Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Development and characterization of microsatellite loci for smooth cordgrass, Spartina alterniflora (Poaceae).

ABSTRACT: UNLABELLED: PREMISE OF THE STUDY:Spartina alterniflora is one of the nine most notoriously invasive plants in China. Microsatellite markers were developed for this species to investigate its invasiveness and genetic diversity. • METHODS AND RESULTS:Fifteen polymorphic and seven monomorphic simple sequence repeat (SSR) markers derived from expressed sequence tags (ESTs) were identified and screened in 60 samples of S. alterniflora. The number of alleles per polymorphic locus ranged from two to eight, with an average of 3.8 alleles per polymorphic locus. The expected heterozygosity and observed heterozygosity based on seven disomic loci ranged from 0.27 to 0.46 and 0.21 to 0.51, respectively. The average Shannon index ranged from 0.26 to 0.94 in eight nondisomic loci. • CONCLUSIONS:The SSR markers described here may be useful for further investigation of population genetics and invasion dynamics of S. alterniflora.

SUBMITTER: Guo W

PROVIDER: S-EPMC4105352 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Development and characterization of microsatellite loci for smooth cordgrass, Spartina alterniflora (Poaceae).

Guo Wuxia W Huang Yelin Y He Ziwen Z Yan Yubin Y Zhou Renchao R Shi Suhua S

Applications in plant sciences 20130102 1

<h4>Unlabelled</h4><h4>Premise of the study</h4>Spartina alterniflora is one of the nine most notoriously invasive plants in China. Microsatellite markers were developed for this species to investigate its invasiveness and genetic diversity. •<h4>Methods and results</h4>Fifteen polymorphic and seven monomorphic simple sequence repeat (SSR) markers derived from expressed sequence tags (ESTs) were identified and screened in 60 samples of S. alterniflora. The number of alleles per polymorphic locus ...[more]

PMID: 25202479

Similar Datasets

Molecular analysis of diazotroph diversity in the rhizosphere of the smooth cordgrass, Spartina alterniflora.

Project description:N(2) fixation by diazotrophic bacteria associated with the roots of the smooth cordgrass, Spartina alterniflora, is an important source of new nitrogen in many salt marsh ecosystems. However, the diversity and phylogenetic affiliations of these rhizosphere diazotrophs are unknown. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified nifH sequence segments was used in previous studies to examine the stability and dynamics of the Spartina rhizosphere diazotroph assemblages in the North Inlet salt marsh, near Georgetown, S.C. In this study, plugs were taken from gel bands from representative DGGE gels, the nifH amplimers were recovered and cloned, and their sequences were determined. A total of 59 sequences were recovered, and the amino acid sequences predicted from them were aligned with sequences from known and unknown diazotrophs in order to determine the types of organisms present in the Spartina rhizosphere. We recovered numerous sequences from diazotrophs in the gamma subdivision of the division Proteobacteria (gamma-Proteobacteria) and from various anaerobic diazotrophs. Diazotrophs in the alpha-Proteobacteria were poorly represented. None of the Spartina rhizosphere DGGE band sequences were identical to any known or previously recovered environmental nifH sequences. The Spartina rhizosphere diazotroph assemblage is very diverse and apparently consists mainly of unknown organisms.

| S-EPMC92225 | biostudies-literature

Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity.

Project description:BackgroundSoil salinity affects growth and yield of crop plants. Plants respond to salinity by physiological and biochemical adjustments through a coordinated regulation and expression of a cascade of genes. Recently, halophytes have attracted attention of the biologists to understand their salt adaptation mechanisms. Spartina alterniflora (smooth cordgrass) is a Louisiana native monocot halophyte that can withstand salinity up to double the strength of sea water. To dissect the molecular mechanisms underlying its salinity adaptation, leaf and root transcriptome of S. alterniflora was sequenced using 454/GS-FLX.ResultsAltogether, 770,690 high quality reads with an average length 324-bp were assembled de novo into 73,131 contigs (average 577-bp long) with 5.9X sequence coverage. Most unigenes (95 %) annotated to proteins with known functions, and had more than 90 % similarity to rice genes. About 28 % unigenes were considered specific to S. alterniflora. Digital expression profiles revealed significant enrichment (P < 0.01) of transporters, vacuolar proton pump members and transcription factors under salt stress, which suggested the role of ion homeostasis and transcriptional regulation in the salinity adaptation of this grass. Also, 10,805 SSRs markers from 9457 unigenes were generated and validated through genetic diversity analysis among 13 accessions of S. alterniflora.ConclusionsThe present study explores the transcriptome of S. alterniflora to understand the gene regulation under salt stress in halophytes. The sequenced transcriptome (control and salt-regulated) of S. alterniflora provides a platform for further gene finding studies in grasses. This study and our previously published studies suggested that S. alterniflora is a rich reservoir of salt tolerance genes that can be used to develop salt tolerant cereal crops, especially rice, a major food crop of global importance.

| S-EPMC4992267 | biostudies-literature

High Genetic Diversity With Weak Phylogeographic Structure of the Invasive Spartina alterniflora (Poaceae) in China.

