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The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies.

O'Rourke JA, Fu F, Bucciarelli B, Yang SS, Samac DA, Lamb JF, Monteros MJ, Graham MA, Gronwald JW, Krom N, Li J, Dai X, Zhao PX, Vance CP - BMC Genomics (2015)

Bottom Line: Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56.Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,241) were identified.The Medicago sativa Gene Index 1.2 increases the expressed sequence data available for alfalfa by ninefold and can be expanded as additional experiments are performed.

View Article: PubMed Central - PubMed

Affiliation: USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA. Jamie.ORourke@ars.usda.gov.

ABSTRACT

Background: Alfalfa (Medicago sativa L.) is the primary forage legume crop species in the United States and plays essential economic and ecological roles in agricultural systems across the country. Modern alfalfa is the result of hybridization between tetraploid M. sativa ssp. sativa and M. sativa ssp. falcata. Due to its large and complex genome, there are few genomic resources available for alfalfa improvement.

Results: A de novo transcriptome assembly from two alfalfa subspecies, M. sativa ssp. sativa (B47) and M. sativa ssp. falcata (F56) was developed using Illumina RNA-seq technology. Transcripts from roots, nitrogen-fixing root nodules, leaves, flowers, elongating stem internodes, and post-elongation stem internodes were assembled into the Medicago sativa Gene Index 1.2 (MSGI 1.2) representing 112,626 unique transcript sequences. Nodule-specific and transcripts involved in cell wall biosynthesis were identified. Statistical analyses identified 20,447 transcripts differentially expressed between the two subspecies. Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56. Comparing transcript abundance in floral tissues of B47 and F56 identified expression differences in sequences involved in anthocyanin and carotenoid synthesis, which determine flower pigmentation. Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,241) were identified.

Conclusions: The Medicago sativa Gene Index 1.2 increases the expressed sequence data available for alfalfa by ninefold and can be expanded as additional experiments are performed. The MSGI 1.2 transcriptome sequences, annotations, expression profiles, and SNPs were assembled into the Alfalfa Gene Index and Expression Database (AGED) at http://plantgrn.noble.org/AGED/ , a publicly available genomic resource for alfalfa improvement and legume research.

No MeSH data available.


Related in: MedlinePlus

Distribution of transcript lengths in the Medicago sativa Gene Index 1.2. The de novo transcriptome was built from 76-bp single-end read sequences from three biological replicates of six tissues (roots, nodules, post-elongation stem internodes, elongating stem internodes, leaves, and flowers) isolated from Medicago sativa ssp. falcata (F56) and M. sativa ssp. sativa (B47) using Velvet/Oases, cd-HIT, and CAP3. The Medicago sativa Gene Index 1.2 (MSGI 1.2) is composed of 112,626 unique sequences ranging from 100 bp to 15,768 bp
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Fig2: Distribution of transcript lengths in the Medicago sativa Gene Index 1.2. The de novo transcriptome was built from 76-bp single-end read sequences from three biological replicates of six tissues (roots, nodules, post-elongation stem internodes, elongating stem internodes, leaves, and flowers) isolated from Medicago sativa ssp. falcata (F56) and M. sativa ssp. sativa (B47) using Velvet/Oases, cd-HIT, and CAP3. The Medicago sativa Gene Index 1.2 (MSGI 1.2) is composed of 112,626 unique sequences ranging from 100 bp to 15,768 bp

Mentions: The MSGI 1.2 transcriptome assembly consists of 112,626 unique sequences (Additional file 1). On average, 15.25 million 76 bp reads were generated for each cDNA library (Additional file 2) and 84 % of the reads generated mapped to the MSGI 1.2 assembly. The average MSGI 1.2 contig size is 1,352 bp, with the largest contig spanning 15,768 bp (Fig. 2). The assembly provides 152,325,272 bp of alfalfa sequence, a significant increase in the publicly available sequence data for this crop. The MSGI 1.2 transcriptome represents 19 % of the predicted 800 Mbp M. sativa genome, which is double the percentage of the M. truncatula genome predicted to be transcriptionally active (8.3 %) [33], but less than that of Arabidopsis (24 %) [34].Fig. 2


The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies.

