Pdf insights into salt tolerance from the genome of thellungiella. Genomewide identification of thellungiella salsuginea. Thellungiella salsuginea is becoming a new model plant because it resembles its relative species, arabidopsis thaliana, in small genome and short life cycle. Genome wide identification of thellungiella salsuginea. Genomewide identification of thellungiella salsuginea micrornas. This genome provides resources and evidence about the nature of defense. Schrenkiella parvula formerly thellungiella parvula, a close relative of arabidopsis arabidopsis thaliana and brassica crop species, thrives on the shores of lake tuz, turkey, where soils accumulate high concentrations of multipleion salts. Thellungiella parvula 1 is related to arabidopsis thaliana and is endemic to saline, resourcepoor habitats 2, making it a model for the evolution of plant adaptation to extreme environments. Wang j, zhang q, cui f, hou l, zhao s, xia h, qiu j, li t, zhang y, wang x and zhao c 2017 genome wide analysis of gene expression provides new insights into cold responses in thellungiella salsuginea. Genome structures and halophytespecific gene expression. The flow chart of genome assembly and annotation is shown in fig. The genome of the extremophile crucifer thellungiella.
Thellungiella salsuginea has attracted interest as an alternative plant model species. Aug 16, 2012 oh dh, dassanayake m, haas js, kropornika a, wright c, durzo mp, hong h, ali s, hernandez a, lambert gm, inan g, galbraith dw, bressan ra, yun dj, zhu jk, cheeseman jm, bohnert hj. The genome of thellungiella parvula, a halophytic relative of arabidopsis arabidopsis thaliana, is being assembled using roche454 sequencing. The genome of the extremophile crucifer thellungiella parvula. To improve the accuracy of sequence assembly, we downloaded the. Thellungiella salsuginea has attracted interest as an alternative plant model species with high tolerance of various abiotic stresses.
Research article open access genomewide identification. Thellungiella salsuginea salt cress exhibits high tolerance to chilling. Insights into salt tolerance from the genome of thellungiella. Here we present the draft genome for this extremophile species. Structural analysis of 83kb genomic dna from thellungiella halophila. This species is endemic to highly saline environments subject to. Genome analysis genome structures and halophytespeci. Expressed sequence tags ests add information on the expressed part of the genome while representing a valuable tool in the identification of new genes, construction of linkage maps, correlation of est map position with the position of mutant loci and the isolation of homologous genes from different but related species. Thellungiella salsuginea eutrema salsugineum, a relative of arabidopsis thaliana, displays an extremely high level of tolerance to salt, drought. Research article open access transcriptome sequencing. Thellungiella salsuginea halophila is a close relative of arabidopsis thaliana but, unlike a.
Thellungiella genes exhibit a high degree of sequence identity with arabidopsis genes 90% at the cdna level. Jul 24, 2012 thellungiella salsuginea, a close relative of arabidopsis, represents an extremophile model for abiotic stress tolerance studies. Jgi arabidopsis lyrata genome the multinational brassica genome project this is a list of researchers who have either taken part in the founding meeting from which thellungiella. Ascorbate peroxidase apx is an enzyme that clears h2o2 in plants. Syntenic orthologs between brassica rapa, arabidopsis thaliana, arabidopsis lyrata, schrenkiella parvula, thellungiella salsuginea, papaya carica papaya, and grape vitis vinifera were identified using the tool synorths cheng et al. The genome of the shandong ecotype has been sequenced twice and published. Luowhole genome sequencing of cultivated and wild peppers provides insights into capsicum domestication and specialization.
Soil salinization is a resource and ecological problem in the world. Dongha oh and colleagues report the draft genome of the extremophile crucifer plant thellungiella parvula. We named the lest fractionized subgenome as lf, the moderate gene fractionized as mf1 and the most gene fractionized as mf2. Despite the stark differences in adaptations to extreme salt stresses, the genomes of s. Analysis of the genome sequence of the flowering plant arabidopsis thaliana samir kaul et al. In order to understand the adaptive evolution of this species in the arid. Genomewide analysis of gene expression provides new insights. The ecotype shandong analysed in this study was initially assigned as t. Thellungiella salsuginea has therefore attracted increasing interest as an alternative plant model species that possesses high tolerance of various abiotic stresses. Global transcriptome analysis provides new insights in.
Little is known about the genes that confer salt tolerance in trees. Nov 19, 20 thellungiella salsuginea has therefore attracted increasing interest as an alternative plant model species that possesses high tolerance of various abiotic stresses. Thellungiella is a genus of plants in the family brassicaceae closely related to arabidopsis, but in the subclade eutremeae. Eutrema parvulum, also called thellungiella parvula, is one of several. The buildup of salt in agricultural soils is a widespread problem that limits the growth and yield of important crop species worldwide. Identity between the arabidopsis genome sequence and t. Sequence features and microcolinearity between salt cress and arabidopsis thaliana.
