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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.


The length distribution of CDSs mapped to know genes.
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Figure 1: The length distribution of CDSs mapped to know genes.

Mentions: In order to predict CDSs, the unigenes for both “Yaan” and “1110” were consolidated into a single set of sequences. We predicted a total of 180,932 CDSs in our study, of which 99,037 CDSs aligned to the eight previously discussed databases. The largest number of CDSs (23,182, 23.41%) was 100–200 nt long (Figure 1). An additional 81,895 CDSs without BLAST hits were predicted by the Getorf software. Interestingly, 100–200 nt long CDSs were also the highest in number in this group (40,973 CDSs, 50.03%; Figure 2).


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)

The length distribution of CDSs mapped to know genes.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: The length distribution of CDSs mapped to know genes.
Mentions: In order to predict CDSs, the unigenes for both “Yaan” and “1110” were consolidated into a single set of sequences. We predicted a total of 180,932 CDSs in our study, of which 99,037 CDSs aligned to the eight previously discussed databases. The largest number of CDSs (23,182, 23.41%) was 100–200 nt long (Figure 1). An additional 81,895 CDSs without BLAST hits were predicted by the Getorf software. Interestingly, 100–200 nt long CDSs were also the highest in number in this group (40,973 CDSs, 50.03%; Figure 2).

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.