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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

Gene ontology analyses of legume transcripts confirm the breadth of the M. sativa transcript assembly. a Total number of transcripts in MSGI 1.2 M. truncatula, G. max, and P. vulgaris with Biological Process (BP) Gene Ontology (GO) Slim annotations. The 2-fold difference in transcript number reflects a polyploid event in M. sativa compared to M. truncatula and a genome duplication event in G. max compared to P. vulgaris. b The percentage of transcripts with each BP GO Slim annotation, from the total number of sequences with BP GO Slim annotations, is consistent across all four legumes, suggesting the MSGI 1.2 assembly represents the majority of transcripts in the M. sativa genome
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Fig3: Gene ontology analyses of legume transcripts confirm the breadth of the M. sativa transcript assembly. a Total number of transcripts in MSGI 1.2 M. truncatula, G. max, and P. vulgaris with Biological Process (BP) Gene Ontology (GO) Slim annotations. The 2-fold difference in transcript number reflects a polyploid event in M. sativa compared to M. truncatula and a genome duplication event in G. max compared to P. vulgaris. b The percentage of transcripts with each BP GO Slim annotation, from the total number of sequences with BP GO Slim annotations, is consistent across all four legumes, suggesting the MSGI 1.2 assembly represents the majority of transcripts in the M. sativa genome

Mentions: To evaluate the breadth of gene function across the MSGI 1.2 assembly, we compared the gene ontology (GO) [38] slim annotations of the MSGI 1.2 assembly and the primary transcripts of M. truncatula, soybean, and P. vulgaris. The total number of transcripts associated with each biological process (BP) GO Slim term is approximately 2-fold greater for M. sativa and G. max than for M. truncatula and P. vulgaris (Fig. 3a). These results provide additional evidence of genome duplication event in soybean and a polyploid event in M. sativa. The percentage of transcripts within each BP GO Slim annotation is similar in all four legumes (Fig. 3b) confirming the MSGI 1.2 assembly encompasses the majority of transcripts in the M. sativa genome.Fig. 3


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)

Gene ontology analyses of legume transcripts confirm the breadth of the M. sativa transcript assembly. a Total number of transcripts in MSGI 1.2 M. truncatula, G. max, and P. vulgaris with Biological Process (BP) Gene Ontology (GO) Slim annotations. The 2-fold difference in transcript number reflects a polyploid event in M. sativa compared to M. truncatula and a genome duplication event in G. max compared to P. vulgaris. b The percentage of transcripts with each BP GO Slim annotation, from the total number of sequences with BP GO Slim annotations, is consistent across all four legumes, suggesting the MSGI 1.2 assembly represents the majority of transcripts in the M. sativa genome
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Gene ontology analyses of legume transcripts confirm the breadth of the M. sativa transcript assembly. a Total number of transcripts in MSGI 1.2 M. truncatula, G. max, and P. vulgaris with Biological Process (BP) Gene Ontology (GO) Slim annotations. The 2-fold difference in transcript number reflects a polyploid event in M. sativa compared to M. truncatula and a genome duplication event in G. max compared to P. vulgaris. b The percentage of transcripts with each BP GO Slim annotation, from the total number of sequences with BP GO Slim annotations, is consistent across all four legumes, suggesting the MSGI 1.2 assembly represents the majority of transcripts in the M. sativa genome
Mentions: To evaluate the breadth of gene function across the MSGI 1.2 assembly, we compared the gene ontology (GO) [38] slim annotations of the MSGI 1.2 assembly and the primary transcripts of M. truncatula, soybean, and P. vulgaris. The total number of transcripts associated with each biological process (BP) GO Slim term is approximately 2-fold greater for M. sativa and G. max than for M. truncatula and P. vulgaris (Fig. 3a). These results provide additional evidence of genome duplication event in soybean and a polyploid event in M. sativa. The percentage of transcripts within each BP GO Slim annotation is similar in all four legumes (Fig. 3b) confirming the MSGI 1.2 assembly encompasses the majority of transcripts in the M. sativa genome.Fig. 3

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