Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica

Glycoside Hydrolase 3 (GH3), a member of the Auxin-responsive gene family, is involved in plant growth, the plant developmental process, and various stress responses. The GH3 gene family has been well-studied in Arabidopsis thaliana and Zea mays. However, the evolution of the GH3 gene family in Oryza species remains unknown and the function of the GH3 gene family in Oryza sativa is not well-documented. Here, a systematic analysis was performed in six Oryza species/subspecies, including four wild rice species and two cultivated rice subspecies. A total of 13, 13, 13, 13, 12, and 12 members were identified in O. sativa ssp. japonica, O. sativa ssp. indica, Oryza rufipogon, Oryza nivara, Oryza punctata, and Oryza glumaepatula, respectively. Gene duplication events, structural features, conserved motifs, a phylogenetic analysis, chromosome locations, and Ka/Ks ratios of this important family were found to be strictly conservative across these six Oryza species/subspecies, suggesting that the expansion of the GH3 gene family in Oryza species might be attributed to duplication events, and this expansion could occur in the common ancestor of Oryza species, even in common ancestor of rice tribe (Oryzeae) (23.07~31.01 Mya). The RNA-seq results of different tissues displayed that OsGH3 genes had significantly different expression profiles. Remarkably, the qRT-PCR result after NaCl treatment indicated that the majority of OsGH3 genes play important roles in salinity stress, especially OsGH3-2 and OsGH3-8. This study provides important insights into the evolution of the GH3 gene family in Oryza species and will assist with further investigation of OsGH3 genes’ functions under salinity stress.

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Temperature affects the dormancy and germination of sympatric annual (Oryza meridionalis) and perennial (O. rufipogon) native Australian rices (Poaceae) and influences their emergence in introduced para grass (Urochloa mutica) swards

Australian Journal of Botany ◽

10.1071/bt15092 ◽

2015 ◽

Vol 63 (8) ◽

pp. 687 ◽

Cited By ~ 2

Author(s):

Sean M. Bellairs ◽

Penelope A. S. Wurm ◽

Beckie Kernich

Keyword(s):

Soil Surface ◽

Field Studies ◽

Oryza Rufipogon ◽

Oryza Species ◽

Northern Australia ◽

Seed Biology ◽

Oryza Meridionalis ◽

Native Grasslands ◽

Wild Rice Species ◽

Soil Temperatures

The seed biology of two ecologically and genetically important sympatric wild rice species from northern Australia was compared – perennial Oryza rufipogon Griff. and annual Oryza meridionalis N.Q.Ng. The aim was to determine mechanisms of dormancy exhibited at seed shed and to identify factors that trigger or inhibit germination. This information was used to investigate the ecology of in situ Oryza populations in introduced para grass swards (Urochloa mutica (Forssk.) T.Q. Nguyen) and to understand interactions between the two sympatric Oryza species. Primary dormancy in the two species is similar, namely, non-deep physiological dormancy, determined by external maternal structures and broken by warm temperature treatments equivalent to dry season soil temperatures. Light quality, smoke water, gibberellic acid and nitric acid treatments had minor influences on germination. Changes to the soil profile and aboveground biomass structure due to swards of U. mutica significantly affected emergence of O. meridionalis. Thus the influence of soil temperature explains the results of previous field studies in which biomass or litter on the soil surface prevented germination. This has implications for biodiversity management on monsoonal floodplains of northern Australia, where introduced pasture species produce greater biomass than native grasslands, reduce soil temperatures and are displacing native rices. There were differences between the Oryza species – dormancy was more quickly broken in annual O. meridionalis, reflecting the reduced need for investment in seed bank persistence for annual species in annually inundated and climatically reliable wetlands.

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Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice

PLoS ONE ◽

10.1371/journal.pone.0182469 ◽

2017 ◽

Vol 12 (8) ◽

pp. e0182469 ◽

Cited By ~ 12

Author(s):

Showkat Ahmad Ganie ◽

Dipti Ranjan Pani ◽

Tapan Kumar Mondal

Keyword(s):

Gene Family ◽

Salinity Stress ◽

Oryza Species ◽

Genome Wide Analysis ◽

Genome Wide

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Characterization and evolutionary analysis of ent-kaurene synthase like genes from the wild rice species Oryza rufipogon

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2016.10.062 ◽

2016 ◽

Vol 480 (3) ◽

pp. 402-408 ◽

Cited By ~ 4

Author(s):

Tomonobu Toyomasu ◽

Koji Miyamoto ◽

Matthew R. Shenton ◽

Arisa Sakai ◽

Chizu Sugawara ◽

...