Project description:Biological invasion represents a global issue of concern due to its large negative impacts on native ecosystems and society. Elucidating the evolutionary history and genetic basis underpinning invasiveness is critical to understanding how alien species invade and adapt to novel environments. Smooth cordgrass (Spartina alterniflora, 2n = 6x = 62) is a notorious invasive species that causes heavily negative effects on native ecosystems worldwide. Here we addressed the evolutionary mechanisms underlying the invasion and dispersal history of this species along the China coast in the past decades. We employed nine microsatellites and three chloroplast fragments to investigate phylogeographic structure and genetic diversity of 11 native US and 11 invasive Chinese S. alterniflora populations. Demographic history simulation was also performed for both the native and invasive populations, respectively. Comparative genetic analyses of these natural populations revealed that although all the Chinese populations were introduced only once, high level of genetic diversity with weak geographic structure was observed. In particular, both the genetic features and mathematical simulation illustrated very recent population expansion in the Chinese populations. We found that genetic variants identified in native US populations were mixed in the Chinese populations, suggesting the recombination of these original variants during the invasion process. These genetic attributes indicate that Chinese populations might not have experienced a genetic bottleneck during the invasion process. High genetic diversity and genetic admixture might have contributed to the success of invasion of S. alterniflora in China. Our study provides a framework of how the smooth cordgrass spreads along the China coast as well as its potential genetic mechanisms underlying the invasion.

| S-EPMC6896949 | biostudies-literature

Tropicalization of the barrier islands of the northern Gulf of Mexico: A comparison of herbivory and decomposition rates between smooth cordgrass (Spartina alterniflora) and black mangrove (Avicennia germinans).

Project description:The expansion of black mangrove Avicennia germinans into historically smooth cordgrass Spartina alterniflora-dominated marshes with warming temperatures heralds the migration of the marsh-mangrove ecotone northward in the northern Gulf of Mexico. With this shift, A. germinans is expected to outcompete S. alterniflora where it is able to establish, offering another prevalent food source to first order consumers. In this study, we find A. germinans leaves to be preferable to chewing herbivores, but simultaneously, chewing herbivores cause more damage to S. alterniflora leaves. Despite higher nitrogen content, A. germinans leaves decomposed slower than S. alterniflora leaves, perhaps due to other leaf constituents or a different microbial community. Other studies have found the opposite in decomposition rates of the two species' leaf tissue. This study provides insights into basic trophic process, herbivory and decomposition, at the initial stages of black mangrove colonization into S. alterniflora salt marsh.

| S-EPMC6322730 | biostudies-literature

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae).

Project description:Spartina species have a critical ecological role in salt marshes and represent an excellent system to investigate recurrent polyploid speciation. Using the 454 GS-FLX pyrosequencer, we assembled and annotated the first reference transcriptome (from roots and leaves) for two related hexaploid Spartina species that hybridize in Western Europe, the East American invasive Spartina alterniflora and the Euro-African S. maritima. The de novo read assembly generated 38 478 consensus sequences and 99% found an annotation using Poaceae databases, representing a total of 16 753 non-redundant genes. Spartina expressed sequence tags were mapped onto the Sorghum bicolor genome, where they were distributed among the subtelomeric arms of the 10 S. bicolor chromosomes, with high gene density correlation. Normalization of the complementary DNA library improved the number of annotated genes. Ecologically relevant genes were identified among GO biological function categories in salt and heavy metal stress response, C4 photosynthesis and in lignin and cellulose metabolism. Expression of some of these genes had been found to be altered by hybridization and genome duplication in a previous microarray-based study in Spartina. As these species are hexaploid, up to three duplicated homoeologs may be expected per locus. When analyzing sequence polymorphism at four different loci in S. maritima and S. alterniflora, we found up to four haplotypes per locus, suggesting the presence of two expressed homoeologous sequences with one or two allelic variants each. This reference transcriptome will allow analysis of specific Spartina genes of ecological or evolutionary interest, estimation of homoeologous gene expression variation using RNA-seq and further gene expression evolution analyses in natural populations.

| S-EPMC3554450 | biostudies-literature