Celebrating 20 Years of Genetic Discoveries in Legume Nodulation and Symbiotic Nitrogen Fixation

Roy, Sonali; Liu, Wei; Nandety, Raja Sekhar; Crook, Ashley D.; Mysore, Kirankumar S.; Pislariu, Catalina I.; Frugoli, Julia; Dickstein, Rebecca; Udvardi, Michael K.

doi:10.1105/tpc.19.00279

Cited by 511 publications

(542 citation statements)

References 299 publications

(326 reference statements)

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“…We found 12 soybean nodule-specific genes within the experimentally validated list of over 200 nodulins described previously (Roy et al, 2019). These 12 genes include the above-mentioned ERF TFs, NIN (Glyma.04G000600), C2H2 (Glyma.07G135800) and GRAS (Glyma.16G008200).…”

Section: Tissuementioning

confidence: 80%

Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

et al. 2020

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SUMMARY Soybean (Glycine max [L.] Merr.) is a major crop in animal feed and human nutrition, mainly for its rich protein and oil contents. The remarkable rise in soybean transcriptome studies over the past 5 years generated an enormous amount of RNA‐seq data, encompassing various tissues, developmental conditions and genotypes. In this study, we have collected data from 1298 publicly available soybean transcriptome samples, processed the raw sequencing reads and mapped them to the soybean reference genome in a systematic fashion. We found that 94% of the annotated genes (52 737/56 044) had detectable expression in at least one sample. Unsupervised clustering revealed three major groups, comprising samples from aerial, underground and seed/seed‐related parts. We found 452 genes with uniform and constant expression levels, supporting their roles as housekeeping genes. On the other hand, 1349 genes showed heavily biased expression patterns towards particular tissues. A transcript‐level analysis revealed that 95% (70 963 of 74 490) of the assembled transcripts have intron chains exactly matching those from known transcripts, whereas 3256 assembled transcripts represent potentially novel splicing isoforms. The dataset compiled here constitute a new resource for the community, which can be downloaded or accessed through a user‐friendly web interface at http://venanciogroup.uenf.br/resources/. This comprehensive transcriptome atlas will likely accelerate research on soybean genetics and genomics.

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Section: Tissuementioning

confidence: 80%

Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

et al. 2020

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“…Medicago truncatula and are essential for nodule differentiation and development 254(Vernié et al, 2008).255 We found 12 soybean nodule-specific genes within the experimentally validated 256 list of over 200 nodulins described previously(Roy et al, 2019). These 12 genes include 257 the above mentioned ERF TFs, NIN (Glyma.04G000600), C2H2 (Glyma.07G135800), and 258 GRAS (Glyma.16G008200).…”

mentioning

confidence: 73%

Systematic analysis of 1,298 RNA-Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

Machado

Moharana

Almeida‐Silva

et al. 2019

Preprint

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20Soybean (Glycine max [L.] Merr.) is a major crop in animal feed and human nutrition, 21 mainly for its rich protein and oil contents. The remarkable rise in soybean transcriptome 22 studies over the past five years generated an enormous amount of RNA-seq data, 23 encompassing various tissues, developmental conditions, and genotypes. In this study, 24we have collected data from 1,298 publicly available soybean transcriptome samples, 25processed the raw sequencing reads, and mapped them to the soybean reference 26 genome in a systematic fashion. We found that 94% of the annotated genes 27(52,737/56,044) had detectable expression in at least one sample. Unsupervised 28 clustering revealed three major groups, comprising samples from aerial, underground, 29and seed/seed-related parts. We found 452 genes with uniform and constant expression 30 levels, supporting their roles as housekeeping genes. On the other hand, 1,349 genes 31 showed heavily biased expression patterns towards particular tissues. A transcript-level 32 analysis revealed that 95% (70,963/74,490) of the known transcripts overlap with those 33 reported here, whereas 3,256 assembled transcripts represent potentially novel splicing 34isoforms. The dataset compiled here constitute a new resource for the community, which 35can be downloaded or accessed through a user-friendly web interface at 36

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“…Legume plants regulate the number of nodules formed through a long distance signal transduction pathway that involves many genes [1]. Earlier work in our lab identified a spontaneous mutant in Medicago truncatula in the Jemalong cultivar, resulting in increased nodulation [2]. Molecular genetic evidence indicated the phenotype of the like-sunn-supernodulator (lss) mutant was due to an unknown lesion resulting in cis-silencing of the SUNN gene, which has a wild type sequence in lss mutants.…”

Section: Objectivementioning

confidence: 99%

Whole genome bisulfite sequencing of Medicago truncatula A17 wild type and lss mutants

Freese¹,

Schnabel²,

Frugoli³

2020

BMC Res Notes

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Objectives: Earlier work in our lab identified a spontaneous mutant (like sunn supernodulator-lss) in Medicago truncatula, resulting in increased nodulation. Molecular genetic evidence indicated the phenotype was due to an unknown lesion resulting in cis-silencing of the SUNN gene. Altered methylation of the promoter was suspected, but analysis of the SUNN promoter by bisulfite sequencing at the time of publication revealed no significant methylation differences between the SUNN promoter in wild type and lss plants. Using advances in methylome generation we compared the methylome of wild type and the lss mutant in the larger 810 kB area of the genome where lss maps. Data description: The data show the distribution of types of methylation across the entire genome between A17 wild type and lss mutants, the number of differentially methylated cytosines between genotypes, and the overall pattern of gene methylation between genotypes. We expect the wild type data will be especially useful as a reference for other investigations of methylation using M. truncatula.

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Celebrating 20 Years of Genetic Discoveries in Legume Nodulation and Symbiotic Nitrogen Fixation

Cited by 511 publications

References 299 publications

Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

Systematic analysis of 1,298 RNA-Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

Whole genome bisulfite sequencing of Medicago truncatula A17 wild type and lss mutants

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