Here we present the draft genome for this extremophile species. Aug 16, 2012 the phylogeny was constructed with sequences corresponding to the nuclear ribosomal its1, 5. Genome analysis genome structures and halophytespeci. Understanding brassicaceae evolution through ancestral genome. The whole genome assembly and comparative genomic research of. Dec 10, 2015 we reconstruct an evolutionary framework of brassicaceae composed of highresolution ancestral karyotypes using the genomes of modern a. Despite the stark differences in adaptations to extreme salt stresses, the genomes of s. The whole genome assembly and comparative genomic research. Thellungiella is an excellent model organism for several other reasons. Lake tuz, shown in this landsat photo june 2009, is one of the worlds largest inland hypersaline lakes, with an area more than 1600 sq. Distinct roles for sos1 in the convergent evolution of salt. Transcriptome sequencing and microarray design for functional. The evolutionary history of pepc genes in green plants we constructed a phylogenetic tree of pepc family members using genomic sequences of representative species fig.
The buildup of salt in agricultural soils is a widespread problem that limits the growth and yield of important crop species worldwide. This species is endemic to highly saline environments subject to. The genome of the extremophile crucifer thellungiella parvula maheshi dassanayake 1,9, dongha oh, jeffrey s. A draft genome for thellungiella parvula was published in 2011 and updated in march, 2012subsequently, the draft genome for t. Haas 1,2, alvaro hernandez 3, hyewon hong 1,4, shahjahan ali 5, daejin yun 4,6, ray a. Insights into salt tolerance from the genome of thellungiella. Dassanayake m1, oh dh, haas js, hernandez a, hong h, ali s, yun dj, bressan ra, zhu jk, bohnert hj, cheeseman jm. Schrenkiella parvula formerly thellungiella parvula, a close relative of arabidopsis arabidopsis thaliana and brassica crop species, thrives on the shores of. The genome of the extremophile crucifer thellungiella parvula maheshi dassanayake et al. The complete chloroplast genome of schrenkiella parvula brassicaceae. Thellungiella parvula is related to arabidopsis thaliana and is endemic to saline, resourcepoor habitats, making it a model for the evolution of plant adaptation to extreme environments. Ppc1 planttype pepc, ppc2 bacterialtype pepc and ppc3. Here, we report a highquality chromosomescale genome assembly of i. Eutrema salsugineum and schrenkiella parvula are salttolerant relatives of the saltsensitive species arabidopsis thaliana.
The genome of the extremophile crucifer thellungiella parvula. The genome of thellungiella parvula, a halophytic relative of arabidopsis arabidopsis thaliana, is being assembled using roche454 sequencing. Schrenkiella parvula, also called thellungiella parvula, is a small herbaceous plant that is closely related to arabidopsis thaliana. Among these three subgenomes, we observed biased gene fractionation gene losing. Complete genome sequence of veillonella parvula type strain. Thellungiella salsuginea has attracted interest as an alternative plant model.
As such comparisons of the thellungialla parvula genome with other crucifers can reveal genomic changes necessary for environmental stress. Mar 28, 2017 schrenkiella parvula growing in situ at tuz gol anatolia, turkey. The feasibility of karyotypebased assembly has been shown in the assembly of thellungiella schrenkiella parvula genome independent of genetic andor physical maps dassanayake et al. Genome structures and halophytespecific gene expression of.
Dongha oh and colleagues report the draft genome of the extremophile crucifer plant thellungiella parvula. Alshehbaz ia, okane sl 1995 placement of arabidopsis parvula in thellungiella brassicaceae. Aug 07, 2011 thellungiella parvula is related to arabidopsis thaliana and is endemic to saline, resourcepoor habitats, making it a model for the evolution of plant adaptation to extreme environments. Thellungiella salsuginea, a close relative of arabidopsis, represents an extremophile model for abiotic stress tolerance studies. The reference genome of the halophytic plant eutrema salsugineum ruolin yang et al.