We previously generated a fulllength enriched cdna library of t. Fei gao, jing chen, tingting ma, huayun li, ning wang, zhanglei li, zichen zhang and yijun zhou college of life and environmental sciences, minzu university of china, beijing 81, china. Insights into salt tolerance from the genome of thellungiella salsuginea huajun wua,1, zhonghui zhanga,1, junyi wangb,1, dongha ohc,1, maheshi dassanayakec,1, binghang liub,1, quanfei huangb,1, haixi sun a, ran xia, yaorong wu a, yinan wang a, zhao yang, yang liu, wanke zhang, huawei zhang a, jinfang chu, cunyu yan a, shuang fang, jinsong zhang, yiqin wanga, fengxia zhanga. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions annabelle haudry et al. Try ncbi datasets a new way to download genome sequence and annotation were. Pdf insights into salt tolerance from the genome of. The query sequence is filtered for low complexity regions by default. Genome structures and halophytespecific gene expression of the extremophile thellungiella parvula in comparison with thellungiella salsuginea thellungiella halophila and arabidopsis. In recent classifications, the genus is no longer recognized, and the formerly included species are now placed in the genus eutrema or schrenkiella they are commonly known as saltwater cresses because of their ability to grow in salty environments. Analyses of a 10mb scaffold revealed synteny with arabidopsis, with recombination and inversion and an uneven distribution of repeat sequences. In addition, functional genomics investigations in this species are. The yellowhorn genome was assembled by integration of illumina short reads, pacbio long reads, 10x genomics link. This species is endemic to highly saline environments subject to extreme temperatures.
Deciphering the diploid ancestral genome of the mesohexaploid. Cold stress increases salt tolerance of the extremophytes eutrema salsugineum thellungiella salsuginea and eutrema thellungiella botschantzevii authors shamustakimova, a. Mar 12, 2020 alkaligrass puccinellia tenuiflora is a monocotyledonous halophytic forage grass widely distributed in northern china. Genome structures and halophytespecific gene expression of the extremophile thellungiella parvula in comparison with thellungiella salsuginea thellungiella. A highquality genome sequence of alkaligrass provides. Thellungiella salsuginea brassiaceae is a typical halophyte which can tolerate extreme cold, drought, and salinity. Genome structures and halophytespecific gene expression of. Micrornas are key regulators of plant growth and development with important roles in environmental adaptation. Using illumina and nanopore reads, we achieved the assembled genome.
Over the last decade, many laboratories have started to use thellungiella to investigate the physiological, metabolic, and molecular mechanisms of abiotic stress tolerance in plants, and new. The genome of the extremophile crucifer thellungiella parvula maheshi dassanayake et al. Thellungiella is an excellent model organism for several other reasons. The complete nucleotide sequences of the mitochondrial mt genome of an extremophile species thellungiella parvula t. Here, we present a highquality chromosomelevel genome sequence of alkaligrass assembled from illumina, pacbio and 10. Substantial reprogramming of the eutrema salsugineum. A highly efficient agrobacteriummediated method for.
Expressed sequence tags from thellungiella halophila, a new. Nov 15, 20 the release of the entire genome sequence of t. Genome wide identification, classification, and gene and protein expression analysis under stress conditions. The reference genome of the halophytic plant eutrema salsugineum. Insights into salt tolerance from the genome of thellungiella salsuginea author. The reference genome of the halophytic plant eutrema salsugineum ruolin yang et al. Pdf thellungiella salsuginea, a close relative of arabidopsis, represents an. The genome was primarily assembled using nextgeneration sequencing data. With few exceptions, crop plants are glycophytes, unable to adapt to the ionic, osmotic, and oxidative stresses induced by elevated levels of salt in the soil. Thellungiella parvula1 is related to arabidopsis thaliana and is endemic to saline, resourcepoor habitats2, making it a. Nov 24, 2010 thellungiella halophila also known as t. Thellungiella parvula genomic data and gene models files available. Oh dh, dassanayake m, haas js, kropornika a, wright c, durzo mp, hong h, ali s, hernandez a, lambert gm, inan g, galbraith dw, bressan ra, yun dj, zhu jk, cheeseman jm, bohnert hj.
It is highly tolerant to salinity and drought stresses. Glutathione peroxidases gpx catalyze the reduction of h2o2 or organic hydroperoxides to water or corresponding alcohols using reduced glutathione, which plays an essential role in ros reactive oxygen species homeostasis and stress signaling. Arabidopsis thaliana is not particularly stress tolerant and may lack protective mechanisms required to survive extreme environmental conditions. Hsfa1d, a protein identified via fox hunting using. The recently sequenced genome of thellungiella parvula exemplifies such efforts, providing resources for highresolution genome wide comparison with its nonextremophile relative, a. Microsatellite dna loci from the typical halophyte. Here, we look at three notable evolutionary features reflected in the genomes that may contribute to adaptations to abiotic stress. Author links open overlay panel zhiyong deng a 1 yin li a 1 ran xia b 1 weiquan wang a xiahe huang b ling zhang a shengli zhang b 2 cuiping yang a yiyue zhang a b mingsheng chen b qi xie a b.
Thellungiella salsuginea, salt cress, cold stress, gene expression. The glutathione peroxidase gene family in thellungiella. Transcriptome sequencing and microarray design for. Thellungiella salsuginea has been studied because its ability, in the natural world, to function in extreme salt, cold, and freezing conditions, and for its efficient mobilization of resources in poor or degraded soils. This genome provides resources and evidence about the nature of defense mechanisms constituting. Among these three subgenomes, we observed biased gene fractionation gene losing. The whole genome assembly and comparative genomic research of. The haploid genome size of yellowhorn was also measured by means of flow cytometry and showed a 1c genomic sequence of 433. The functional and regulatory mechanisms of the thellungiella. It belongs to the gramineae family and shares a close phylogenetic relationship with the cereal crops, wheat and barley. Thellungiella salsuginea, a close relative of arabidopsis, represents an extremophile model for abiotic stress tolerance studies.
Structural analysis of 83kb genomic dna from thellungiella. Filter low complexity mask for lookup table only expect 0. Genome structures and halophytespecific gene expression of the. About thellungiella and why it is the upandcoming tool for plant molecular genetics. Insights into salt tolerance from the genome of thellungiella salsuginea huajun wu et al.
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