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De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species.

Huang X, Yan HD, Zhang XQ, Zhang J, Frazier TP, Huang DJ, Lu L, Huang LK, Liu W, Peng Y, Ma X, Yan YH - Front Plant Sci (2016)

Bottom Line: In addition, a total of 86,731 "Yaan" and 48,645 "1110" unigenes were successfully annotated.We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product.The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.

View Article: PubMed Central - PubMed

Affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University Chengdu, China.

ABSTRACT
Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa "Yaan" and H. altissima "1110." Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for "Yaan" and "1110," respectively. In addition, a total of 86,731 "Yaan" and 48,645 "1110" unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11-87.04%) of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.

No MeSH data available.


KEGG classification of H. compressa (“Yaan”) unigenes and H. altissima (“1110”) unigenes.
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Figure 6: KEGG classification of H. compressa (“Yaan”) unigenes and H. altissima (“1110”) unigenes.

Mentions: To systematically understand the biological pathways activated in Hemarthria roots and leaves, a KEGG analysis of the assembled unigenes of “Yaan” and “1110” was performed. A total of 18,148 and 8434 unigenes for “Yaan” and “1110,” respectively, were assigned to 121 biological pathways including transcription and translation, protein processing and modification, biosynthesis of secondary metabolites, signal transduction, replication and repair, transport and catabolism, immune system function, amino acid metabolism, and several others. The six major pathway groups for “Yaan” and “1110” were ribosomal [2832 (15.60%); 994 (11.79%)], oxidative phosphorylation [789 (4.35%); 324 (3.84%)], protein processing in the endoplasmic reticulum [798 (4.40%); 246 (2.92%)], RNA transport [739 (4.07%); 293 (3.47%)], spliceosomal [617 (3.40%); 247 (2.93%)], and glycolysis/gluconeogenesis [469 (2.58%); 234 (2.77%)] (Figure 6). These findings revealed a high level of protein synthesis occurring during the growth and development of Hemarthria species, and reflect the reliability of the KEGG orthology-based annotation. Furthermore, these data may provide reference information for future experiments such as gene expression analyses and gene cloning.


De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species.

Huang X, Yan HD, Zhang XQ, Zhang J, Frazier TP, Huang DJ, Lu L, Huang LK, Liu W, Peng Y, Ma X, Yan YH - Front Plant Sci (2016)

KEGG classification of H. compressa (“Yaan”) unigenes and H. altissima (“1110”) unigenes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4834353&req=5

Figure 6: KEGG classification of H. compressa (“Yaan”) unigenes and H. altissima (“1110”) unigenes.
Mentions: To systematically understand the biological pathways activated in Hemarthria roots and leaves, a KEGG analysis of the assembled unigenes of “Yaan” and “1110” was performed. A total of 18,148 and 8434 unigenes for “Yaan” and “1110,” respectively, were assigned to 121 biological pathways including transcription and translation, protein processing and modification, biosynthesis of secondary metabolites, signal transduction, replication and repair, transport and catabolism, immune system function, amino acid metabolism, and several others. The six major pathway groups for “Yaan” and “1110” were ribosomal [2832 (15.60%); 994 (11.79%)], oxidative phosphorylation [789 (4.35%); 324 (3.84%)], protein processing in the endoplasmic reticulum [798 (4.40%); 246 (2.92%)], RNA transport [739 (4.07%); 293 (3.47%)], spliceosomal [617 (3.40%); 247 (2.93%)], and glycolysis/gluconeogenesis [469 (2.58%); 234 (2.77%)] (Figure 6). These findings revealed a high level of protein synthesis occurring during the growth and development of Hemarthria species, and reflect the reliability of the KEGG orthology-based annotation. Furthermore, these data may provide reference information for future experiments such as gene expression analyses and gene cloning.

Bottom Line: In addition, a total of 86,731 "Yaan" and 48,645 "1110" unigenes were successfully annotated.We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product.The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.

View Article: PubMed Central - PubMed

Affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University Chengdu, China.

ABSTRACT
Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa "Yaan" and H. altissima "1110." Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for "Yaan" and "1110," respectively. In addition, a total of 86,731 "Yaan" and 48,645 "1110" unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11-87.04%) of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.

No MeSH data available.