scholarly journals Discovery and analysis of NBS-LRR gene family in sweet potato genome

2020 ◽  
Vol 46 (8) ◽  
pp. 1195-1207
Author(s):  
Cai-Xiao LIANG ◽  
Yuan-Yuan SHI ◽  
Xiao-Fang HUANG ◽  
Li-Xiang ZHOU ◽  
Shi-Qiang LIN ◽  
...  
Keyword(s):  
Gene Family ◽  
Sweet Potato ◽  
Potato Genome

scholarly journals Haplotype-resolved sweet potato genome traces back its hexaploidization history

Nature Plants ◽  
2017 ◽  
Vol 3 (9) ◽  
pp. 696-703 ◽  
Author(s):  
Jun Yang ◽  
M-Hossein Moeinzadeh ◽  
Heiner Kuhl ◽  
Johannes Helmuth ◽  
Peng Xiao ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Potato Genome

scholarly journals Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuxia Li ◽  
Lei Zhang ◽  
Panpan Zhu ◽  
Qinghe Cao ◽  
Jian Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Sweet Potato ◽  
Gene Structure ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Functional Evaluation ◽  
Ipomoea Trifida ◽  
Wild Ancestor ◽  
Genome Wide ◽  
A Genome

Abstract Background WRKY DNA-binding protein (WRKY) is a large gene family involved in plant responses and adaptation to salt, drought, cold and heat stresses. Sweet potato from the genus Ipomoea is a staple food crop, but the WRKY genes in Ipomoea species remain unknown to date. Hence, we carried out a genome-wide analysis of WRKYs in Ipomoea trifida (H.B.K.) G. Don., the wild ancestor of sweet potato. Results A total of 83 WRKY genes encoding 96 proteins were identified in I. trifida, and their gene distribution, duplication, structure, phylogeny and expression patterns were studied. ItfWRKYs were distributed on 15 chromosomes of I. trifida. Gene duplication analysis showed that segmental duplication played an important role in the WRKY gene family expansion in I. trifida. Gene structure analysis showed that the intron-exon model of the ItfWRKY gene was highly conserved. Meanwhile, the ItfWRKYs were divided into five groups (I, IIa + IIb, IIc, IId + IIe and III) on the basis of the phylogenetic analysis on I. trifida and Arabidopsis thaliana WRKY proteins. In addition, gene expression profiles confirmed by quantitative polymerase chain reaction showed that ItfWRKYs were highly up-regulated or down-regulated under salt, drought, cold and heat stress conditions, implying that these genes play important roles in response and adaptation to abiotic stresses. Conclusions In summary, genome-wide identification, gene structure, phylogeny and expression analysis of WRKY gene in I. trifida provide basic information for further functional studies of ItfWRKYs and for the molecular breeding of sweet potato.

scholarly journals Genome-Wide Identification and Analysis of the NF-Y Gene Family in Potato (Solanum tuberosum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhen Liu ◽  
Yuanming Li ◽  
Jinyong Zhu ◽  
Wenjing Ma ◽  
Zhitao Li ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Solanum Tuberosum L ◽  
Abiotic Stress Tolerance ◽  
Maturation Stage ◽  
Rna Seq ◽  
Potato Genome ◽  
Potato Genome Sequencing Consortium

Nuclear factor Y (NF-Y) is a ubiquitous transcription factor in eukaryotes, which is composed of three subunits (NF-YA, NF-YB, and NF-YC). NF-Y has been identified as a key regulator of multiple pathways in plants. Although the NF-Y gene family has been identified in many plants, it has not been reported in potato (Solanum tuberosum). In the present study, a total of 41 NF-Y proteins in potato (StNF-Ys) were identified, including 10 StNF-YA, 22 StNF-YB, and nine StNF-YC subunits, and their distribution on chromosomes, gene structure, and conserved motif was analyzed. A synteny analysis indicated that 14 and 38 pairs of StNF-Y genes were orthologous to Arabidopsis and tomato (Solanum lycopersicum), respectively, and these gene pairs evolved under strong purifying selection. In addition, we analyzed the expression profiles of NF-Y genes in different tissues of double haploid (DM) potato, as well as under abiotic stresses and hormone treatments by RNA-seq downloaded from the Potato Genome Sequencing Consortium (PGSC) database. Furthermore, we performed RNA-seq on white, red, and purple tuber skin and flesh of three potato cultivars at the tuber maturation stage to identify genes that might be involved in anthocyanin biosynthesis. These results provide valuable information for improved understanding of StNF-Y gene family and further functional analysis of StNF-Y genes in fruit development, abiotic stress tolerance, and anthocyanin biosynthesis in potato.

scholarly journals Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shutao He ◽  
Xiaomeng Hao ◽  
Shuli He ◽  
Xiaoge Hao ◽  
Xiaonan Chen
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Gene Family ◽  
Sweet Potato ◽  
Stress Responses ◽  
Expression Patterns ◽  
Gene Promoters ◽  
Biotic And Abiotic Stress ◽  
Protein Motifs ◽  
Genome Wide