Eutrema salsugineum is a halophytic species in the brassicaceae that can naturally tolerate multiple types of abiotic stresses that typically limit crop productivity, including extreme salinity and cold. Endnote generated xml zipped resources thellungiella parvula genome sequences. Pdf thellungiella parvula is related to arabidopsis thaliana and is endemic to saline, resourcepoor habitats, making it a model for the. The impact of genome triplication on tandem gene evolution in. Pdf thellungiella parvula is related to arabidopsis thaliana and is endemic to. Overview of the thellungiella parvula mitochondrial genome sequence. Veillonella parvula veillon and zuber 1898 prevot 1933 is the type species of the genus veillonella in the family veillonellaceae within the order clostridiales.
To improve the accuracy of sequence assembly, we downloaded the. Analyses of a 10mb scaffold revealed synteny with arabidopsis, with recombination and inversion and an uneven distribution of repeat sequences. Try ncbi datasets a new way to download genome sequence and annotation were. Pdf the genome of the extremophile crucifer thellungiella parvula. Arabidopsis thaliana u43225, arabidopsis lyrata dq165338, thellungiella parvula blast search on t. Nov 29, 2012 whole genome duplication wgd and tandem duplication td are both important modes of gene expansion. Eutrema parvulum, also called thellungiella parvula, is one of several. Genome structures and transcriptomes signify niche adaptation for.
The micrornas from the halophyte species thellungiella salsuginea salt cress, which exhibits extreme salt stress tolerance, remain to be investigated. Halophytes are plants that can naturally tolerate high concentrations of salt in the soil, and their tolerance to salt stress may occur through various evolutionary and molecular mechanisms. Genomewide identification of thellungiella salsuginea. We thus selected the genomes of five sequenced extant brassicaceae a. Prime among the extremophyte crucifers for genomic resources are available are two species which were moved to the genus thellungiella, only to be moved again and again. The genus thellungiella is closely related to arabidopsis thaliana but its species are endemic to saline, resourcepoor habitats, making them good models for the evolution of plant adaptation to extreme environments. Sequencing information such as uniquely aligned reads and average read depth of gene. Thellungiella salsuginea has attracted interest as an alternative plant model species. Thellungiella parvula genomic data and gene models files available.
Insights into salt tolerance from the genome of thellungiella salsuginea. Here, we report a highquality draft genome of a chinese radish raphanus sativus cultivar. 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. Nov 15, 20 micrornas are key regulators of plant growth and development with important roles in environmental adaptation.
The complete nucleotide sequences of the mitochondrial mt genome of an extremophile species thellungiella parvula t. The reference genome of the halophytic plant eutrema salsugineum. It is often used as a model organism for environmental stress responses due to its small genome size, similarity to a. Deciphering the diploid ancestral genome of the mesohexaploid. However, how wgd influences tandemly duplicated genes is not well studied. The tpck genome structure was recently confirmed by whole genome sequencing of schrenkiella parvula synonym of thellungiella parvula, formerly placed in the eutremeae dassanayake et al. Taking this advantage, we developed the kgbassembler, a tool to assemble full chromosomes from scaffolds if a karyotype is provided. Evolutionary history of pepc genes in green plants. We used brassica rapa, which has undergone an additional genome triplication wgt and shares a common ancestor with arabidopsis thaliana, arabidopsis lyrata, and thellungiella parvula, to investigate the impact of. This genome provides resources and evidence about the nature of defense mechanisms constituting. Thellungiella salsuginea has been studied because its ability, in the natural world, to function in extreme. The genome of thellungiella parvula, a halophytic relative of arabidopsis arabidopsis thaliana, is being assembled using roche454. The ancestral brassicaceae karyotype brassicaceae lineages i and ii is composed of eight protochromosomes and 20,037.785 123 1155 1534 1397 1453 967 639 986 208 557 976 1427 171 1120 1163 871 1405 295 581 1352 792 865 483 129 956 1592 595 598 45 368 1482 1418 677 62 915 992 1136