Species in this database

Studies in this database

Arabidopsis thaliana

Pignatta et al. 2014

eLife,
Pubmed ID: 24994762 , DOI
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Species: A. thaliana
Strain: Ler, Col, Cvi

This study compared imprinting in Arabidopsis thaliana endosperm across multiple accessions with different seed phenotypes (Col, Ler and Cvi) to identify shared and accession-specific imprinted genes. RNA-seq was performed on endosperm from reciprocal crosses between all pairs of these three accessions (Col-Ler, Col-Cvi, Ler-Cvi), with three biological replicates per comparison. A total of 285 maternally expressed genes (MEGs) and 103 paternally expressed genes (PEGs) were identified across all three accession comparisons, with 28 MEGs and 6 PEGs identified in all three comparisons.

Gehring et al. 2011

PLoS ONE,
Pubmed ID: 21858209 , DOI
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Species: A. thaliana
Strain: Col, Ler

This study examined imprinting in the embryo and endosperm of A. thaliana reciprocal Col-Ler hybrids. Seeds from crosses were manually dissected into embryo and endosperm at the torpedo stage, and RNA was extracted for RNA-seq. A total of 18 imprinted genes were identified in embryo (17 MEGs and 1 PEG) and 208 imprinted genes were identified in endosperm (165 MEGs, 43 PEGs).

Hsieh et al. 2011

PNAS,
Pubmed ID: 21257907 , DOI
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Species: A. thaliana
Strain: Col, Ler fie-1, Ler, Col-gl dme-2, Col-gl met1-6

This study examined imprinting in Arabidopsis thaliana endosperm using RNA-seq of dissected endosperm from reciprocal crosses between accessions Col and Ler. Two sets of replicates were generated, the first using endosperm dissected without the chalazal endosperm to minimize seed coat contamination ("pure" endosperm sample), and the second using the entire dissected endosperm ("full" endosperm). This study identified 114 maternally expressed and 10 paternally expressed genes in A. thaliana endosperm after strict filtering. Additionally, this study did not find evidence of imprinting in embryo. This study also sequenced data from paternal met1 and maternal dme and fie endosperm. Imprinting is not directly assessed in these genotypes (no reciprocal cross data available), but these data are used to identify MEGs among the 114 identified in WT whose imprinting is affected by these mutations (see "notes" field).

Wolff et al. 2011

PLoS Genetics,
Pubmed ID: 21698132 , DOI
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Species: A. thaliana
Strain: Col, Bur-0

This study examined imprinting in Arabidopsis thaliana endosperm using whole-seed RNA-seq of reciprocal Col, Bur-0 crosses. A total of 39 high-confidence MEGs and 27 PEGs were identified after filtering.

Arabidopsis lyrata

Klosinska et al. 2016

Nature Plants,
Pubmed ID: 27643534 , DOI
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Species: A. lyrata
Strain: MN47, Kar

This study examined imprinting in Arabidopsis lyrata, an obligate outcrosser that diverged from A. thaliana approximately 10 million years ago, using RNA-seq of reciprocal crosses between A. lyrata strains MN47 and Kar. The authors obtained 3 replicates each of MNxKar embryo, KarxMN embryo, and MNxKar endosperm, as well as 4 replicates of KarxMN endosperm. Imprinting was determined by examining all possible combinations of reciprocal crosses, producing 9 (3x3) comparisons in embryo and 12 (3x4) comparisons in endosperm. Genes highly expressed in the seed coat relative to embryo or endosperm were censored (see "notes" column for each comparison). A custom set of gene annotations were made for this study. For compatibility, these gene IDs have been converted to match the gene IDs used in Phytozome (drawn from Rawat et al. 2015, PLoS ONE); the gene IDs originally used in the paper are visible in the "notes" column.

