Annotation, phylogeny and expression analysis of the nuclear factor Y gene families in common bean (Phaseolus vulgaris)

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

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Genome-wide characterization and expression analysis of citrus NUCLEAR FACTOR-Y (NF-Y) transcription factors identified a novel NF-YA gene involved in drought-stress response and tolerance

PLoS ONE ◽

10.1371/journal.pone.0199187 ◽

2018 ◽

Vol 13 (6) ◽

pp. e0199187 ◽

Cited By ~ 7

Author(s):

Suzam L. S. Pereira ◽

Cristina P. S. Martins ◽

Aurizangela O. Sousa ◽

Luciana R. Camillo ◽

Caroline P. Araújo ◽

...

Keyword(s):

Transcription Factors ◽

Drought Stress ◽

Stress Response ◽

Expression Analysis ◽

Nuclear Factor ◽

Nuclear Factor Y ◽

Genome Wide

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Comparative bioinformatic analysis of genes expressed in common bean (Phaseolus vulgaris L.) seedlings

Genome ◽

10.1139/g05-010 ◽

2005 ◽

Vol 48 (3) ◽

pp. 562-570 ◽

Cited By ~ 31

Author(s):

Maeli Melotto ◽

Claudia B Monteiro-Vitorello ◽

Adriano G Bruschi ◽

Luis E.A Camargo

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Expressed Sequence Tag ◽

Gene Families ◽

Bioinformatic Analysis ◽

Colletotrichum Lindemuthianum ◽

Cdna Libraries ◽

Nucleotide Polymorphisms ◽

Phaseolus Vulgaris L ◽

Single Nucleotide

To rapidly and cost-effectively generate gene expression data, we developed an annotated unigene database of common bean (Phaseolus vulgaris L.). In this study, 3 cDNA libraries were constructed from the bean breeding line SEL1308, 1 from young leaf and 2 from seedlings inoculated or not inoculated with the fungal pathogen Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara, which causes anthracnose in common bean. To this date, 5255 single-pass sequences have been included in the database after selection based on sequence quality. These ESTs were trimmed and clustered using the computer programs Phred and CAP3 to form a unigene collection of 3126 unique sequences. Within clusters, 318 single nucleotide polymorphisms (SNPs) and 68 insertions–deletions (indels) were found, indicating the presence of paralogous gene families in our database. Each unigene sequence was analyzed for possible function using their similarity to known genes represented in the GenBank database and classified into 14 categories. Only 314 unigenes showed significant similarities to Phaseolus genomic sequences and P. vulgaris ESTs, which indicates that 90% (2818 unigenes) of our database represent newly discovered common bean genes. In addition, 12% (387 unigenes) were shown to be specific to common bean. This study represents a first step towards the discovery of novel genes in beans and a valuable source of molecular markers for expressed gene tagging and mapping.Key words: expressed sequence tag (EST), Colletotrichum lindemuthianum, Phaseolus vulgaris, simple sequence repeat (SSR), single nucleotide polymorphism (SNP).

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Isolation, structural analysis, and expression characteristics of the maize nuclear factor Y gene families

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2016.08.020 ◽

2016 ◽

Vol 478 (2) ◽

pp. 752-758 ◽

Cited By ~ 13

Author(s):

Zhongbao Zhang ◽

Xianglong Li ◽

Chun Zhang ◽

Huawen Zou ◽

Zhongyi Wu

Keyword(s):

Structural Analysis ◽

Gene Families ◽

Nuclear Factor ◽

Nuclear Factor Y ◽

Expression Characteristics

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Cloning and Expression Analysis of Fusarium Wilt Resistance-Related Gene PvCaM1 in Common Bean (Phaseolus vulgaris L.)

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2012.00606 ◽

2013 ◽

Vol 38 (4) ◽

pp. 606-613

Author(s):

Ren-Feng XUE ◽

Zhen-Dong ZHU ◽

Xiao-Ming WANG ◽

Lan-Fen WANG ◽

Xiao-Fei WU ◽

...

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Fusarium Wilt ◽

Expression Analysis ◽

Cloning And Expression ◽

Related Gene ◽

Wilt Resistance ◽

Fusarium Wilt Resistance

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Fe and Zn stress induced gene expression analysis unraveled mechanisms of mineral homeostasis in common bean (Phaseolus vulgaris L.)

Scientific Reports ◽

10.1038/s41598-021-03506-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Uneeb Urwat ◽

Syed Mudasir Ahmad ◽

Antonio Masi ◽

Nazir Ahmad Ganai ◽

Imtiyaz Murtaza ◽

...

Keyword(s):

Gene Expression ◽

Phaseolus Vulgaris ◽

Common Bean ◽

Candidate Genes ◽

Expression Analysis ◽

French Bean ◽

Physiological Processes ◽

Mineral Stress ◽

Zn Stress

AbstractIron (Fe) and zinc (Zn) stress significantly affects fundamental metabolic and physiological processes in plants that results in reduction of plant growth and development. In the present study, common bean variety; Shalimar French Bean-1 (SFB-1) was used as an experimental material. Four different MGRL media i.e. normal MGRL medium (Control), media without Fe (0-Fe), media without Zn (0-Zn) and media with excess Zn (300-Zn) were used for growing seeds of SFB-1 under in vitro condition for three weeks under optimum conditions. Three week old shoot and root tissues were harvested from the plants grown in these four different in vitro conditions and were, subjected to Fe and Zn estimation. Further, extraction of total RNA for differential gene expression of ten candidate genes selected based on our in silico investigation and their classification, phylogeny and expression pattern was unraveled. Expression analysis of three candidate genes (OPT3, NRAMP2 and NRAMP3) in roots revealed possible cross talk among Fe/Zn stress that was further confirmed by observing less accumulation of Fe in roots under both these conditions. However, we observed, higher accumulation of Fe in shoots under 0-Fe condition compared to control that suggests precise sensing for priority based compartmentalization and partitioning leading to higher accumulation of Fe in shoots. Furthermore, the expression analysis of IRT1, FRO1 and Ferritin 1 genes under Fe/Zn stress suggested their role in uptake/transport and signaling of Fe and Zn, whereas the expression of ZIP2, NRAMP1, HA2 and GLP1 genes were highly responsive to Zn in Phaseolus vulgaris. The identified genes highly responsive to Fe and Zn stress condition can be potential candidates for overcoming mineral stress in dicot crop plants.

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