Genome Structures and Transcriptomes Signify Niche Adaptation for the Multiple-Ion-Tolerant Extremophyte <i>Schrenkiella parvula</i>

Oh, Dong Ha; Hong, Hyewon; Lee, Sang Yeol; Yun, Dae‐Jin; Bohnert, Hans J.; Dassanayake, Maheshi

doi:10.1104/pp.113.233551

Cited by 74 publications

(138 citation statements)

References 85 publications

Supporting

Mentioning

131

Contrasting

Order By: Relevance

“…This emphasizes the importance of multiple levels of fine-tuning of stress responses. More broadly, the characterization of halophytes such as Eutrema salsugineum has highlighted the importance of CNV and neofunctionalization in salinity tolerance 143 , and these and other extremophiles may provide novel alleles of conserved determinant genes for crop improvement 144 . Environmental stresses can be concurrent or sequential, and stress tolerances can be independent or interconnected, posing the additional challenge of proper stacking or pyramiding of traits that are synergistic or at least not antagonistic.…”

Section: Winter Varietiesmentioning

confidence: 99%

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability

2015

View full text Add to dashboard Cite

Crop yield reduction as a consequence of increasingly severe climatic events threatens global food security. Genetic loci that ensure productivity in challenging environments exist within the germplasm of crops, their wild relatives and species that are adapted to extreme environments. Selective breeding for the combination of beneficial loci in germplasm has improved yields in diverse environments throughout the history of agriculture. An effective new paradigm is the targeted identification of specific genetic determinants of stress adaptation that have evolved in nature and their precise introgression into elite varieties. These loci are often associated with distinct regulation or function, duplication and/or neofunctionalization of genes that maintain plant homeostasis.

show abstract

Section: Winter Varietiesmentioning

confidence: 99%

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability

2015

View full text Add to dashboard Cite

show abstract

“…Deposited ESTs in TAIR, as well as RNA-seq data (Oh et al., 2014), indicate that transcription of the AtβCA1 gene may result in two different mRNAs (Figure 4). The RNA variants arise from the splicing of the ninth and tenth exons, where one variant has all 10 exons, and the other has an extended ninth exon, making proteins that differ slightly at their C termini.…”

Section: Evidence Of Alternative Splicing Of β Carbonic Anhydrase Tramentioning

confidence: 99%

Plant Carbonic Anhydrases: Structures, Locations, Evolution, and Physiological Roles

et al. 2017

View full text Add to dashboard Cite

Carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the interconversion of CO2 and HCO3− and are ubiquitous in nature. Higher plants contain three evolutionarily distinct CA families, αCAs, βCAs, and γCAs, where each family is represented by multiple isoforms in all species. Alternative splicing of CA transcripts appears common; consequently, the number of functional CA isoforms in a species may exceed the number of genes. CAs are expressed in numerous plant tissues and in different cellular locations. The most prevalent CAs are those in the chloroplast, cytosol, and mitochondria. This diversity in location is paralleled in the many physiological and biochemical roles that CAs play in plants. In this review, the number and types of CAs in C3, C4, and crassulacean acid metabolism (CAM) plants are considered, and the roles of the α and γCAs are briefly discussed. The remainder of the review focuses on plant βCAs and includes the identification of homologs between species using phylogenetic approaches, a consideration of the inter- and intracellular localization of the proteins, along with the evidence for alternative splice forms. Current understanding of βCA tissue-specific expression patterns and what controls them are reviewed, and the physiological roles for which βCAs have been implicated are presented.

show abstract

“…japonica (International Rice Genome Sequencing Project, 2005), Oryza sativa ssp. indica (Yu et al, 2002), Brachypodium distachyon (International Brachypodium Initiative, 2010), Zea mays (Schnable et al, 2009), Sorghum bicolor , Setaria italica , Solanum tuberosum (Xu et al, 2011), Solanum lycopersicum (Tomato Genome Consortium, 2012), Vitis vinifera (Jaillon et al, 2007), Lotus japonicus (Sato et al, 2008), Cajanus cajan (Varshney et al, 2012), Arabidopsis thaliana (Arabidopsis Genome Initiative, 2000), Arabidopsis lyrata , Schrenkiella parvula (a synonym is Eutrema parvula; we used the nomenclature from Oh et al [2014]; Dassanayake et al, 2011), Eutrema salsugineum (a synonym is Thellungiella halophila; we chose the nomenclature according to Phytozome [http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Esalsugineum]; Wu et al, 2012), Brassica rapa , Populus trichocarpa (Tuskan et al, 2006), Glycine max (Schmutz et al, 2010), Medicago truncatula (Young et al, 2011), Prunus persica (Ahmad et al, 2011), Malus 3 domestica (Velasco et al, 2010), Ricinus communis (Chan et al, 2010), Jatropha curcas (Sato et al, 2011), Manihot esculenta (Prochnik et al, 2012), Cucumis sativus (Huang et al, 2009), Cucumis melo (GarciaMas et al, 2012), Carica papaya (Ming et al, 2008), Gossypium raimondii , and Theobroma cacao (Argout et al, 2011). We also extracted LRR-RLKs from the moss Physcomitrella patens (Rensing et al, 2008) and the spikemoss Selaginella moellendorffii (Banks et al, 2011).…”

Section: Studied Genomesmentioning

confidence: 99%

Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms

et al. 2016

View full text Add to dashboard Cite

Gene duplications are an important factor in plant evolution, and lineage-specific expanded (LSE) genes are of particular interest. Receptor-like kinases expanded massively in land plants, and leucine-rich repeat receptor-like kinases (LRR-RLK) constitute the largest receptor-like kinases family. Based on the phylogeny of 7,554 LRR-RLK genes from 31 fully sequenced flowering plant genomes, the complex evolutionary dynamics of this family was characterized in depth. We studied the involvement of selection during the expansion of this family among angiosperms. LRR-RLK subgroups harbor extremely contrasting rates of duplication, retention, or loss, and LSE copies are predominantly found in subgroups involved in environmental interactions. Expansion rates also differ significantly depending on the time when rounds of expansion or loss occurred on the angiosperm phylogenetic tree. Finally, using a d N /d S -based test in a phylogenetic framework, we searched for selection footprints on LSE and single-copy LRR-RLK genes. Selective constraint appeared to be globally relaxed at LSE genes, and codons under positive selection were detected in 50% of them. Moreover, the leucine-rich repeat domains, and specifically four amino acids in them, were found to be the main targets of positive selection. Here, we provide an extensive overview of the expansion and evolution of this very large gene family.

show abstract

Genome Structures and Transcriptomes Signify Niche Adaptation for the Multiple-Ion-Tolerant Extremophyte Schrenkiella parvula

Cited by 74 publications

References 85 publications

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability

Plant Carbonic Anhydrases: Structures, Locations, Evolution, and Physiological Roles

Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms

Contact Info

Product

Resources

About