Limits...
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.


Schematic model for Miscanthus Hd1 evolution. Blue indicates functional alleles and red indicates non-functional alleles. The whole genome duplication of Miscanthus resulted in Hd1a and Hd1b loci. Accumulation of deleterious mutations caused pseudogenization of Hd1b in M. sinensis. By additional local duplication, Hd1a increased in copy number (duplicated genes designated as Hd1a’ and Hd1a’’ in figure). After the last glacial maximum, the number of functional Hd1a alleles in the Asian mainland population of M. sinensis was high, whereas, in the Japanese population, the number of functional alleles decreased due to the accumulation of alleles with MITE insertions and/or other deleterious mutations. This difference suggests that dependency on the gene function of Hd1a is different between M. sinensis populations from the Asian mainland and the Japanese archipelago.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: Schematic model for Miscanthus Hd1 evolution. Blue indicates functional alleles and red indicates non-functional alleles. The whole genome duplication of Miscanthus resulted in Hd1a and Hd1b loci. Accumulation of deleterious mutations caused pseudogenization of Hd1b in M. sinensis. By additional local duplication, Hd1a increased in copy number (duplicated genes designated as Hd1a’ and Hd1a’’ in figure). After the last glacial maximum, the number of functional Hd1a alleles in the Asian mainland population of M. sinensis was high, whereas, in the Japanese population, the number of functional alleles decreased due to the accumulation of alleles with MITE insertions and/or other deleterious mutations. This difference suggests that dependency on the gene function of Hd1a is different between M. sinensis populations from the Asian mainland and the Japanese archipelago.

Mentions: The NJ tree showed that 20 of the 44 Miscanthus accessions that were analysed had two diverged loci, Hd1a and Hd1b (Fig. 3; see Supplementary Fig. S2 at JXB online). Although their positions on the Miscanthus genome are unknown, the existence of duplicated Hd1 loci can be considered to be universal within the genus Miscanthus, in contrast to sorghum, maize, and rice which have only one Hd1 locus. The recent genome duplication of Miscanthus relative to sorghum (Kim et al., 2012; Ma et al., 2012; Swaminathan et al., 2012) can at least partially account for differences in the number of Hd1 loci. Large-scale genomic analyses of M. sinensis have revealed that M. sinensis (x=19) is a diploidized tetraploid species formed by the duplication of chromosomes after the divergence from an x=10 ancestor (Kim et al., 2012; Ma et al., 2012; Swaminathan et al., 2012). The three or more loci of MsiHd1 identified by this study in M. sinensis might have been caused in part by the whole genome duplication (MsiHd1a and MsiHd1b) and also by local gene duplications (multiple MsiHd1a) via unequal crossing-over (Fig. 6). Although gene duplication can be an evolutionary process to gain new function (Ohno, 1970), a duplicated gene can alternatively be subjected to inactivation by mutations and genetic drift (Hughes, 1994; Force et al., 1999). Redundancy of gene functions among multiple MsiHd1 loci through polyploidization might have allowed pseudogenization of MsiHd1b. The precise number of MsiHd1a loci in Miscanthus remains unknown. In two Japanese accessions, JM0190-5 and JM0091-2, five copies of MsiHd1a were detected, suggesting the possibility of additional duplications in MsiHd1a. The M. floridulus Hd1 locus, having a revertant allele, showed the greatest sequence similarity to the M. sinensis Hd1 locus (Fig. 3) of the species evaluated. McoHd1b and Msa(4x)Hd1b in M. sinensis spp. condensatus and M. sacchariflorus (4x), respectively, each had three alleles, suggesting at least two loci, in contrast to the putative single locus in M. sinensis. The observation of five alleles of Msa(4x)Hd1a within one individual M. sacchariflorus (4x) indicates that there are at least three Msa(4x)Hd1a loci in this individual. As observed above, copy number of Hd1a/b varies among species in the genus Miscanthus.


