New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics

Hu, Weichang; Hua, Xiuting; Zhang, Qing; Wang, Jianping; Shen, Qiaochu; Zhang, Xingtan; Wang, Kai; Yu, Qingyi; Lin, Yi Ru; Ming, Ray; Zhang, Jisen

doi:10.1186/s12870-018-1495-y

Cited by 58 publications

(59 citation statements)

References 93 publications

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“…Analysis of the expression profiling of HAKs in Saccharum based on RNA-seq RNA preparation, cDNA libraries construction and RNA-seq libraries sequencing were performed as previously described [51,52]. Raw data were aligned to available S. spontaneum AP85-441 reference gene models using Trinity (https:// github.com/trinityrnaseq/trinityrnaseq/wiki).…”

Section: Sequence and Phylogenetic Analysesmentioning

confidence: 99%

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Genome-wide systematic characterization of the HAK/KUP/KT gene family and its expression profile during plant growth and in response to low-K+ stress in Saccharum

Feng¹,

Wang

Zhang³

et al. 2020

BMC Plant Biol

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Background: Plant genomes contain a large number of HAK/KUP/KT transporters, which play important roles in potassium uptake and translocation, osmotic potential regulation, salt tolerance, root morphogenesis and plant development. Potassium deficiency in the soil of a sugarcane planting area is serious. However, the HAK/KUP/KT gene family remains to be characterized in sugarcane (Saccharum). Results: In this study, 30 HAK/KUP/KT genes were identified in Saccharum spontaneum. Phylogenetics, duplication events, gene structures and expression patterns were analyzed. Phylogenetic analysis of the HAK/KUP/KT genes from 15 representative plants showed that this gene family is divided into four groups (clades I-IV). Both ancient wholegenome duplication (WGD) and recent gene duplication contributed to the expansion of the HAK/KUP/KT gene family. Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that purifying selection was the main force driving the evolution of HAK/KUP/KT genes. The divergence time of the HAK/KUP/KT gene family was estimated to range from 134.8 to 233.7 Mya based on Ks analysis, suggesting that it is an ancient gene family in plants. Gene structure analysis showed that the HAK/KUP/KT genes were accompanied by intron gain/loss in the process of evolution. RNA-seq data analysis demonstrated that the HAK/KUP/KT genes from clades II and III were mainly constitutively expressed in various tissues, while most genes from clades I and IV had no or very low expression in the tested tissues at different developmental stages. The expression of SsHAK1 and SsHAK21 was upregulated in response to low-K + stress. Yeast functional complementation analysis revealed that SsHAK1 and SsHAK21 could rescue K + uptake in a yeast mutant. Conclusions: This study provided insights into the evolutionary history of HAK/KUP/KT genes. HAK7/9/18 were mainly expressed in the upper photosynthetic zone and mature zone of the stem. HAK7/9/18/25 were regulated by sunlight. SsHAK1 and SsHAK21 played important roles in mediating potassium acquisition under limited K + supply. Our results provide valuable information and key candidate genes for further studies on the function of HAK/KUP/KT genes in Saccharum.

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Section: Sequence and Phylogenetic Analysesmentioning

confidence: 99%

“…Raw data were aligned to available S. spontaneum AP85-441 reference gene models using Trinity (https:// github.com/trinityrnaseq/trinityrnaseq/wiki). Fragments per kilobase per million mapped fragments (FPKM) values were calculated to represent gene expression levels as previously described [51,52].…”

Section: Sequence and Phylogenetic Analysesmentioning

confidence: 99%

Genome-wide systematic characterization of the HAK/KUP/KT gene family and its expression profile during plant growth and in response to low-K+ stress in Saccharum

Feng¹,

Wang

Zhang³

et al. 2020

BMC Plant Biol

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“…For analyzing transcription levels of SsDof genes in different tissues and stages: root samples were obtained from root in seedling stage (45 days old), including the top of root (below the root hair, root-t), the middle of root (root-m) and the base of the root (root-b). Stem and leaf samples were from 9 months old premature internode (pre-m-stem3, pre-m-stem6 and prem-stem9), 12 months old mature internode (m-stem3, m-stem6 and m-stem9) and leaf (leafb, leaf-m and leaf-u) as previously described [17][18][19].…”

Section: Plant Materials and Treatmentsmentioning

confidence: 99%

“…For instance, in group Ⅰ, 10 motifs (1,4,7,8,10,11,15,16,21,25) were the conserved motifs. There were 12 conserved motifs (1,7,8,11,12,13,14,15,16,18,21,24) in group Ⅱ. And group Ⅲ…”

