are discriminated unambiguously from MsiHd1a by a common MsiMITE2 insertion and additional indels with deleterious mutations, including one crucial, 1bp insertion that causes a premature stop codon. The positions of the start and stop codon and polyA addition site are shown. Insertional sites of five miniature inverted transposable elements (MITEs) (MsiMITE1–5) are indicated by filled triangles. Miscanthus accessions in which MITE sequences were detected are indicated in parentheses below the names of the MITEs. All PCR products from the genus Miscanthus in this study were amplified by a pair of primers, F14 and R17, depicted as arrowheads above the figure.

Mentions: To isolate CO/Hd1 homologues of M. sinensis, PCR amplification was carried out for 23 accessions derived from the Japanese archipelago, three accessions from South Korea, and 14 from China. Specific 2–2.5kb PCR products were amplified from all accessions. Based on the results of RT-PCR, the M. sinensis CO/Hd1 sequence consisting of two exons and one intron in the PCR fragment was identified and named as MsiHd1 (Fig. 2). The MsiHd1 encoded approximately 400 amino acids with two conserved B-box zinc finger domains, which may be responsible for protein–protein interactions (Ben-Naim et al., 2006; Wenkel et al., 2006), and a CCT domain, which is involved with nuclear localization signal (Robson et al., 2001) (see Supplementary Fig. S1 at JXB online). Both domains are features of CO/Hd1. Splicing sites of MsiHd1 matched to those of sorghum and rice. PolyA addition sites were 159bp downstream of the stop codon (Fig. 2).


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 gene structure of Miscanthus CO/Hd1 homologues, MsiHd1. Two types of homologues, MsiHd1a and MsiHd1b, were detected. MsiHd1b is a putative pseudogene, given that its sequences are discriminated unambiguously from MsiHd1a by a common MsiMITE2 insertion and additional indels with deleterious mutations, including one crucial, 1bp insertion that causes a premature stop codon. The positions of the start and stop codon and polyA addition site are shown. Insertional sites of five miniature inverted transposable elements (MITEs) (MsiMITE1–5) are indicated by filled triangles. Miscanthus accessions in which MITE sequences were detected are indicated in parentheses below the names of the MITEs. All PCR products from the genus Miscanthus in this study were amplified by a pair of primers, F14 and R17, depicted as arrowheads above the figure.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: The gene structure of Miscanthus CO/Hd1 homologues, MsiHd1. Two types of homologues, MsiHd1a and MsiHd1b, were detected. MsiHd1b is a putative pseudogene, given that its sequences are discriminated unambiguously from MsiHd1a by a common MsiMITE2 insertion and additional indels with deleterious mutations, including one crucial, 1bp insertion that causes a premature stop codon. The positions of the start and stop codon and polyA addition site are shown. Insertional sites of five miniature inverted transposable elements (MITEs) (MsiMITE1–5) are indicated by filled triangles. Miscanthus accessions in which MITE sequences were detected are indicated in parentheses below the names of the MITEs. All PCR products from the genus Miscanthus in this study were amplified by a pair of primers, F14 and R17, depicted as arrowheads above the figure.
Mentions: To isolate CO/Hd1 homologues of M. sinensis, PCR amplification was carried out for 23 accessions derived from the Japanese archipelago, three accessions from South Korea, and 14 from China. Specific 2–2.5kb PCR products were amplified from all accessions. Based on the results of RT-PCR, the M. sinensis CO/Hd1 sequence consisting of two exons and one intron in the PCR fragment was identified and named as MsiHd1 (Fig. 2). The MsiHd1 encoded approximately 400 amino acids with two conserved B-box zinc finger domains, which may be responsible for protein–protein interactions (Ben-Naim et al., 2006; Wenkel et al., 2006), and a CCT domain, which is involved with nuclear localization signal (Robson et al., 2001) (see Supplementary Fig. S1 at JXB online). Both domains are features of CO/Hd1. Splicing sites of MsiHd1 matched to those of sorghum and rice. PolyA addition sites were 159bp downstream of the stop codon (Fig. 2).

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.