Miscanthus sacchariflorus x Miscanthus sinensis cultivar:PF30022 x PMS-014
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ABSTRACT:
PROVIDER: PRJNA582435 | ENA |
REPOSITORIES: ENA
Dataset's files
primary
| Action | DRS | |||
|---|---|---|---|---|
| SRR10672775_1.fastq.gz | Fastqsanger.gz | |||
| SRR10672775_2.fastq.gz | Fastqsanger.gz |
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Project description:The genome sizes of five Miscanthus species, including 79 accessions of M. lutarioriparius, 8 of M. floridulus, 6 of M. sacchariflorus, 7 of M. sinensis, and 4 of M. × giganteus were examined using flow cytometry. The overall average nuclear DNA content were 4.256?±?0.6 pg/2C in M. lutarioriparius, 5.175?±?0.3 pg/2C in M. floridulus, 3.956?±?0.2 pg/2C in M. sacchariflorus, 5.272?±?0.2 pg/2C in M. sinensis, and 6.932?±?0.1 pg/2C in M. × giganteus. Interspecific variation was found at the diploid level, suggesting that DNA content might be a parameter that can be used to differentiate the species. Tetraploid populations were found in M. lutarioriparius, M. sacchariflorus, and M. sinensis, and their DNA content were 8.34?±?1.2, 8.52, and 8.355 pg, respectively. The association between the DNA content of M. lutarioriparius, collected from representative ranges across the Yangtze River, and its geographic distribution was statistically analyzed. A consistent pattern of DNA content variation in 79 M. lutarioriparius accessions across its entire geographic range was found in this study. Along the Yangtze River, the DNA content of M. lutarioriparius tended to increase from the upstream to the downstream areas, and almost all tetraploids gathered in the upstream area extended to coastal regions.
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Project description:<i>Miscanthus</i> species are perennial C4 grasses that are considered promising energy crops because of their high biomass yields, excellent adaptability and low management costs. <i>Miscanthus lutarioriparius</i> and <i>Miscanthus sacchariflorus</i> are closely related subspecies that are distributed in different habitats. However, there are only a few reports on the mechanisms by which <i>Miscanthus</i> adapts to different environments. Here, comparative transcriptomic and morphological analyses were used to study the evolutionary adaptation of <i>M. lutarioriparius</i> and <i>M. sacchariflorus</i> to different habitats. In total, among 7586 identified orthologs, 2060 orthologs involved in phenylpropanoid biosynthesis and plant hormones were differentially expressed between the two species. Through an analysis of the Ka/Ks ratios of the orthologs, we estimated that the divergence time between the two species was approximately 4.37 Mya. In addition, 37 candidate positively selected orthologs (PSGs) that played important roles in the adaptation of these species to different habitats were identified. Then, the expression levels of 20 PSGs in response to flooding and drought stress were analyzed, and the analysis revealed significant changes in their expression levels. These results facilitate our understanding of the evolutionary adaptation to habitats and the speciation of <i>M. lutarioriparius</i> and <i>M. sacchariflorus</i>. We hypothesise that lignin synthesis genes are the main cause of the morphological differences between the two species. In summary, the plant nonspecific phospholipase C gene family and the receptor-like protein kinase gene family played important roles in the evolution of these two species.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1007/s12298-021-01030-1.
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Project description:Lignocellulose content is an important factor affecting the conversion efficiency of biomass energy plants. In this study, 179 <i>Miscanthus</i> accessions in China were used to determine the content of lignocellulose components in stems via acid hydrolysis and high-performance liquid chromatography. Results showed that the average lignocellulose content of wild <i>Miscanthus</i> germplasm resources was 80.27 ± 6.51%, and the average content of cellulose, hemicellulose, lignin, extracts, and total ash was 38.38 ± 3.52, 24.23 ± 4.21, 17.66 ± 1.56, 14.50 ± 5.60, and 2.53 ± 0.59%, respectively. The average lignocellulose content of <i>M. sinensis, M. floridulus, M. nudipes, M. sacchariflorus, M. lutarioriparius</i>, and the hybrids was 77.94 ± 6.06, 75.16 ± 4.98, 75.68 ± 3.02, 83.71 ± 4.78, 81.50 ± 5.23, and 74.72 ± 7.13%, respectively. In all the tested materials, the highest cellulose content was 48.52%, and the lowest was 29.79%. Hemicellulose had the maximum content of 34.23% and a minimum content of 15.71%. The highest lignin content was 23.75%, and the lowest was 13.01%. The lignocellulosic components of different ploidy materials were compared. The content of lignocellulosic components of diploid <i>M. sacchariflorus</i> was higher than that of tetraploid <i>M. sacchariflorus</i>, and the content of lignocellulosic components of diploid <i>M. lutarioriparius</i> was lower than that of tetraploid <i>M. lutarioriparius</i>. Analysis of the relationship between the changes in lignocellulosic components and geographical locations of <i>Miscanthus</i> showed that the holocellulose and hemicellulose content was significantly positive correlated with the latitude of the original growth location. Results indicated that the lignocellulosic components of <i>Miscanthus</i> resources in China are rich in genetic diversity.
