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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.


Comparative distribution of GO categories for H. compressa (“Yaan”) and H. altissima (“1110”).
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Figure 4: Comparative distribution of GO categories for H. compressa (“Yaan”) and H. altissima (“1110”).

Mentions: GO annotation is an international gene functional classification system that provides a controlled vocabulary that is able to comprehensively describe properties of the uncharacterized sequences in any organism (Gene Ontology Consortium, 2004; Tang et al., 2014). Based on sequence homology, 50,638 “Yaan” unigenes (36.92% of all the assembled “Yaan” unigenes) and 30,538 “1110” unigenes (39.58% of all the assembled “1110” unigenes) were assigned to at least one GO term and were classified into three groups: biological processes, molecular function, and cellular component. The distribution of GO groups for the two Hemarthria materials was extremely similar. As described in Figure 4, most of the unigenes were classified into the cellular components of cell part, cell, organelle, and membrane. In the molecular function group, binding, catalytic activity, structural molecules and transporter activity were found to be the four most frequent classes. Among 25 different biological process categories, the metabolic processes category was the most represented followed by cellular processes, response to stimuli, and biological regulation. With the help of GO functional classification, a large number of the unigenes were assigned to a wide range of biological processes, molecular functions, and cellular components. This information can provide a valuable resource for gene expression profile analysis, gene location, and gene isolation in Hemarthria species. In addition, the main GO classifications identified in this study pertained to fundamental biological processes. These results are similar to previously reported studies of de novo transcriptome analyses in the taproots of radish and the leaves of young tea plant (Wang et al., 2013; Wu et al., 2014).


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)

Comparative distribution of GO categories for H. compressa (“Yaan”) and H. altissima (“1110”).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Comparative distribution of GO categories for H. compressa (“Yaan”) and H. altissima (“1110”).
Mentions: GO annotation is an international gene functional classification system that provides a controlled vocabulary that is able to comprehensively describe properties of the uncharacterized sequences in any organism (Gene Ontology Consortium, 2004; Tang et al., 2014). Based on sequence homology, 50,638 “Yaan” unigenes (36.92% of all the assembled “Yaan” unigenes) and 30,538 “1110” unigenes (39.58% of all the assembled “1110” unigenes) were assigned to at least one GO term and were classified into three groups: biological processes, molecular function, and cellular component. The distribution of GO groups for the two Hemarthria materials was extremely similar. As described in Figure 4, most of the unigenes were classified into the cellular components of cell part, cell, organelle, and membrane. In the molecular function group, binding, catalytic activity, structural molecules and transporter activity were found to be the four most frequent classes. Among 25 different biological process categories, the metabolic processes category was the most represented followed by cellular processes, response to stimuli, and biological regulation. With the help of GO functional classification, a large number of the unigenes were assigned to a wide range of biological processes, molecular functions, and cellular components. This information can provide a valuable resource for gene expression profile analysis, gene location, and gene isolation in Hemarthria species. In addition, the main GO classifications identified in this study pertained to fundamental biological processes. These results are similar to previously reported studies of de novo transcriptome analyses in the taproots of radish and the leaves of young tea plant (Wang et al., 2013; Wu et al., 2014).

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.