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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.


Neighbor–Joining (NJ) tree showing the relationships among 54 CO/Hd1 alleles of 16 accessions of Miscanthus sinensis, six CO/Hd1 alleles from one of M. floridulus, five CO/Hd1 alleles from one of M. sinensis spp. condensatus, three CO/Hd1 alleles from one of M. sacchariflorus (2×), and eight CO/Hd1 alleles from one of M. sacchariflorus (4x). To facilitate viewing this figure on a single page, only about half of the accessions analysed are shown here (see Supplementary Fig. S2 at JXB online for the complete tree). Sixteen accessions of M. sinensis that represent a range of MITE insertions and latitudes of origin were included in this figure. Sorghum bicolor was used as an out-group. The phylogenetic tree was split largely into two clades, which were classified as two loci, Hd1a and Hd1b. All detected alleles of Hd1b in M. sinensis were non-functional. Major mutations that caused loss-of-function are shown to the right of the red circles, which represent non-functional alleles. The double slash on the out-group branch indicates shortening of the branch length by approximately half. Bootstrap values for nodes supported in >50% of 1000 bootstrap replicates are shown. The unnumbered squares, circles, and triangles represent the geographic origin of accessions, putative gene function, and the existence of MsiMITE1, respectively. The numbered triangles show MsiMITE2 to MsiMITE5.
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Figure 3: Neighbor–Joining (NJ) tree showing the relationships among 54 CO/Hd1 alleles of 16 accessions of Miscanthus sinensis, six CO/Hd1 alleles from one of M. floridulus, five CO/Hd1 alleles from one of M. sinensis spp. condensatus, three CO/Hd1 alleles from one of M. sacchariflorus (2×), and eight CO/Hd1 alleles from one of M. sacchariflorus (4x). To facilitate viewing this figure on a single page, only about half of the accessions analysed are shown here (see Supplementary Fig. S2 at JXB online for the complete tree). Sixteen accessions of M. sinensis that represent a range of MITE insertions and latitudes of origin were included in this figure. Sorghum bicolor was used as an out-group. The phylogenetic tree was split largely into two clades, which were classified as two loci, Hd1a and Hd1b. All detected alleles of Hd1b in M. sinensis were non-functional. Major mutations that caused loss-of-function are shown to the right of the red circles, which represent non-functional alleles. The double slash on the out-group branch indicates shortening of the branch length by approximately half. Bootstrap values for nodes supported in >50% of 1000 bootstrap replicates are shown. The unnumbered squares, circles, and triangles represent the geographic origin of accessions, putative gene function, and the existence of MsiMITE1, respectively. The numbered triangles show MsiMITE2 to MsiMITE5.

Mentions: An NJ tree indicated that at least one of the multiple MsiHd1 loci was a pseudogene locus with deleterious mutations, forming a distinctive monophyletic clade (Fig. 3; see Supplementary Fig. S2 at JXB online). The pseudogene locus was named as MsiHd1b and the others were considered alleles of the MsiHd1a multi-locus family. All 46 alleles of MsiHd1a detected in accessions from China and South Korea appeared to be functional based on their sequence, whereas about half of the alleles of MsiHd1a from Japanese accessions had putative loss-of-function mutations (35 functional alleles/68 total alleles=51.5%). Thus, a strikingly large difference was observed in the number of putative functional alleles between accessions from the Asian mainland and the Japanese archipelago (Fig. 4), although no clear difference for Hd1a alleles was observed among northern, middle, and southern latitudinal regions.


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)

Neighbor–Joining (NJ) tree showing the relationships among 54 CO/Hd1 alleles of 16 accessions of Miscanthus sinensis, six CO/Hd1 alleles from one of M. floridulus, five CO/Hd1 alleles from one of M. sinensis spp. condensatus, three CO/Hd1 alleles from one of M. sacchariflorus (2×), and eight CO/Hd1 alleles from one of M. sacchariflorus (4x). To facilitate viewing this figure on a single page, only about half of the accessions analysed are shown here (see Supplementary Fig. S2 at JXB online for the complete tree). Sixteen accessions of M. sinensis that represent a range of MITE insertions and latitudes of origin were included in this figure. Sorghum bicolor was used as an out-group. The phylogenetic tree was split largely into two clades, which were classified as two loci, Hd1a and Hd1b. All detected alleles of Hd1b in M. sinensis were non-functional. Major mutations that caused loss-of-function are shown to the right of the red circles, which represent non-functional alleles. The double slash on the out-group branch indicates shortening of the branch length by approximately half. Bootstrap values for nodes supported in >50% of 1000 bootstrap replicates are shown. The unnumbered squares, circles, and triangles represent the geographic origin of accessions, putative gene function, and the existence of MsiMITE1, respectively. The numbered triangles show MsiMITE2 to MsiMITE5.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: Neighbor–Joining (NJ) tree showing the relationships among 54 CO/Hd1 alleles of 16 accessions of Miscanthus sinensis, six CO/Hd1 alleles from one of M. floridulus, five CO/Hd1 alleles from one of M. sinensis spp. condensatus, three CO/Hd1 alleles from one of M. sacchariflorus (2×), and eight CO/Hd1 alleles from one of M. sacchariflorus (4x). To facilitate viewing this figure on a single page, only about half of the accessions analysed are shown here (see Supplementary Fig. S2 at JXB online for the complete tree). Sixteen accessions of M. sinensis that represent a range of MITE insertions and latitudes of origin were included in this figure. Sorghum bicolor was used as an out-group. The phylogenetic tree was split largely into two clades, which were classified as two loci, Hd1a and Hd1b. All detected alleles of Hd1b in M. sinensis were non-functional. Major mutations that caused loss-of-function are shown to the right of the red circles, which represent non-functional alleles. The double slash on the out-group branch indicates shortening of the branch length by approximately half. Bootstrap values for nodes supported in >50% of 1000 bootstrap replicates are shown. The unnumbered squares, circles, and triangles represent the geographic origin of accessions, putative gene function, and the existence of MsiMITE1, respectively. The numbered triangles show MsiMITE2 to MsiMITE5.
Mentions: An NJ tree indicated that at least one of the multiple MsiHd1 loci was a pseudogene locus with deleterious mutations, forming a distinctive monophyletic clade (Fig. 3; see Supplementary Fig. S2 at JXB online). The pseudogene locus was named as MsiHd1b and the others were considered alleles of the MsiHd1a multi-locus family. All 46 alleles of MsiHd1a detected in accessions from China and South Korea appeared to be functional based on their sequence, whereas about half of the alleles of MsiHd1a from Japanese accessions had putative loss-of-function mutations (35 functional alleles/68 total alleles=51.5%). Thus, a strikingly large difference was observed in the number of putative functional alleles between accessions from the Asian mainland and the Japanese archipelago (Fig. 4), although no clear difference for Hd1a alleles was observed among northern, middle, and southern latitudinal regions.

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.