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Genes expression during stem growth of Populus alba x Populus tremula var. glandulosa

ABSTRACT: To obtain genes expression in different parts of 84k poplar stems, transcriptome sequencing was performed using Illumina Novaseq 6000 second-generation sequencing platform from Shanghai BIOZERON Co. Ltd (www.biozeron.com). Selecte three stem segments of plants REPEAT 1, 2 and 3 with good and similar growth to use: 2nd-3rd internodes (poplar stem top: PST1, PST2, PST3); 9th-10th internodes (poplar stem middle: PSM1, PSM2, PSM3); 14th-15th internodes (poplar stem bottom: PSB1, PSB2, PSB3). [Or the three repeating organisms are also called poplar A, B, C. From top to bottom, the three parts of the stem are also called stem 1, 2, 3.]

ORGANISM(S): Populus alba x Populus glandulosa

PROVIDER: GSE186743 | GEO | 2021/10/28

REPOSITORIES: GEO

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Project description:Hybrid poplar (Populus alba?×?grandidentata; p39) wild type (WT) and QsuB transgenic low-lignin lines were previously described (Unda et al., 2022). WT and lines QsuB1, QsuB5, and QsuB15 were grown in a greenhouse as described in Lin et al., 2022. Samples for metabolomic analyses were collected after a growth period of six months. Stems were cut 5 cm above the root collar and segments of 5 cm were collected above the 1st (bottom), 20th (middle), and 40th (top) internodes. The bark was peeled and developing xylem tissue was collected by scraping the surface of the debarked segments using a razor blade. This approach generated developing xylem samples from the mature (bottom segment), intermediate (middle segment), and immature (top segment) parts of the stem. All the samples were immediately placed in liquid nitrogen, and stored at ?80 °C until time of use. Frozen samples were pulverized with a ball mill (Retsch) using stainless steel jars and grinding balls. Four biological replicates from each transgenic poplar line and WT control were used for metabolomic analyses. The data showed that some changes in metabolite abundance occur only in a specific tissue such as the xylem, phloem, or periderm. In the poplar line that exhibits the strongest reduction of lignin, we found that ~19% of the detected metabolite ions had different abundances in the xylem from mature stems. Changes affect predominantly the shikimate and phenylpropanoid pathways, secondary cell wall metabolism, and result in significant accumulation of hydroxybenzoates that derive from protocatechuate and salicylate. Unda et al., 2022: https://doi.org/10.1111/nph.18136 Lin et al., 2022: https://doi.org/10.1186/s13068-022-02245-4. The work (proposal:https://doi.org/10.46936/10.25585/60000514) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

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Genes expression during stem growth of Populus alba x Populus tremula var. glandulosa

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