In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula

Song, Jianbo; Zeng, Liming; Chen, Rongrong; Wang, Yihua; Zhou, Yong

doi:10.1007/s13205-018-1373-1

Cited by 31 publications

(44 citation statements)

References 36 publications

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“…However, Cu/ZnSODs subfamily genes possessed seven to eight exons. These results are in line with previous reports (Song et al, 2018), and further confirmed that three subfamilies may displayed a great diversity in soybean. Thirdly, the conserved motifs further revealed the varied widely from different subfamilies, especially MnSODs and Cu/ZnSODs subfamily (Fig.…”

Section: Discussionsupporting

confidence: 93%

“…Whereas, almost all the expression levels of soybean SOD genes displayed no significant change under cold stress, except for a slightly up-regulation (|Log 2 fold change| > 1) of GmFSD2. This indicated that the soybean SOD genes may play different roles under cold stress, which also consistent with previous research (Song et al, 2018). In addition, we also examined the expression patterns of soybean SOD genes under water-deficit stress (Fig.…”

Section: Discussionsupporting

confidence: 90%

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Genome-wide identification and characterization of the soybean SOD family during alkaline stress

Duanmu

Qiao

et al. 2020

PeerJ

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Background Superoxide dismutase (SOD) proteins, as one kind of the antioxidant enzymes, play critical roles in plant response to various environment stresses. Even though its functions in the oxidative stress were very well characterized, the roles of SOD family genes in regulating alkaline stress response are not fully reported. Methods We identified the potential family members by using Hidden Markov model and soybean genome database. The neighbor-joining phylogenetic tree and exon-intron structures were generated by using software MEGA 5.0 and GSDS online server, respectively. Furthermore, the conserved motifs were analyzed by MEME online server. The syntenic analysis was conducted using Circos-0.69. Additionally, the expression levels of soybean SOD genes under alkaline stress were identified by qRT-PCR. Results In this study, we identified 13 potential SOD genes in soybean genome. Phylogenetic analysis suggested that SOD genes could be classified into three subfamilies, including MnSODs (GmMSD1–2), FeSODs (GmFSD1–5) and Cu/ZnSODs (GmCSD1–6). We further investigated the gene structure, chromosomal locations and gene-duplication, conserved domains and promoter cis-elements of the soybean SOD genes. We also explored the expression profiles of soybean SOD genes in different tissues and alkaline, salt and cold stresses, based on the transcriptome data. In addition, we detected their expression patterns in roots and leaves by qRT-PCR under alkaline stress, and found that different SOD subfamily genes may play different roles in response to alkaline stress. These results also confirmed the hypothesis that the great evolutionary divergence may contribute to the potential functional diversity in soybean SOD genes. Taken together, we established a foundation for further functional characterization of soybean SOD genes in response to alkaline stress in the future.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionsupporting

confidence: 90%

Genome-wide identification and characterization of the soybean SOD family during alkaline stress

Duanmu

Qiao

et al. 2020

PeerJ

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“…In the present study, AOS was also encoded by a single gene, but the HPL genes existed in multiple copies. According to the criteria in a previous report [27], two tandem duplication events and one segmental duplication event were identified (Figure 1). A previous study showed that a single amino acid exchange leads to the conversion of an AOS to an HPL [43].…”

Section: Discussionmentioning

confidence: 99%

“…The subcellular localization of the watermelon CYP74 proteins was predicted using ProtComp 9.0 (http://linux1.softberry.com/). The chromosomal locations of watermelon CYP74 genes were obtained from watermelon (97103) v1 genome database, and the segmental and tandem duplications were checked based on the methodology in a previous study [27]. To identify the putative cis-acting regulatory elements of the promoter regions of watermelon CYP74 genes, the 1,500-bp sequences upstream the start codon of watermelon CYP74 genes were retrieved and analyzed using PlantCARE tool (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/).…”

Section: Protein Properties Chromosomal Locations and Promoter Analmentioning

confidence: 99%

The CYP74 Gene Family in Watermelon: Genome-Wide Identification and Expression Profiling Under Hormonal Stress and Root-Knot Nematode Infection