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)

Schematic model for Miscanthus Hd1 evolution. Blue indicates functional alleles and red indicates non-functional alleles. The whole genome duplication of Miscanthus resulted in Hd1a and Hd1b loci. Accumulation of deleterious mutations caused pseudogenization of Hd1b in M. sinensis. By additional local duplication, Hd1a increased in copy number (duplicated genes designated as Hd1a’ and Hd1a’’ in figure). After the last glacial maximum, the number of functional Hd1a alleles in the Asian mainland population of M. sinensis was high, whereas, in the Japanese population, the number of functional alleles decreased due to the accumulation of alleles with MITE insertions and/or other deleterious mutations. This difference suggests that dependency on the gene function of Hd1a is different between M. sinensis populations from the Asian mainland and the Japanese archipelago.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: Schematic model for Miscanthus Hd1 evolution. Blue indicates functional alleles and red indicates non-functional alleles. The whole genome duplication of Miscanthus resulted in Hd1a and Hd1b loci. Accumulation of deleterious mutations caused pseudogenization of Hd1b in M. sinensis. By additional local duplication, Hd1a increased in copy number (duplicated genes designated as Hd1a’ and Hd1a’’ in figure). After the last glacial maximum, the number of functional Hd1a alleles in the Asian mainland population of M. sinensis was high, whereas, in the Japanese population, the number of functional alleles decreased due to the accumulation of alleles with MITE insertions and/or other deleterious mutations. This difference suggests that dependency on the gene function of Hd1a is different between M. sinensis populations from the Asian mainland and the Japanese archipelago.
Mentions: The NJ tree showed that 20 of the 44 Miscanthus accessions that were analysed had two diverged loci, Hd1a and Hd1b (Fig. 3; see Supplementary Fig. S2 at JXB online). Although their positions on the Miscanthus genome are unknown, the existence of duplicated Hd1 loci can be considered to be universal within the genus Miscanthus, in contrast to sorghum, maize, and rice which have only one Hd1 locus. The recent genome duplication of Miscanthus relative to sorghum (Kim et al., 2012; Ma et al., 2012; Swaminathan et al., 2012) can at least partially account for differences in the number of Hd1 loci. Large-scale genomic analyses of M. sinensis have revealed that M. sinensis (x=19) is a diploidized tetraploid species formed by the duplication of chromosomes after the divergence from an x=10 ancestor (Kim et al., 2012; Ma et al., 2012; Swaminathan et al., 2012). The three or more loci of MsiHd1 identified by this study in M. sinensis might have been caused in part by the whole genome duplication (MsiHd1a and MsiHd1b) and also by local gene duplications (multiple MsiHd1a) via unequal crossing-over (Fig. 6). Although gene duplication can be an evolutionary process to gain new function (Ohno, 1970), a duplicated gene can alternatively be subjected to inactivation by mutations and genetic drift (Hughes, 1994; Force et al., 1999). Redundancy of gene functions among multiple MsiHd1 loci through polyploidization might have allowed pseudogenization of MsiHd1b. The precise number of MsiHd1a loci in Miscanthus remains unknown. In two Japanese accessions, JM0190-5 and JM0091-2, five copies of MsiHd1a were detected, suggesting the possibility of additional duplications in MsiHd1a. The M. floridulus Hd1 locus, having a revertant allele, showed the greatest sequence similarity to the M. sinensis Hd1 locus (Fig. 3) of the species evaluated. McoHd1b and Msa(4x)Hd1b in M. sinensis spp. condensatus and M. sacchariflorus (4x), respectively, each had three alleles, suggesting at least two loci, in contrast to the putative single locus in M. sinensis. The observation of five alleles of Msa(4x)Hd1a within one individual M. sacchariflorus (4x) indicates that there are at least three Msa(4x)Hd1a loci in this individual. As observed above, copy number of Hd1a/b varies among species in the genus Miscanthus.

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.