Keyword(s):

Wild Rice ◽

Oryza Rufipogon ◽

Evolutionary Analysis ◽

Wild Rice Species

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Molecular Evolutionary Analysis of the HCRTR Gene Family in Vertebrates

BioMed Research International ◽

10.1155/2018/8120263 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9

Author(s):

Zhen Cai ◽

Hehe Liu ◽

Liyun Wang ◽

Xinxin Li ◽

Lili Bai ◽

...

Keyword(s):

Gene Family ◽

Functional Differentiation ◽

Evolution Process ◽

Evolutionary Analysis ◽

Vital Functions ◽

Evolutionary Force ◽

The Family ◽

Duplication Events ◽

Molecular Evolutionary Analysis ◽

Insight Into

Hypocretin system is composed of hypocretins (hcrts) and their receptors (hcrtrs), which has multiple vital functions. Hypocretins work via hypocretin receptors and it is reported that functional differentiation occurred in hcrtrs. It is necessary to figure out the evolution process of hypocretin receptors. In our study, we adopt a comprehensive approach and various bioinformatics tools to analyse the evolution process of HCRTR gene family. It turns out that the second round of whole genome duplication in early vertebrate ancestry and the independent round in fish ancestry may contribute to the diversity of HCRTR gene family. HCRTR1 of fishes and mammals are not the same receptor, which means that there are three members in the family. HCRTR2 is proved to be the most ancient one in HCRTR gene family. After duplication events, the structure of HCRTR1 diverged from HCRTR2 owing to relaxed selective pressure. Negative selection is the predominant evolutionary force acting on the HCRTR gene family but HCRTR1 of mammals is found to be subjected to positive selection. Our study gains insight into the molecular evolution process of HCRTR gene family, which contributes to the further study of the system.

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Interrelationships of Oryza species based on electrophoretic patterns of alcohol dehydrogenase

Canadian Journal of Botany ◽

10.1139/b92-047 ◽

1992 ◽

Vol 70 (2) ◽

pp. 352-358 ◽

Cited By ~ 8

Author(s):

Anil Grover ◽

Deepak Pental

Keyword(s):

Alcohol Dehydrogenase ◽

Oryza Rufipogon ◽

Band Pattern ◽

Oryza Species ◽

Oryza Glaberrima ◽

Cultivated Rice ◽

Major Band ◽

Electrophoretic Patterns ◽

Oryza Punctata ◽

Germinating Seeds

Nineteen different species belonging to the genus Oryza were studied for variation in electrophoretic patterns of alcohol dehydrogenase (ADH) extracted from germinating seeds. The ADH patterns were similar for aerobically and anaerobically germinating seeds of all the species. Oryza saliva accessions, both indica and japonica, revealed a five-band pattern on polyacrylamide gels. African cultivated rice, Oryza glaberrima, had an alcohol dehydrogenase pattern similar to that of O. sativa. Oryza perennis complex comprising of Oryza nivara, Oryza rufipogon in Asia, Oryza barthii, Oryza longistaminata in Africa, and some of the accessions of O. rufipogon from America had ADH patterns similar to that of O. sativa. In a few accessions of O. rufipogon from America, only three bands were visualized. Oryza minuta, Oryza officinalis, Oryza punctata, Oryza alta, Oryza grandiglumis, and Oryza latifolia had similar patterns with one major band at the same Rf value as the major band of O. sativa and two minor bands corresponding to the two bands found in O. sativa. Oryza australiensis, Oryza brachyantha, and Oryza granulata had distinct patterns. Oryza ridleyi had a six-band pattern with three major and three minor bands. The three major bands correspond to the major band of O. granulata, O. officinalis, and O. australiensis. Based on alcohol dehydrogenase data, six major groups were identified amongst Oryza species. Key words: Oryza species, alcohol dehydrogenase, phylogenetics.

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Expansion and Evolutionary Patterns of Glycosyltransferase Family 8 in Gramineae Crop Genomes and Their Expression under Salt and Cold Stresses in Oryza sativa ssp. japonica

Biomolecules ◽

10.3390/biom9050188 ◽

2019 ◽

Vol 9 (5) ◽

pp. 188 ◽

Cited By ~ 9

Author(s):

Weilong Kong ◽

Ziyun Gong ◽

Hua Zhong ◽

Yue Zhang ◽

Gangqing Zhao ◽

...

