Developmental variation in DNA methylation in poplar (Populus trichocarpa)

نویسندگان

  • Kelly Vining
  • Kyle R Pomraning
  • Larry Wilhelm
  • Henry D Priest
  • Cathleen Ma
  • Ruoqing Zhu
  • Elizabeth Etherington
  • Matteo Pellegrini
  • Todd Mockler
  • Michael Freitag
  • Steven H Strauss
چکیده

Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we analyzed DNA methylation patterns in the P. trichocarpa genome in relation to four biological processes: bud dormancy and release, mature organ maintenance, in vitro organogenesis, and methylation suppression. Here, we report results from Illumina sequencing of nine sampled tissues, each representing 1 to 2 biological replicates. We sequenced 26M – 97M reads per tissue type, and validated our MeDIP-seq results using bisulfite sequencing of selected targets. Unique MeDIP-seq reads covered ~30-60% of genome space at an average depth of 4 to 12 reads/nucleotide. Transposons and other repeat elements were enriched within the methylated fraction of the genome. The pattern of gene model methylation showed higher methylation at promoters, in the middle of coding regions, and 3’ to ends of genes, similar to that observed in other plant and animal species. Numbers of methylated genes identified varied widely by tissue type. We produced summary data for genome methylation in P. trichocarpa, including the distribution of methylation across chromosomes (Fig. 1) and in and around genes. The intensity of methylation was highly heterogeneous within and between chromosomes. One-third of the genome, analyzed as 1 kb tiled windows, was differentially methylated among tissues. An example of a chromosomal region with differential methylation is shown in Fig. 2. Promoter methylation was more frequent than gene body methylation. Male catkins differed from the other tissues in that gene body methylation was more prevalent than promoter methylation, and two

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation

Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the ...

متن کامل

Site-Dependent Differences in DNA Methylation and Their Impact on Plant Establishment and Phosphorus Nutrition in Populus trichocarpa

The propagation via clonal stem cuttings is a frequent practice in tree plantations. Despite their clonal origin, the trees establish differently according to weather, temperature and nutrient availability, as well as the presence of various stresses. Here, clonal Populus trichocarpa (cv. Muhle Larson) cuttings from different sites were transferred into a common, fully nutrient supplied environ...

متن کامل

Natural acetylation impacts carbohydrate recovery during deconstruction of Populus trichocarpa wood

BACKGROUND Significant variation in the inherent degree of acetylation naturally exists in the xylem cell walls of Populus trichocarpa. During pretreatment, endogenous acetate hydrolyzes to acetic acid that can subsequently catalyze the breakdown of poplar wood, increasing the efficiency of biomass pretreatment. RESULTS Poplar genotypes varying in cell wall composition were pretreated in 0.3%...

متن کامل

Variation in Genomic Methylation in Natural Populations of Chinese White Poplar

BACKGROUND It is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic met...

متن کامل

Rapid alkalinization factors in poplar cell cultures. Peptide isolation, cDNA cloning, and differential expression in leaves and methyl jasmonate-treated cells.

A family of peptides inducing rapid pH alkalinization in hybrid poplar (Populus trichocarpa x Populus deltoides) cell culture medium was isolated from hybrid poplar leaves. Five related approximately 5-kD peptides were purified by high-performance liquid chromatography and analyzed by matrix-assisted laser desorption ionization-mass spectrometry. The N-terminal sequence of one of the isolated p...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:

دوره 5  شماره 

صفحات  -

تاریخ انتشار 2011