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

Jamie A. O'Rourke; Fengli Fu; Bruna Bucciarelli; S. Sam Yang; Deborah A. Samac; Jo Ann F.S. Lamb; Maria J. Monteros; Michelle A. Graham; John W. Gronwald; Nick Krom; Jun Li; Xinbin Dai; Patrick X. Zhao; Carroll P. Vance

doi:10.1186/s12864-015-1718-7

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

Jamie A. O'Rourke, Fengli Fu, Bruna Bucciarelli, S. Sam Yang, Deborah A. Samac, Jo Ann F.S. Lamb, Maria J. Monteros, Michelle A. Graham, John W. Gronwald, Nick Krom, Jun Li, Xinbin Dai, Patrick X. Zhao, Carroll P. Vance

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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.

Original language	English (US)
Article number	502
Journal	BMC Genomics
Volume	16
Issue number	1
DOIs	https://doi.org/10.1186/s12864-015-1718-7
State	Published - Jul 7 2015

Bibliographical note

Funding Information:
This work was performed in part using resources at the University of Minnesota Supercomputing Institute. This project was supported by USDA-ARS projects 3640-12210-002-00D, 3640-21000-029-00D and 3625-21220-005-00D. The USDA is an equal opportunity provider and employer. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U. S. Department of Agriculture.

Publisher Copyright:
© 2015 O'Rourke et al.

Keywords

Cysteine cluster protein
Gene expression atlas
Illumina
Medicago sativa
Nodule-specific cysteine-rich peptide
RNA-seq

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O'Rourke, J. A., Fu, F., Bucciarelli, B., Yang, S. S., Samac, D. A., Lamb, J. A. F. S., Monteros, M. J., Graham, M. A., Gronwald, J. W., Krom, N., Li, J., Dai, X., Zhao, P. X., & Vance, C. P. (2015). The Medicago sativa gene index 1.2: A web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies. BMC Genomics, 16(1), Article 502. https://doi.org/10.1186/s12864-015-1718-7

O'Rourke, JA, Fu, F, Bucciarelli, B, Yang, SS, Samac, DA, Lamb, JAFS, Monteros, MJ, Graham, MA, Gronwald, JW, Krom, N, Li, J, Dai, X, Zhao, PX & Vance, CP 2015, 'The Medicago sativa gene index 1.2: A web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies', BMC Genomics, vol. 16, no. 1, 502. https://doi.org/10.1186/s12864-015-1718-7

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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.",

keywords = "Cysteine cluster protein, Gene expression atlas, Illumina, Medicago sativa, Nodule-specific cysteine-rich peptide, RNA-seq",

author = "O'Rourke, {Jamie A.} and Fengli Fu and Bruna Bucciarelli and Yang, {S. Sam} and Samac, {Deborah A.} and Lamb, {Jo Ann F.S.} and Monteros, {Maria J.} and Graham, {Michelle A.} and Gronwald, {John W.} and Nick Krom and Jun Li and Xinbin Dai and Zhao, {Patrick X.} and Vance, {Carroll P.}",

note = "Funding Information: This work was performed in part using resources at the University of Minnesota Supercomputing Institute. This project was supported by USDA-ARS projects 3640-12210-002-00D, 3640-21000-029-00D and 3625-21220-005-00D. The USDA is an equal opportunity provider and employer. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U. S. Department of Agriculture. Publisher Copyright: {\textcopyright} 2015 O'Rourke et al.",

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T2 - A web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies

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AU - Fu, Fengli

AU - Bucciarelli, Bruna

AU - Yang, S. Sam

AU - Samac, Deborah A.

AU - Lamb, Jo Ann F.S.

AU - Monteros, Maria J.

AU - Graham, Michelle A.

AU - Gronwald, John W.

AU - Krom, Nick

AU - Li, Jun

AU - Dai, Xinbin

AU - Zhao, Patrick X.

AU - Vance, Carroll P.

N1 - Funding Information: This work was performed in part using resources at the University of Minnesota Supercomputing Institute. This project was supported by USDA-ARS projects 3640-12210-002-00D, 3640-21000-029-00D and 3625-21220-005-00D. The USDA is an equal opportunity provider and employer. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U. S. Department of Agriculture. Publisher Copyright: © 2015 O'Rourke et al.

PY - 2015/7/7

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N2 - 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.

AB - 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.

KW - Cysteine cluster protein

KW - Gene expression atlas

KW - Illumina

KW - Medicago sativa

KW - Nodule-specific cysteine-rich peptide

KW - RNA-seq

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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

Abstract

Bibliographical note

Keywords

Access

OpenUrl availability

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