Keyword(s):

Oryza Sativa ◽

Gene Family ◽

Plant Cell ◽

Plant Cell Wall ◽

Brachypodium Distachyon ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Oryza Rufipogon ◽

Potential Candidate ◽

Evolutionary Patterns

Plant cell walls play a fundamental role in several ways, providing structural support for cells, resistance against pathogens and facilitating the communication between cells. The glycosyltransferase family 8 (GT8) is involved in the formation of the plant cell wall. However, the evolutionary relationship and the functional differentiation of this important gene family remain obscure in Gramineae crop genomes. In the present investigation, we identified 269 GT8 genes in the seven Gramineae representative crop genomes, namely, 33 in Hordeum vulgare, 37 in Brachypodium distachyon, 40 in Oryza sativa ssp. japonica, 41 in Oryza rufipogon, 36 in Setaria italica, 37 in Sorghum bicolor, and 45 in Zea mays. Phylogenetic analysis suggested that all identified GT8 proteins belonged to seven subfamilies: galacturonosyltransferase (GAUT), galacturonosyltransferase-like (GATL), GATL-related (GATR), galactinol synthase (GolS), and plant glycogenin-like starch initiation proteins A (PGSIP-A), PGSIP-B, and PGSIP-C. We estimated that the GAUT subfamily might be further divided into four subgroups (I–IV) due to differentiation of gene structures and expression patterns. Our orthogroup analysis identified 22 orthogroups with different sizes. Of these orthogroups, several orthogroups were lost in some species, such as S. italica and Z. mays. Moreover, lots of duplicate pairs and collinear pairs were discovered among these species. These results indicated that multiple duplication modes led to the expansion of this important gene family and unequal loss of orthogroups and subfamilies might have happened during the evolutionary process. RNA-seq, microarray analysis, and qRT-PCR analyses indicated that GT8 genes are critical for plant growth and development, and for stresses responses. We found that OsGolS1 was significantly up-regulated under salt stress, while OsGAUT21, OsGATL2, and OsGATL5 had remarkable up-regulation under cold stress. The current study highlighted the expansion and evolutionary patterns of the GT8 gene family in these seven Gramineae crop genomes and provided potential candidate genes for future salt- and cold- resistant molecular breeding studies in O. sativa.

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Genome-Wide Identification and Evolutionary Analysis of AOMT Gene Family in Pomegranate (Punica granatum)

Agronomy ◽

10.3390/agronomy11020318 ◽

2021 ◽

Vol 11 (2) ◽

pp. 318

Author(s):

Xinhui Zhang ◽

Weicheng Yuan ◽

Yujie Zhao ◽

Yuan Ren ◽

Xueqing Zhao ◽

...

Keyword(s):

Gene Family ◽

Gene Evolution ◽

Punica Granatum ◽

Gene Family Evolution ◽

Raw Material ◽

Whole Genome ◽

Evolutionary Analysis ◽

New Genes ◽

Genome Wide ◽

Duplication Events

Gene duplication is the major resource with which to generate new genes, which provide raw material for novel functions evolution. Thus, to elucidate the gene family evolution after duplication events is of vital importance. Anthocyanin O-methyltransferases (AOMTs) have been recognized as being capable of anthocyanin methylation, which increases anthocyanin diversity and stability and improves the protection of plants from environmental stress. Meanwhile, no detailed identification or genome-wide analysis of the AOMT gene family members in pomegranate (Punicagranatum) have been reported. Three published pomegranate genome sequences offer substantial resources with which to explore gene evolution based on the whole genome. Altogether, 58 identified OMTs from pomegranate and five other species were divided into the AOMT group and the OMT group, according to their phylogenetic tree and AOMTs derived from OMTs. AOMTs in the same subclade have a similar gene structure and protein conserved motifs. The PgAOMT family evolved and expanded primarily via whole-genome duplication (WGD) and tandem duplication. PgAOMTs expression pattern in peel and aril development by qRT-PCR verification indicated that PgAOMTs had tissue-specific patterns. The main fates of AOMTs were neo- or non-functionalization after duplication events. High expression genes of PgOMT04 and PgOMT09 were speculated to contribute to “Taishanhong” pomegranate’s bright red peel color. Finally, we integrated the above analysis in order to infer the evolutionary scenario of AOMT family.

