Plant Species In Families Research Articles

Phylogenetic, Structural and Functional Evolution of the LHC Gene Family in Plant Species.

Light-harvesting chlorophyll a/b-binding (LHC) superfamily proteins play a vital role in photosynthesis. Although the physiological and biochemical functions of LHC genes have been well-characterized, the structural evolution and functional differentiation of the products need to be further studied. In this paper, we report the genome-wide identification and phylogenetic analysis of LHC genes in photosynthetic organisms. A total of 1222 non-redundant members of the LHC family were identified from 42 species. According to the phylogenetic clustering of their homologues with Arabidopsis thaliana, they can be divided into four subfamilies. In the subsequent evolution of land plants, a whole-genome replication (WGD) event was the driving force for the evolution and expansion of the LHC superfamily, with its copy numbers rapidly increasing in angiosperms. The selection pressure of photosystem II sub-unit S (PsbS) and ferrochelatase (FCII) families were higher than other subfamilies. In addition, the transcriptional expression profiles of LHC gene family members in different tissues and their expression patterns under exogenous abiotic stress conditions significantly differed, and the LHC genes are highly expressed in mature leaves, which is consistent with the conclusion that LHC is mainly involved in the capture and transmission of light energy in photosynthesis. According to the expression pattern and copy number of LHC genes in land plants, we propose different evolutionary trajectories in this gene family. This study provides a basis for understanding the molecular evolutionary characteristics and evolution patterns of plant LHCs.

Genome-Wide Analysis of von Willebrand Factor A Gene Family in Rice for Its Role in Imparting Biotic Stress Resistance with Emphasis on Rice Blast Disease

von Willebrand factor A (vWA) genes are well characterized in humans except for few BONZAI genes, but the vWA genes are least explored in plants. Considering the novelty and vital role of vWA genes, this study aimed at characterization of vWA superfamily in rice. Rice genome was found to have 40 vWA genes distributed across all the 12 chromosomes, and 20 of the 40 vWA genes were unique while the remaining shared large fragment similarities with each other, indicating gene duplication. In addition to vWA domain, vWA proteins possess other different motifs or domains, such as ubiquitin interacting motif in protein degradation pathway, and RING finger in protein-protein interaction. Expression analysis of vWA genes in available expression data suggested that they probably function in biotic and abiotic stress responses including hormonal response and signaling. The frequency of transposon elements in the entire 3K rice germplasm was negligible except for 9 vWA genes, indicating the importance of these genes in rice. Structural and functional diversities showed that the vWA genes in a blast-resistant rice variety Tetep had huge variations compared to blast-susceptible rice varieties HP2216 and Nipponbare. qRT-PCR analysis of vWA genes in Magnaporthe oryzae infected rice tissues indicated OsvWA9, OsvWA36, OsvWA37 and OsvWA18 as the optimal candidate genes for disease resistance. This is the first attempt to characterize vWA gene family in plant species.

NGHIÊN CỨU MỨC ĐỘ BIỂU HIỆN CỦA CÁC GEN LẶP TRONG HỌ NHÂN TỐ PHIÊN MÃ NAC LIÊN QUAN ĐẾN ĐÁP ỨNG HẠN Ở CÂY LẠC (Arachis hypogaea)

NAC has been considered one of the largest transcription factor families in plant species. In peanut (Arachis hypogaea), 29 members of the AhNAC gene family have been identified and characterized. However, the information of their functions related to the mechanism of the stress response has been reported. In this study, a total of seven duplication events, which occurred from the segmental duplication, has been predicted in the AhNAC gene family in peanuts. The Ka\Ks ratios revealed that natural selection prevented the presence of the point mutations in the most duplicated genes, consequently, maintaining their structure and function during evolution. Based on the unrooted phylogenetic tree between AhNAC proteins in peanuts and 23 drought-responsive CaNAC in chickpea (Cicer arietinum), we proposed 12 members of the AhNAC that potentially share similar functions with well-characterized NAC in chickpea. Furthermore, various hormone- and drought-responsive cis-regulatory elements have been found in the promoter regions of these candidate genes. Re-analysis of the previous RNA-Seq demonstrated that the majority of the candidate AhNAC genes were responsive to the osmotic stress. Taken together, our study could provide an important foundation for further functional characterization towards the improvement of stress tolerance in peanuts.

Prospective Plants with Corroborated Antimalarial Actions: A Review

Malaria is a serious illness resulted from parasites that are communicated to people through the bites of infected female Anopheles mosquitoes. Malaria is still in a worrying trend, particularly in tropical and subtropical climates although it is curable and preventable. In spite of a noteworthy abetment in incidence and death rates caused by malaria, even in 2017, a big number of people (219 million) have been affected by it along with 435 thousand confirmed death cases. Though a lot of synthetic drugs have been commercialized to treat malaria, those are compromised with some serious side effects. On the contrary, plant sources are always getting a big focus to develop novel and effective therapeutics in the treatment of different ailments i.e. quinine and artemisinin to treat malarial complications. The usage of herbal plants against malaria has also a very ancient root. Several families of plant species have showed potential antimalarial activities in previous research works. In this review work, families of these plants have been compiled so that prospective researchers can find a hint to discover more effective and safer plant-derived therapeutic options against malaria. Bangladesh Pharmaceutical Journal 24(2): 180-193, 2021

An Investigation on the Forest and Savanna Vegetation Types in Nnamdi Azikiwe University, Awka Campus, in Anambra State of Nigeria

