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Characterization of the complete plastome of Elymus tangutorum (Poaceae: Triticeae).

ABSTRACT: Elymus tangutorum (Nevski) Handel-Mazzetti (Poaceae: Triticeae), a hexaploid perennial herb, is a kind of forage plant with large biomass. In this study, the complete plastome sequence of E. tangutorum was reported. The size of the plastome is 134,949?bp in length, including a large single copy region (LSC) of 80,556?bp, a small single copy region (SSC) of 12,767?bp, and a pair of inverted repeat (IR) regions with 20,813?bp. Moreover, a total of 131 functional genes were annotated, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The maximum likelihood (ML) phylogenetic tree suggested that E. tangutorum was closely related to Elymus libanoticus and Dasypyrum villosum.

SUBMITTER: Jing M

PROVIDER: S-EPMC7707338 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Characterization of the complete plastome of Elymus tangutorum (Poaceae: Triticeae).

Jing Meiling M Ma Yushou Y Li Huimei H Wang Jiuli J

Mitochondrial DNA. Part B, Resources 20191004 2

Elymus tangutorum (Nevski) Handel-Mazzetti (Poaceae: Triticeae), a hexaploid perennial herb, is a kind of forage plant with large biomass. In this study, the complete plastome sequence of E. tangutorum was reported. The size of the plastome is 134,949 bp in length, including a large single copy region (LSC) of 80,556 bp, a small single copy region (SSC) of 12,767 bp, and a pair of inverted repeat (IR) regions with 20,813 bp. Moreover, a total of 131 functional genes were annotated, ...[more]

PMID: 33365991

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Project description:BackgroundElymus L. is the largest genus in the Triticeae tribe. Most species in this genus are highly stress resistant, with excellent forage value. Elymus breviaristatus, a rare species endemic to the Qinghai-Tibet Plateau (QTP), is declining due to habitat fragmentation. However, genetic data for E. breviaristatus are limited, with expressed sequence tag (EST) markers being particularly rare, hampering genetic studies and protection measures.ResultsWe obtained 9.06 Gb clean sequences from the transcriptome of E. breviaristatus, generating 171,522 unigenes, which were assembled and functionally annotated against five public databases. We identified 30,668 SSRs in the E. breviaristatus transcriptome, from which 103 EST-SSR primer pairs were randomly selected. Of these, 58 pairs of amplified products of the expected size, and 18 of the amplified products were polymorphic. Model-based Bayesian clustering, the unweighted pair group method with arithmetic average (UPGMA), and principal coordinate analysis (PCoA) of 179 wild E. breviaristatus in 12 populations using these EST-SSRs were generally consistent, grouping the 12 populations into two major clades. Analysis of molecular variance (AMOVA) found 70% of the genetic variation among the 12 populations and 30% within the populations, indicating a high level of genetic differentiation (or low gene exchange) among the 12 populations. The transferability of the 58 successful EST-SSR primers to 22 related hexaploid species was 86.2-98.3%. UPGMA analysis generally grouped species with similar genome types together.ConclusionsHere, we developed EST-SSR markers from the transcriptome of E. breviaristatus. The transferability of these markers was evaluated, and the genetic structure and diversity of E. breviaristatus were explored. Our results provide a basis for the conservation and management of this endangered species, and the obtained molecular markers represent valuable resources for the exploration of genetic relationships among species in the Elymus genus.

Project description:Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread Elymus species. Elymus excelsus Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of E. excelsus germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of E. excelsus from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei's genetic diversity (H) and Shannon's diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of E. excelsus germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (F st = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (H e = 0.197) was greater than that of the GSC (H e = 0.176) and XJC (H e = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that E. excelsus accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable E. excelsus germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.

Dataset Information

Characterization of the complete plastome of Elymus tangutorum (Poaceae: Triticeae).

Publications

Characterization of the complete plastome of <i>Elymus tangutorum</i> (Poaceae: Triticeae).

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