O'Rourke JA, Fu F, Bucciarelli B, Yang SS, Samac DA, Lamb JF, Monteros MJ, Graham MA, Gronwald JW, Krom N, Li J, Dai X, Zhao PX, Vance CP - BMC Genomics (2015)

Distribution of transcript lengths in the Medicago sativa Gene Index 1.2. The de novo transcriptome was built from 76-bp single-end read sequences from three biological replicates of six tissues (roots, nodules, post-elongation stem internodes, elongating stem internodes, leaves, and flowers) isolated from Medicago sativa ssp. falcata (F56) and M. sativa ssp. sativa (B47) using Velvet/Oases, cd-HIT, and CAP3. The Medicago sativa Gene Index 1.2 (MSGI 1.2) is composed of 112,626 unique sequences ranging from 100 bp to 15,768 bp
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4492073&req=5

Fig2: Distribution of transcript lengths in the Medicago sativa Gene Index 1.2. The de novo transcriptome was built from 76-bp single-end read sequences from three biological replicates of six tissues (roots, nodules, post-elongation stem internodes, elongating stem internodes, leaves, and flowers) isolated from Medicago sativa ssp. falcata (F56) and M. sativa ssp. sativa (B47) using Velvet/Oases, cd-HIT, and CAP3. The Medicago sativa Gene Index 1.2 (MSGI 1.2) is composed of 112,626 unique sequences ranging from 100 bp to 15,768 bp
Mentions: The MSGI 1.2 transcriptome assembly consists of 112,626 unique sequences (Additional file 1). On average, 15.25 million 76 bp reads were generated for each cDNA library (Additional file 2) and 84 % of the reads generated mapped to the MSGI 1.2 assembly. The average MSGI 1.2 contig size is 1,352 bp, with the largest contig spanning 15,768 bp (Fig. 2). The assembly provides 152,325,272 bp of alfalfa sequence, a significant increase in the publicly available sequence data for this crop. The MSGI 1.2 transcriptome represents 19 % of the predicted 800 Mbp M. sativa genome, which is double the percentage of the M. truncatula genome predicted to be transcriptionally active (8.3 %) [33], but less than that of Arabidopsis (24 %) [34].Fig. 2

Bottom Line: Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56.Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,241) were identified.The Medicago sativa Gene Index 1.2 increases the expressed sequence data available for alfalfa by ninefold and can be expanded as additional experiments are performed.

View Article: PubMed Central - PubMed

Affiliation: USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA. Jamie.ORourke@ars.usda.gov.

ABSTRACT

Background: Alfalfa (Medicago sativa L.) is the primary forage legume crop species in the United States and plays essential economic and ecological roles in agricultural systems across the country. Modern alfalfa is the result of hybridization between tetraploid M. sativa ssp. sativa and M. sativa ssp. falcata. Due to its large and complex genome, there are few genomic resources available for alfalfa improvement.

Results: A de novo transcriptome assembly from two alfalfa subspecies, M. sativa ssp. sativa (B47) and M. sativa ssp. falcata (F56) was developed using Illumina RNA-seq technology. Transcripts from roots, nitrogen-fixing root nodules, leaves, flowers, elongating stem internodes, and post-elongation stem internodes were assembled into the Medicago sativa Gene Index 1.2 (MSGI 1.2) representing 112,626 unique transcript sequences. Nodule-specific and transcripts involved in cell wall biosynthesis were identified. Statistical analyses identified 20,447 transcripts differentially expressed between the two subspecies. Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56. Comparing transcript abundance in floral tissues of B47 and F56 identified expression differences in sequences involved in anthocyanin and carotenoid synthesis, which determine flower pigmentation. Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,241) were identified.

Conclusions: The Medicago sativa Gene Index 1.2 increases the expressed sequence data available for alfalfa by ninefold and can be expanded as additional experiments are performed. The MSGI 1.2 transcriptome sequences, annotations, expression profiles, and SNPs were assembled into the Alfalfa Gene Index and Expression Database (AGED) at http://plantgrn.noble.org/AGED/ , a publicly available genomic resource for alfalfa improvement and legume research.

No MeSH data available.


Related in: MedlinePlus