A transcriptional timetable of autumn senescence

Andersson, Anders F.; Keskitalo, Johanna; Sjödin, Andreas; Bhalerao, Rupali; Sterky, Fredrik; Wissel, Kirsten; Tandre, Karolina; Aspeborg, Henrik; Moyle, Richard; Ohmiya, Yasunori; Bhalerao, Rishikesh P.; Brunner, Amy M.; Gustafsson, Petter; Karlsson, Jan; Lundeberg, Joakim; Nilsson, Ove; Sandberg, Göran; Strauss, Steven H.; Sundberg, Björn; Uhlén, Mathias; Jansson, Stefan; Nilsson, Peter

doi:10.1186/gb-2004-5-4-r24

Cited by 227 publications

(58 citation statements)

References 28 publications

(45 reference statements)

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“…Mining of POPULUSDB for specific orthologs will also give researchers working with other plant species information about tissue specificity. We have established a platform for transcript analysis with cDNA microarrays that contain Ͼ13 000 clones (13); and using the data set presented here, we have increased the number of clones on microarrays to almost 25,000 (the list of selected clones is found in Table 9, which is published as supporting information on the PNAS web site). We have also shown that Populus species are highly conserved in DNA sequence, and in preliminary studies have found that the DNA microarrays can be effectively hybridized with RNA prepared from different Populus species and related genera, including Salix viminalis and Salix caprea (Salicaceae).…”

Section: Discussionmentioning

confidence: 99%

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A Populus EST resource for plant functional genomics

Sterky

Bhalerao

Unneberg

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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271

261

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Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide >4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (POPULUSDB) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.A fter the completion of the Arabidopsis genome sequence (1) and the publication of near-complete sequences of indica and japonica rice (2, 3), plant researchers have been able to scan these genomes to identify and compare genes of interest. Arabidopsis and rice represent the two major angiosperm phylogenetic groups, dicotyledons and monocotyledons, respectively. They diverged Ϸ170 million years ago (4) and differ in numerous physiological traits. Within these groups, however, great diversity also exists in life history and plant structure. Some of the most striking differences observed are those between woody (trees and shrubs) and herbaceous species. Trees and shrubs form hard, long-lasting structures that are distinct from the soft stems and branches of herbs, especially annuals. The lignocellulosic cell walls of trees and shrubs are critical for their survival, stature, competitive ability, and provision of habitat, and they have a dramatic influence on ecosystem cycles. Trees and shrubs are found intermixed with herbaceous plants in many phylogenetic groups within the angiosperms, showing that the tree growth habit has been lost or acquired many times during evolution (5). The herbaceous life form is often considered to be the derived state, evolving numerous times from tree-like ancestors (6).The tree life form imposes several different physiological and morphological constraints compared with those of herbaceous plants. Many of the processes that distinguish trees from herbs take years to fully develop and express themselves (e.g., wood formation, vegetative phenology, maturation, and the juvenility͞maturity transition) and are therefore not easily studied in herbs. The need for a tree model system for functional genomics has therefore become evident (7). The genus Populus, consisting of Ϸ40 species distributed i...

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Section: Discussionmentioning

confidence: 99%

“…Sequences were run on Beckman SEQ2000, MegaBACE, ABI3700, and ABI377. The 5Ј and 3Ј end sequences from the confirmatory resequencing of the clones selected for microarray production (12,13) were also included in the assembly. Sequence reads obtained from the ABI3700 and ABI377 sequencers were base-called by using TRACETUNER (www.paracel.com).…”

Section: Methodsmentioning

confidence: 99%

A Populus EST resource for plant functional genomics

Sterky

Bhalerao

Unneberg

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

271

261

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“…Downstream from photoperiod sensing both involve a plethora of genes that execute the respective programmes with negative and positive elements, e.g. down regulation of photosynthesis and up regulation of functions of breakdown and remobilisation (BuchananWollaston 1997; Andersson et al 2004;Keskitalo et al 2005;Lim et al 2007). …”