Brassica Napus

Liu et al. 2018

DNA Research,
Pubmed ID: 30272113 , DOI
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Species: B. napus
Strain: 93275, YN171

This study examined imprinting in rapeseed (Brassica napus L.) endosperm using reciprocal crosses between the two inbred lines 93275 and YN171. Two replicates were generated in each direction of the cross. A total of 167 MEGs and 16 PEGs were identified.

Capsella rubella

Hatorangan et al. 2016

Plant Cell,
Pubmed ID: 27465027 , DOI
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Species: C. rubella
Strain: Cr A, Cr B

This study examined imprinting in the endosperm of Capsella rubella, using reciprocal crosses between two accessions: Cr A (Cr48.2-1, from Tuscany, Italy) and Cr B (Cr75.2-3, from Trapeza, Greece). Imprinting could be assessed for 15,293 genes, and a total of 77 MEGs and 52 PEGs were reported.

Solanum chilense

Florez-Rueda et al. 2016

Mol. Biol. Evol.,
Pubmed ID: 27601611 , DOI
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Species: S. chilense
Strain: LA4329 (4329B), LA4329 (4329K)

This study assessed imprinting in two species of tomato - Solanum peruvianum and S. chilense. Imprinting in S. peruvianum was assessed using two individuals from accession LA1616 (Lima, Peru), named 1616A and 1616J. Imprinting in S. chilense was assessed using two individuals from accesssion LA4329 (Antofagasta, Chile), named 4329B and 4329K. Fruits were collected at 14 DAP (corresponding to the globular embryo stage) and endosperm was isolated using laser-assisted microdissection. 351 candidate MEGs and 172 candidate PEGs were identified in S. peruvianum. 40 candidate MEGs and 70 candidate PEGs were identified in S. chilense.

Solanum peruvianum

Florez-Rueda et al. 2016

Mol. Biol. Evol.,
Pubmed ID: 27601611 , DOI
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Species: S. peruvianum
Strain: LA1616 (1616A), LA1616 (1616J)

This study assessed imprinting in two species of tomato - Solanum peruvianum and S. chilense. Imprinting in S. peruvianum was assessed using two individuals from accession LA1616 (Lima, Peru), named 1616A and 1616J. Imprinting in S. chilense was assessed using two individuals from accesssion LA4329 (Antofagasta, Chile), named 4329B and 4329K. Fruits were collected at 14 DAP (corresponding to the globular embryo stage) and endosperm was isolated using laser-assisted microdissection. 351 candidate MEGs and 172 candidate PEGs were identified in S. peruvianum. 40 candidate MEGs and 70 candidate PEGs were identified in S. chilense.

Zea mays

Waters et al. 2013

Proc. Natl. Acad. Sci. USA,
Pubmed ID: 24218619 , DOI
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Species: Z. mays
Strain: B73, Ki11, Mo17

This study evaluated imprinting in the endosperm of maize kernels at 14 DAP, a time point after endosperm cellularization but before significant starch accumulation. Reciprocal crosses among 4 diverse maize genotypes were examined. MEGs and PEGs were identified as moderate, strong, or complete depending on the chi-square value and the fraction of maternal reads in each reciprocal cross. 69 MEGs (strong+complete MEGs) and 108 PEGs (strong+complete PEGs) were identified, with a few hundred other genes identified as maternally or paternally biased (moderate MEGs or PEGs).

Waters et al. 2011

Plant Cell,
Pubmed ID: 22198147 , DOI
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Species: Z. mays
Strain: B73, Mo17

This study evaluated imprinting in the embryo and endosperm of maize, using reciprocal crosses between accessions B73 and Mo17. Ears were harvested at 14 days after pollination (DAP) and dissected into embryo and endosperm before preparing RNA-seq libraries. In endosperm, ~12,500 genes could be evaluated for imprinting, and 54 MEGs and 46 PEGs were identified.

Homology Mapping

Download a copy of all homology mappings in this database. This file maps genes in each species with their known homologs in other species in the database, using homology information from araport/thalemine (https://www.araport.org/).