Section: Motif Composition and Gene Structure Of Sugarcane Dof Gene Fmentioning

confidence: 99%

Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane

Cai¹,

Lin²,

Li³

et al. 2020

PLoS ONE

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Dof transcription factors plant-specific and associates with growth and development in plants. We conducted comprehensive and systematic analyses of Dof transcription factors in sugarcane, and identified 29 SsDof transcription factors in sugarcane genome. Those SsDof genes were divided into five groups, with similar gene structures and conserved motifs within the same groups. Segmental duplications are predominant in the evolution of Dof in sugarcane. Cis-element analysis suggested that the functions of SsDofs were involved in growth and development, hormones and abiotic stresses responses in sugarcane. Expression patterns indicated that SsDof7, SsDof23 and SsDof24 had a comparatively high expression in all detected tissues, indicating these genes are crucial in sugarcane growth and development. Moreover, we examined the transcription levels of SsDofs under four plant hormone treatments, SsDof7-3 and SsDof7-4 were down-regulated after ABA treatment, while SsDof7-1 and SsDof7-2 were induced after the same treatment, indicating different alleles may play different roles in response to plant hormones. We also analyzed SsDofs' expression profiling under four abiotic stresses, SsDof5 and SsDof28 significantly responded to these four stresses, indicating they are associate with abiotic stresses responses. Collectively, our results yielded allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane, and their cis-elements could be crucial for sugarcane improvement. et al. (2020) Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane. PLoS ONE 15(1): e0227716. https://

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“…These leaves were cut into 15 1-cm segments and pooled from 4 plants per biological replicate with 3 biological replicates for each tissue type being prepared [49]. The different developmental tissue stages were prepared according to the methods previously described [50,51].…”

Section: Plant Materialsmentioning

confidence: 99%

NAC transcription factors in autopolyploid Saccharum spontaneum: genome-wide identification, expression pattern and a ‘Dry’ orthologous gene

Wang

Naiyan

et al. 2019

Preprint

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Background: The NAC acronym originates from these three genes (NAM, ATA1/2 and CUC2), and were proved to participate in plant development, sugar accumulation and stress tolerance. However, little information is available regarding these genes in sugarcane. The newly published sugarcane genome provided an opportunity to identify the SsNAC transcription factors. Results: In this study, a total of 151 NAC genes including 327 alleles were identified in the autopolyploid S. spontaneum genome and were distributed unevenly on eight chromosomes with the majority located on Chr 5(54, 16.51%), Chr 1(51, 15.60%) and Chr 2(51, 15.60%). 71.6%(234) and 12.53%(41) of SsNAC genes were mainly derived from segmental duplication and tandem duplication. Phylogeny analysis of NAC TF proteins by comparing NAC between sugarcane and Arabidopsis thaliana suggested that the NAC family can be divided into 15 subgroups with one subgroup unclassified. RNA-seq data analysis revealed that 82 SsNAC were expressed in 15 segments of the developmental gradient of the leaf and 74 SsNAC were presented in 12 different developmental stages, respectively. Remarkably, SsNAC genes of the ATAF subgroup presented the highest expression levels among the subgroups, and seven of eight SsNAC genes from the ATAF subgroup excluding SsNAC30 were present at much higher expression levels in the developmental gradient of the leaf than those in different developmental tissues types, indicating that the ATAF subgroup may have significant roles and participate in leaf growth and development and photosynthesis. Importantly, the NAC1 subgroup SsNAC91 gene, being orthologous to Sobic.006G147400 ( Dry gene ), displayed significantly higher expression levels in premature and mature stems of the low sucrose and low water content species S. spontaneum as opposed to the orthologous gene in the high sugar and high water content species S. officinarum . This suggests that the SsNAC91 gene may also play important roles in cellulose biosynthesis and water transport in sugarcane as it does in sorghum. Conclusions: This study provided the basis for the comprehensive genomic study of the SsNAC gene family and thus established a good foundation for the functional analyses of SsNAC genes which can be utilized to breed new varieties of sugarcane.

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New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics

Cited by 58 publications

References 93 publications

Genome-wide systematic characterization of the HAK/KUP/KT gene family and its expression profile during plant growth and in response to low-K+ stress in Saccharum

Genome-wide systematic characterization of the HAK/KUP/KT gene family and its expression profile during plant growth and in response to low-K+ stress in Saccharum

Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane

NAC transcription factors in autopolyploid Saccharum spontaneum: genome-wide identification, expression pattern and a ‘Dry’ orthologous gene

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