Zhou

Guang

et al. 2019

Agronomy

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Allene oxide synthase (AOS) and hydroperoxide lyase (HPL), members of the CYP74 gene family, are branches of the oxylipin pathway and play vital roles in plant responses to a number of stresses. In this study, four HPL genes and one AOS gene were identified in the watermelon genome, which were clustered into three subfamilies (CYP74A, CYP74B and CYP74C). Sequence analysis revealed that most HPL and AOS proteins from various plants contain representative domains, including Helix-I region, Helix-K region (ExxR) and Heme-binding domain. A number of development-, stress-, and hormone-related cis-elements were found in the promoter regions of the ClAOS and ClHPL genes, and the detected ClAOS and ClHPL genes were differentially expressed in different tissues and fruit development stages, as well as in response to various hormones. In addition, red light could enhance the expression of ClAOS in root-knot nematode-infected leaves and roots of watermelon, implying that ClAOS might play a primary role in red light-induced resistance against root-knot nematodes. These findings lay a foundation for understanding the specific function of CYP74 genes in watermelon.Agronomy 2019, 9, 872 2 of 17 isomerization or dehydration of fatty acid hydroperoxides and require neither molecular oxygen nor NAD(P)H-dependent cytochrome P450-reductase [1,2,6].CYP74 enzymes are broadly classified into four subfamilies (CYP74A, CYP74B, CYP74C, and CYP74D) based on their evolutionary heritage and relationship with the diversity of oxylipin structure [6]. AOS and DES members constitute the CYP74A and CYP74D subfamily, respectively, while CYP74B and CYP74C subfamilies contain enzymes with HPL activity [5,7]. In addition, AOS enzymes can be classified into three different types: The first two types can use either 13-hydroperoxide derivatives or 9-hydroperoxide derivatives as the substrate (13-AOS and 9-AOS, respectively), while the third type can use both of them (9/13-AOS) as the substrate [4,8]. Similarly, three types of HPL enzymes named as 13-HPL, 9-HPL, and 9/13-HPL were also reported in a number of plant species [9]. To date, AOS and HPL genes have been cloned and functionally characterized from a number of plant species, such as tomato (Solanum lycopersicum L. (Solanaceae)) [10,11], tobacco (Nicotiana attenuate Torr. ex S.Watson) [12], rice (Oryza sativa L.) [13,14], and barrel medic (Medicago truncatula Gaertn.) [15], whereas DES genes have been isolated in very few plants [16][17][18][19][20]. These findings reveal that plant CYP74 family genes are indispensable for oxylipin biosynthesis, and play important roles in plant growth and development, as well as in plant defense to various abiotic and biotic stresses.Watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) is an agricultural crop with high nutritional and economic values, but it is rather susceptible to various biotic and abiotic stresses during growth and development [21]. The root-knot nematodes (RKNs, Meloidogyne incognita) mainly infect the roots of host plants and increase sus...

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“…Another SOD, nickel superoxide dismutase (NiSOD), has not been found in plants (Dupont et al, 2008). For the three main types of SODs identified in plants, Cu/ZnSOD is the most abundant, and is mainly distributed in the chloroplasts, plants cytoplasm, peroxisomes, and/or the extracellular space (Song et al, 2018). FeSOD is considered the oldest type of SOD, and is mainly localized in the chloroplast with a few proteins found in the cytoplasm, whereas MnSOD typically has a mitochondrial localization (Pan et al, 2019;Perry et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress

Zang

Shang

et al. 2020

PeerJ

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Superoxide dismutases (SODs) serve as the first line of defense in the plant antioxidant enzyme system, and play a primary role in the removal of reactive oxygen species (ROS). However, our understanding of the functions of the SOD family in Zostera marina is limited. In this study, a systematic analysis was conducted on the characteristics of the SOD genes in Z. marina at the whole-genome level. Five SOD genes were identified, consisting of two Cu/ZnSODs, two FeSODs, and one MnSOD. Phylogenetic analysis showed that ZmSOD proteins could be divided into two major categories (Cu/ZnSODs and Fe-MnSODs). Sequence motifs, gene structure, and the 3D-modeled protein structures further supported the phylogenetic analysis, with each subgroup having similar motifs, exon-intron structures, and protein structures. Additionally, several cis-elements were identified that may respond to biotic and abiotic stresses. Transcriptome analysis revealed expression diversity of ZmSODs in various tissues. Moreover, qRT-PCR analysis showed that the expression level of most ZmSOD genes trended to decreased expression with the increase of temperature, indicating that heat stress inhibits expression of ZmSODs and may result in reduced ability of ZmSODs to scavenge ROS. Our results provide a basis for further functional research on the SOD gene family in Z. marina, which will help to determine the molecular mechanism of ZmSOD genes in response to environmental stress.

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In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula

Cited by 31 publications

References 36 publications

Genome-wide identification and characterization of the soybean SOD family during alkaline stress

Genome-wide identification and characterization of the soybean SOD family during alkaline stress

The CYP74 Gene Family in Watermelon: Genome-Wide Identification and Expression Profiling Under Hormonal Stress and Root-Knot Nematode Infection

Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress

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