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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 distributions of KOG categories for H. compressa (“Yaan”) and H. altissima (“1110”).
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Figure 5: Comparative distributions of KOG categories for H. compressa (“Yaan”) and H. altissima (“1110”).

Mentions: For KOG analyses, 42,047 unigenes from “Yaan” were classified into 25 functional categories under four larger groups (metabolism, cellular processes and signaling, information storage and processing, and poorly characterized). Among these functional categories, the top three largest KOG categories were: 1) the prediction of general function only (6604 unigenes, 15.71%), 2) translation, ribosomal structure, and biogenesis (4730 unigenes, 11.25%), and 3) post-translational modification, protein turnover, and chaperones (4113 unigenes, 9.78%). Interestingly, only a few unigenes were assigned to extracellular structures (232 unigenes, 0.55%), nuclear structure (55 unigenes, 0.13%), and cell motility (20 unigenes, 0.05%). We identified several differences between the results from the KOG analyses for the “1110” unigenes and the “Yaan” unigenes. A total of 21,867 of the “1110” unigenes were distributed into 25 functional categories with the top three categories being: (1) general function prediction only (18.42%), (2) signal transduction mechanisms (8.99%), and (3) post-translational modification, protein turnover, and chaperones (8.88%). In both the “1110” and “Yaan” data, extracellular structures, nuclear structure, and cell motility categories had the smallest number of unigenes (Figure 5).


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 distributions of KOG 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 5: Comparative distributions of KOG categories for H. compressa (“Yaan”) and H. altissima (“1110”).
Mentions: For KOG analyses, 42,047 unigenes from “Yaan” were classified into 25 functional categories under four larger groups (metabolism, cellular processes and signaling, information storage and processing, and poorly characterized). Among these functional categories, the top three largest KOG categories were: 1) the prediction of general function only (6604 unigenes, 15.71%), 2) translation, ribosomal structure, and biogenesis (4730 unigenes, 11.25%), and 3) post-translational modification, protein turnover, and chaperones (4113 unigenes, 9.78%). Interestingly, only a few unigenes were assigned to extracellular structures (232 unigenes, 0.55%), nuclear structure (55 unigenes, 0.13%), and cell motility (20 unigenes, 0.05%). We identified several differences between the results from the KOG analyses for the “1110” unigenes and the “Yaan” unigenes. A total of 21,867 of the “1110” unigenes were distributed into 25 functional categories with the top three categories being: (1) general function prediction only (18.42%), (2) signal transduction mechanisms (8.99%), and (3) post-translational modification, protein turnover, and chaperones (8.88%). In both the “1110” and “Yaan” data, extracellular structures, nuclear structure, and cell motility categories had the smallest number of unigenes (Figure 5).

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.