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Project description:BACKGROUND AND AIMS:Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sacchariflorus has a broad geographic range, is used to produce paper in China and is one of the parents (along with Miscanthus sinensis) of the important biomass species Miscanthus × giganteus. The largest study of M. sacchariflorus population genetics to date is reported here. METHODS:Collections included 764 individuals across East Asia. Samples were genotyped with 34 605 single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RAD-seq) and ten plastid microsatellites, and were subjected to ploidy analysis by flow cytometry. KEY RESULTS:Six major genetic groups within M. sacchariflorus were identified using SNP data: three diploid groups, comprising Yangtze (M. sacchariflorus ssp. lutarioriparius), N China and Korea/NE China/Russia; and three tetraploid groups, comprising N China/Korea/Russia, S Japan and N Japan. Miscanthus sacchariflorus ssp. lutarioriparius was derived from the N China group, with a substantial bottleneck. Japanese and mainland tetraploids originated from independent polyploidization events. Hybrids between diploid M. sacchariflorus and M. sinensis were identified in Korea, but without introgression into either parent species. In contrast, tetraploid M. sacchariflorus in southern Japan and Korea exhibited substantial hybridization and introgression with local diploid M. sinensis. CONCLUSIONS:Genetic data indicated that the land now under the Yellow Sea was a centre of diversity for M. sacchariflorus during the last glacial maximum, followed by a series of migrations as the climate became warmer and wetter. Overall, M. sacchariflorus has greater genetic diversity than M. sinensis, suggesting that breeding and selection within M. sacchariflorus will be important for the development of improved M. × giganteus. Ornamental M. sacchariflorus genotypes in Europe and North America represent a very narrow portion of the species' genetic diversity, and thus do not well represent the species as a whole.
| S-EPMC6821896 | BioStudies
Project description:Chromosomes of four <i>Miscanthus</i> (Andersson, 1855) species including <i>M. sinensis</i> (Andersson, 1855), <i>M. floridulus</i> (Schumann & Lauterb, 1901), <i>M. sacchariflorus</i> (Hackel, 1882) and <i>M. lutarioriparius</i> (Chen & Renvoize, 2005) were analyzed using sequentially combined PI and DAPI (CPD) staining and fluorescence <i>in situ</i> hybridization (FISH) with 45S rDNA probe. To elucidate the phylogenetic relationship among the four <i>Miscanthus</i> species, the homology of repetitive sequences among the four species was analyzed by comparative genomic <i>in situ</i> hybridization (cGISH). Subsequently four <i>Miscanthus</i> species were clustered based on the internal transcribed spacer (ITS) of 45S rDNA. Molecular cytogenetic karyotypes of the four <i>Miscanthus</i> species were established for the first time using chromosome measurements, fluorochrome bands and 45S rDNA FISH signals, which will provide a cytogenetic tool for the identification of these four species. All the four have the karyotype formula of <i>Miscanthus</i> species, which is 2n = 2x = 38 = 34m(2SAT) + 4sm, and one pair of 45S rDNA sites. The latter were shown as strong red bands by CPD staining. A non-rDNA CPD band emerged in <i>M. floridulus</i> and some blue DAPI bands appeared in <i>M. sinensis</i> and <i>M. floridulus</i>. The hybridization signals of <i>M. floridulus</i> genomic DNA to the chromosomes of <i>M. sinensis</i> and <i>M. lutarioriparius</i> genomic DNA to the chromosomes of <i>M. sacchariflorus</i> were stronger and more evenly distributed than other combinations. Molecular phylogenetic trees showed that <i>M. sinensis</i> and <i>M. floridulus</i> were closest relatives, and <i>M. sacchariflorus</i> and <i>M. lutarioriparius</i> were also closely related. These findings were consistent with the phylogenetic relationships inferred from the cGISH patterns.
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Project description:Miscanthus sacchariflorus lutarioriparius PF30022 x Miscanthus sinensis PMS-014 F1 Population Resequencing - 14UI-026.324 genome sequencing
| PRJNA582136 | ENA
Project description:Miscanthus sacchariflorus lutarioriparius PF30022 x Miscanthus sinensis PMS-014 F1 Population Resequencing - 14UI-026.242 genome sequencing
| PRJNA582138 | ENA
Project description:Miscanthus sacchariflorus lutarioriparius PF30022 x Miscanthus sinensis PMS-014 F1 Population Resequencing - 14UI-026.094 genome sequencing
| PRJNA582397 | ENA