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Sugar Transporter Proteins (STPs) in Gramineae Crops: Comparative Analysis, Phylogeny, Evolution, and Expression Profiling

Cells ◽

10.3390/cells8060560 ◽

2019 ◽

Vol 8 (6) ◽

pp. 560 ◽

Cited By ~ 2

Author(s):

Weilong Kong ◽

Baoguang An ◽

Yue Zhang ◽

Jing Yang ◽

Shuangmiao Li ◽

...

Keyword(s):

Gene Family ◽

Evolutionary Dynamics ◽

Brachypodium Distachyon ◽

Oryza Rufipogon ◽

Comparative Genomic ◽

Sugar Transporter ◽

Transporter Proteins ◽

Genomic Study ◽

Duplication Events ◽

Selective Forces

Sugar transporter proteins (STPs), such as H+/sugar symporters, play essential roles in plants’ sugar transport, growth, and development, and possess an important potential to enhance plants’ performance of multiple agronomic traits, especially crop yield and stress tolerance. However, the evolutionary dynamics of this important gene family in Gramineae crops are still not well-documented and functional differentiation of rice STP genes remain unclear. To address this gap, we conducted a comparative genomic study of STP genes in seven representative Gramineae crops, which are Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Setaria italica (Si), Sorghum bicolor (Sb), Zea mays (Zm), Oryza rufipogon (Or), and Oryza sativa ssp. japonica (Os). In this case, a total of 177 STP genes were identified and grouped into four clades. Of four clades, the Clade I, Clade III, and Clade IV showed an observable number expansion compared to Clade II. Our results of identified duplication events and divergence time of duplicate gene pairs indicated that tandem, Whole genome duplication (WGD)/segmental duplication events play crucial roles in the STP gene family expansion of some Gramineae crops (expect for Hv) during a long-term evolutionary process. However, expansion mechanisms of the STP gene family among the tested species were different. Further selective force studies revealed that the STP gene family in Gramineae crops was under purifying selective forces and different clades and orthologous groups with different selective forces. Furthermore, expression analysis showed that rice STP genes play important roles not only in flower organs development but also under various abiotic stresses (cold, high-temperature, and submergence stresses), blast infection, and wounding. The current study highlighted the expansion and evolutionary patterns of the STP gene family in Gramineae genomes and provided some important messages for the future functional analysis of Gramineae crop STP genes.

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Genome-Wide Identification and Expansion Patterns of SULTR Gene Family in Gramineae Crops and Their Expression Profiles under Abiotic Stress in Oryza sativa

Genes ◽

10.3390/genes12050634 ◽

2021 ◽

Vol 12 (5) ◽

pp. 634

Author(s):

Zhengqing Yuan ◽

Weixiong Long ◽

Haifei Hu ◽

Ting Liang ◽

Xiaoyun Luo ◽

...

Keyword(s):

Oryza Sativa ◽

Stress Responses ◽

Expression Profiles ◽

Functional Differentiation ◽

Rice Seedling ◽

Oryza Rufipogon ◽

Evolutionary Patterns ◽

Duplication Events ◽

High Selenium ◽

Low Selenium

Sulfate transporters (SULTRs), also known as H+/SO42− symporters, play a key role in sulfate transport, plant growth and stress responses. However, the evolutionary relationships and functional differentiation of SULTRs in Gramineae crops are rarely reported. Here, 111 SULTRs were retrieved from the genomes of 10 Gramineae species, including Brachypodium disachyon, Hordeum vulgare, Setaria italica, Sorghum bicolor, Zea mays, Oryza barthii, Oryza rufipogon, Oryza glabbermia and Oryza sativa (Oryza sativa ssp. indica and Oryza sativa ssp. japonica). The SULTRs were clustered into five clades based on a phylogenetic analysis. Syntheny analysis indicates that whole-genome duplication/segmental duplication and tandem duplication events were essential in the SULTRs family expansion. We further found that different clades and orthologous groups of SULTRs were under a strong purifying selective force. Expression analysis showed that rice SULTRs with high-affinity transporters are associated with the functions of sulfate uptake and transport during rice seedling development. Furthermore, using Oryza sativa ssp. indica as a model species, we found that OsiSULTR10 was significantly upregulated under salt stress, while OsiSULTR3 and OsiSULTR12 showed remarkable upregulation under high temperature, low-selenium and drought stresses. OsiSULTR3 and OsiSULTR9 were upregulated under both low-selenium and high-selenium stresses. This study illustrates the expression and evolutionary patterns of the SULTRs family in Gramineae species, which will facilitate further studies of SULTR in other Gramineae species.

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