Abstract Background In recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress responses. Although AP2/ERFs have been thoroughly characterised in many plant species, the knowledge about this family in the sweet potato, which is a vital edible and medicinal crop, is still limited. In this study, a comprehensive genome-wide investigation was conducted to characterise the AP2/ERF gene family in the sweet potato. Results Here, 198 IbAP2/ERF transcription factors were obtained. Phylogenetic analysis classified the members of the IbAP2/ERF family into three groups, namely, ERF (172 members), AP2 (21 members) and RAV (5 members), which was consistent with the analysis of gene structure and conserved protein domains. The evolutionary characteristics of these IbAP2/ERF genes were systematically investigated by analysing chromosome location, conserved protein motifs and gene duplication events, indicating that the expansion of the IbAP2/ERF gene family may have been caused by tandem duplication. Furthermore, the analysis of cis-acting elements in IbAP2/ERF gene promoters implied that these genes may play crucial roles in plant growth, development and stress responses. Additionally, the available RNA-seq data and quantitative real-time PCR (qRT-PCR) were used to investigate the expression patterns of IbAP2/ERF genes during sweet potato root development as well as under multiple forms of abiotic stress, and we identified several developmental stage-specific and stress-responsive IbAP2/ERF genes. Furthermore, g59127 was differentially expressed under various stress conditions and was identified as a nuclear protein, which was in line with predicted subcellular localization results. Conclusions This study originally revealed the characteristics of the IbAP2/ERF superfamily and provides valuable resources for further evolutionary and functional investigations of IbAP2/ERF genes in the sweet potato.

scholarly journals Genome-wide identification, structural and gene expression analysis of the nitrate transporters (NRTs) family in potato (Solanum tuberosum L.)

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0257383
Author(s):  
Jingying Zhang ◽  
Zhijun Han ◽  
Yue Lu ◽  
Yanfei Zhao ◽  
Yaping Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Solanum Tuberosum L ◽  
Functional Characterization ◽  
Solanum Melongena ◽  
Distribution Analysis ◽  
Mineral N ◽  
Potato Genome ◽  
Genome Wide ◽  
Subfamily Classification ◽  
Nitrate Transporters

Nitrogen (N2) is the most important source of mineral N for plant growth, which was mainly transported by nitrate transporters (NRTs). However, little is known about the NRT gene family in potato. In this study, StNRT gene family members were identified in potato. In addition, we performed StNRT subfamily classification, gene structure and distribution analysis, and conserved domain prediction using various bioinformatics tools. Totally, 39 StNRT gene members were identified in potato genome, including 33, 4 and 2 member belong to NRT1, NRT2, and NRT3, respectively. These 39 StNRT genes were randomly distributed on all chromosomes. The collinearity results show that StNRT members in potato are closely related to Solanum lycopersicum and Solanum melongena. For the expression, different members of StNRT play different roles in leaves and roots. Especially under sufficient nitrogen conditions, different members have a clear distribution in different tissues. These results provide valuable information for identifying the members of the StNRT family in potato and could provide functional characterization of StNRT genes in further research.

scholarly journals Identification and localisation of the NB-LRR gene family within the potato genome

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 75 ◽  
Author(s):  
Florian Jupe ◽  
Leighton Pritchard ◽  
Graham J Etherington ◽  
Katrin MacKenzie ◽  
Peter JA Cock ◽  
...  
Keyword(s):  
Gene Family ◽  
Potato Genome

scholarly journals Occurrence of LINE, gypsy-like, and copia-like retrotransposons in the clonally propagated sweet potato (Ipomoea batatas L.)

Genome ◽  
2011 ◽  
Vol 54 (7) ◽  
pp. 603-609
Author(s):  
Tom Okpul ◽  
Robert M. Harding ◽  
Mark J. Dieters ◽  
Ian D. Godwin
Keyword(s):  
Sweet Potato ◽  
Ipomoea Batatas ◽  
Blot Hybridization ◽  
Dot Blot ◽  
Hordeum Vulgare L ◽  
Future Studies ◽  
Potato Genome ◽  
Cdna Sequences ◽  
Copy Numbers ◽  
Long Interspersed Element

Retrotransposons are a class of transposable elements that represent a major fraction of the repetitive DNA of most eukaryotes. Their abundance stems from their expansive replication strategies. We screened and isolated sequence fragments of long terminal repeat (LTR), gypsy-like reverse transcriptase (rt) and gypsy-like envelope (env) domains, and two partial sequences of non-LTR retrotransposons, long interspersed element (LINE), in the clonally propagated allohexaploid sweet potato (Ipomoea batatas (L.) Lam.) genome. Using dot-blot hybridization, these elements were found to be present in the ~1597 Mb haploid sweet potato genome with copy numbers ranging from ~50 to ~4100 as observed in the partial LTR (IbLtr-1) and LINE (IbLi-1) sequences, respectively. The continuous clonal propagation of sweet potato may have contributed to such a multitude of copies of some of these genomic elements. Interestingly, the isolated gypsy-like env and gypsy-like rt sequence fragments, IbGy-1 (~2100 copies) and IbGy-2 (~540 copies), respectively, were found to be homologous to the Bagy-2 cDNA sequences of barley (Hordeum vulgare L.). Although the isolated partial sequences were found to be homologous to other transcriptionally active elements, future studies are required to determine whether they represent elements that are transcriptionally active under normal and (or) stressful conditions.

Sign in / Sign up

Export Citation Format

Share Document