Section: Autumnal Leaf Senescence and Abscissionmentioning

confidence: 99%

Diurnal and annual rhythms in trees

Lüttge

Hertel

2009

Trees

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Trees, perennial phanerophytes, display a rich variety of rhythmic phenomena. These are either due to exclusive environmental entrainment or due to the functioning of endogenous oscillators independent of the environment. Both types of rhythms are covered in this review. Purely environment controlled rhythms may be considered as a prelude to endogenous rhythms. Environment controlled rhythms discussed are (i) the diurnal rhythms of nyctinastic and heliotropic leaf movements and oscillatory phenomena of photosynthesis, such as the midday depression and Crassulacean acid metabolism (CAM), and (ii) the annual rhythms of annual growth ring formation, autumnal leaf senescence, over wintering mechanisms and flowering. Among the diurnal rhythms, nyctinastic movements and CAM are also free-running endogenous rhythms showing the operation of circadian clocks in trees. In leaf senescence, over wintering, and flowering control, photoperiod sensing is involved which suggests the participation of endogenous clocks. A question asked is if diurnal and annual rhythms are mechanistically correlated. Evidently, phenological phenomena based on photoperiodism (as dependent on measurement of night length) are co-ordinately regulated by the phytochrome system and the circadian clocks and many aspects of annual developments and over wintering are linked to photoperiodism. The existence in trees of circadian clock genes as known to be anchored in the genome of A. thaliana can be assessed by attempts of alignment with the sequenced genome of Populus or by isolating cDNA clones from trees to check them against the genome of A. thaliana. At extreme latitudes near the equator and north of the polar circle trees also display photoperiod-independent phenological phenomena. In the polar region, total irradiance of red and far red light could possibly be involved and the signalling pathway then involves phytochrome, and thus, may still be similar to that of photoperiodism. At the equator, total daily light irradiance received or sensing the dynamics of daily changes in solar irradiance are essential and it remains enigmatic whether signalling cascades are either attached to the circadian clocks in a still unknown way or totally independent of circadian clocks.

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“…For traditional isolation studies 1) One tree on the Umeå University campus, designated the UCT (see Andersson et al 2004 for further details) was sampled on June 20th and August 30th; 2) Twelve clones in the Sävar common garden Swedish aspen (SwAsp) collection (that had been root propagated and transplanted into the garden in 2004 (Luquez et al 2008), designated SwAsp(Field), was sampled on July 30th and September 15th; and 3) Fifteen clones from the SwAsp collection grown in a glasshouse since 2004, designated SwAsp(Gh) was sampled only on July 1st.…”

Section: Biological Materialsmentioning

confidence: 99%

Endophytic fungi in European aspen (Populus tremula) leaves—diversity, detection, and a suggested correlation with herbivory resistance

et al. 2010

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Fungal endophytes are found in most seed plants, but their ecological function mainly remains elusive, except in pooid (or clavicipitalean) systems. The diversity and dynamics of endophytes in non clavicipitalean plants make studies of their ecological function challenging. This paper describes the advantage of using molecular techniques to survey the ecological function of endophytes in Populus tremula clones. About 1,000 endophyte isolates were distinguished using traditional methods; these isolates represented approximately 100 morphologically distinct groups. We generated 73 DNA-sequences (18S and ITS rDNA) from these groups and determined 33 distinct taxa. They represented the Basidiomycota and Ascomycota, including diverse Sordariomycetes and Dothideomycetes, and three sequences that were identified, by their ITS sequences, as a species of Epicoccum (a genus of supposedly unknown relation within the Ascomycota) were placed within the Pleosporales, in the 18S phylogeny. Primer pairs were designed for eleven of the fungi. Of these, three primers produced bands for a subset of Aspen samples. The primer pairs allowed endophytes in field samples to be readily identified, with a detection limit of 0.15 percent fungal DNA. The presence of fungi in Aspen clones was related to field damage by herbivores and the pathogen Venturia tremula. A negative association was found in two separate surveys between Aureobasidium sp. and herbivore damage, but we found no evidence that endophyte presence was related to a history of Venturia symptoms. This approach promises to enhance greatly the scope for qualitative and quantitative detection of endophyte communities, and to improve our ability to elucidate the ecological function of non clavicipitalean endophytes.

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A transcriptional timetable of autumn senescence

Abstract: A microarray has been created from 36,354 ESTs from Populus species and used to study autumn senescence in the leaves of the aspen tree Populus tremula.

Cited by 227 publications

References 28 publications

A Populus EST resource for plant functional genomics

A Populus EST resource for plant functional genomics

Diurnal and annual rhythms in trees

Endophytic fungi in European aspen (Populus tremula) leaves—diversity, detection, and a suggested correlation with herbivory resistance

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