3 research outputs found
Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean
The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires
relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced
floral initiation depends on the differentiation and maintenance of meristems. In this study, the
global changes in transcript expression profiles were analyzed in two meristematic tissues corresponding
to the vegetative and inflorescence meristems of two genotypes with different sensitivities
to photoperiods. A total of 3396 differentially expressed genes (DEGs) were identified, and 1271 and
1533 were found to be up-regulated and down-regulated, respectively, whereas 592 genes showed
discordant expression patterns between both genotypes. Arabidopsis homologues of DEGs were
identified, and most of them were not previously involved in Arabidopsis floral transition, suggesting
an evolutionary divergence of the transcriptional regulatory networks of the flowering process of
both species. However, some genes belonging to the photoperiod and flower development pathways
with evolutionarily conserved transcriptional profiles have been found. In addition, the flower
meristem identity genes APETALA1 and LEAFY, as well as CONSTANS-LIKE 5, were identified as
markers to distinguish between the vegetative and reproductive stages. Our data also indicated
that the down-regulation of the photoperiodic genes seems to be directly associated with promoting
floral transition under inductive short-day lengths. These findings provide valuable insight into
the molecular factors that underlie meristematic development and contribute to understanding the
photoperiod adaptation in the common bean.MCIN/AEI PDI2020-114115RB-100MAPAERDF A way of making Europe
European Commission
European Union NextGenera-tionEU/PRT
Functional characterization of the tomato HAIRPLUS gene reveals the implication of the epigenome in the control of glandular trichome formation
This research was supported by the Spanish Ministry of Science, Innovation and Universities (grants AGL2017-88702-C2-1-R and AGL2017-88702-C2-2-R). Funding was also received from the BRESOV (Breeding for resilient, efficient, and sustainable organic vegetable production) project. BRESOV was funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No. 774244. We would also like to thank research facilities provided by the Campus de Excelencia Internacional Agroalimentario (CeiA3). PhD fellowships were funded by the FPU (R.F., R.Le.) Programmes of the Ministerio de Ciencia e Innovacion and the LASPAU (J.L.Q.).Trichomes are specialised epidermal cells developed in the aerial surface of almost every terrestrial plant. These structures form
physical barriers, which combined with their capability of synthesis of complex molecules, prevent plagues from spreading and
confer trichomes a key role in the defence against herbivores. In this work, the tomato gene HAIRPLUS (HAP) that controls glandular
trichome density in tomato plants was characterised. HAP belongs to a group of proteins involved in histone tail modifications
although some also bind methylated DNA. HAP loss of function promotes epigenomic modifications in the tomato genome reflected
in numerous differentially methylated cytosines and causes transcriptomic changes in hap mutant plants. Taken together, these
findings demonstrate that HAP links epigenome remodelling withmulticellular glandular trichome development and reveal that HAP
is a valuable genomic tool for pest resistance in tomato breeding.Spanish Government AGL2017-88702-C2-1-R
AGL2017-88702-C2-2-REuropean Commission 774244FPU Programmes of the Ministerio de Ciencia e InnovacionLASPAUBRESOV (Breeding for resilient, efficient, and sustainable organic vegetable production) projec
sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression
Since the original publication of sRNAtoolbox in
2015, small RNA research experienced notable advances
in different directions. New protocols for
small RNA sequencing have become available to
address important issues such as adapter ligation
bias, PCR amplification artefacts or to include internal
controls such as spike-in sequences. New microRNA
reference databases were developed with
different foci, either prioritizing accuracy (low number
of false positives) or completeness (low number
of false negatives). Additionally, other small RNA
molecules as well asmicroRNA sequence and length
variants (isomiRs) have continued to gain importance.
Finally, the number of microRNA sequencing
studies deposited in GEO nearly triplicated from
2014 (280) to 2018 (764). These developments imply
that fast and easy-to-use tools for expression profiling
and subsequent downstream analysis of miRNAseq
data are essential to many researchers. Key features
in this sRNAtoolbox release include addition of
all major RNA library preparation protocols to sRNAbench
and improvements in sRNAde, a tool that
summarizes several aspects of small RNA sequencing
studies including the detection of consensus differential
expression. A special emphasis was put on
the user-friendliness of the tools, for instance sRNAbench
now supports parallel launching of several
jobs to improve reproducibility and user time efficiency.European Union [765492 to M.H.]; Spanish Government
[AGL2017-88702-C2-2-R to M.H., J.L.O.]; Instituto de
Salud Carlos III, FEDER funds [PIE16/00045 to J.A.M.];
Chair ‘Doctors Galera-Requena in cancer stem cell research’
to JMA and by the Ministry of Education of
Spain [FPU13/05662 to R.L., IFI16/00041 to E.A.]; Strategic
Research Area (SFO) program of the Swedish Research
Council (to V.R.) through Stockholm University (to
B.F.). Funding for open access charge: SpanishGovernment
[AGL2017-88702-C2-2-R]