An investigation on the forest and savanna vegetation types in NnamdiAzikiwe University, Awka campus, in Anambra state was carried out. This study was conducted on two communities (Science village forest vegetation type and Bank site savanna vegetation type) both located within the University Awka campus. The plot size of 5000 m-2 (50 m × 100 m) for the forest and 650 m-2 (25 m × 26 m) for savanna being their respective minimal areas were used. An analysis of the abundance of plant species above 1m in height in the forest vegetation type revealed that Elaeis Guineensis had the highest basal area (2268.59 M2ha-1) and the Gambeya Albida had the lowest basal area (0.72 M2ha-1). It also revealed that Elaeis Guineensis had the highest important value index (35.7778 %) and Gambeya Albida had the least significant important value index (0.7589 %). The results further revealed that there were 38 families identified in the community. An analysis of the abundance of plant species above 1 metre in height in the savanna vegetation type revealed that 15 families of plant species were identified in the community. It also revealed that Rothmannia Hispida(61.53M2ha-1), had the highest basal area while Napoleana Vogelii had the lowest basal area (1.03M2ha-1). It also showed that Terminalia Ivorensis (51.63%) had the highest important value index while Cnestis Ferruginia(1.03%) had the lowest important value index. A critical look at the abundance of undergrowth plant species in the forest vegetation type revealed that 12 families of plant species were identified in the community. It further showed that Setaria Longista had the higher significant relative density (31.38%) and Combretum Racemosum (0.42%), Cola hispid a(0.42%), Andropogangayanus(0.42%), Glyphaea Brevis(0.42%), and Holarrhaeno Flouribunda(0.42%) had the least relative density. The abundance of undergrowth plant species in the savanna vegetation type showed that 9 families of plant species were identified. The result also showed that the community had the plant species diversity value of 0.88. Since soil pH, N, P, K and organic carbon are the five main contributing factors for plant growth and diversity in the study area, natural resources managers must consider the budget and balance of these resources for protection and to ameliorate soil, vegetation degradation and nutrient limitation.

Integrated physiologic, genomic and transcriptomic strategies involving the adaptation of allotetraploid rapeseed to nitrogen limitation

BackgroundNitrogen (N) is a macronutrient that is essential for optimal plant growth and seed yield. Allotetraploid rapeseed (AnAnCnCn, 2n = 4x = 38) has a higher requirement for N fertilizers whereas exhibiting a lower N use efficiency (NUE) than cereal crops. N limitation adaptation (NLA) is pivotal for enhancing crop NUE and reducing N fertilizer use in yield production. Therefore, revealing the genetic and molecular mechanisms underlying NLA is urgent for the genetic improvement of NUE in rapeseed and other crop species with complex genomes.ResultsIn this study, we integrated physiologic, genomic and transcriptomic analyses to comprehensively characterize the adaptive strategies of oilseed rape to N limitation stresses. Under N limitations, we detected accumulated anthocyanin, reduced nitrate (NO3−) and total N concentrations, and enhanced glutamine synthetase activity in the N-starved rapeseed plants. High-throughput transcriptomics revealed that the pathways associated with N metabolism and carbon fixation were highly over-represented. The expression of the genes that were involved in efficient N uptake, translocation, remobilization and assimilation was significantly altered. Genome-wide identification and molecular characterization of the microR827-NLA1-NRT1.7 regulatory circuit indicated the crucial role of the ubiquitin-mediated post-translational pathway in the regulation of rapeseed NLA. Transcriptional analysis of the module genes revealed their significant functional divergence in response to N limitations between allotetraploid rapeseed and the model Arabidopsis. Association analysis in a rapeseed panel comprising 102 genotypes revealed that BnaC5.NLA1 expression was closely correlated with the rapeseed low-N tolerance.ConclusionsWe identified the physiologic and genome-wide transcriptional responses of oilseed rape to N limitation stresses, and characterized the global members of the BnamiR827-BnaNLA1s-BnaNRT1.7s regulatory circuit. The transcriptomics-assisted gene co-expression network analysis accelerates the rapid identification of central members within large gene families of plant species with complex genomes. These findings would enhance our comprehensive understanding of the physiologic responses, genomic adaptation and transcriptomic alterations of oilseed rape to N limitations and provide central gene resources for the genetic improvement of crop NLA and NUE.

Comprehensive analysis of small RNAs expressed in developing male strobili of Cryptomeria japonica.

Deep sequencing of small RNAs (sRNAs) in developing male strobili of second-generation offspring originating from a nuclear genic male sterile tree of Cryptomeria japonica were performed to characterize sRNA populations in the male strobili at early pollen developmental stages. Comparing to sequences of microRNA (miRNA) families of plant species and sRNAs expressed in the reproductive organs of representative vascular plants, 37 conserved miRNA families were detected, of which eight were ubiquitously expressed in the reproductive organs of land plant species. In contrast, miR1083 was common in male reproductive organs of gymnosperm species but absent in angiosperm species. In addition to conserved miRNAs, 199 novel miRNAs candidates were predicted. The expression patterns of the obtained sRNAs were further investigated to detect the differentially expressed (DE) sRNAs between genic male sterile and fertile individuals. A total of 969 DE sRNAs were obtained and only three known miRNA families were included among them. These results suggest that both conserved and species-specific sRNAs contribute to the development of male strobili in C. japonica.

Characterization of the polyphenol oxidase gene family reveals a novel microRNA involved in posttranscriptional regulation of PPOs in Salvia miltiorrhiza

Salvia miltiorrhiza is a well-known material of traditional Chinese medicine. Understanding the regulatory mechanisms of phenolic acid biosynthesis and metabolism are important for S. miltiorrhiza quality improvement. We report here that S. miltiorrhiza contains 19 polyphenol oxidases (PPOs), forming the largest PPO gene family in plant species to our knowledge. Analysis of gene structures and sequence features revealed the conservation and divergence of SmPPOs. SmPPOs were differentially expressed in plant tissues and eight of them were predominantly expressed in phloem and xylem, indicating that some SmPPOs are functionally redundant, whereas the others are associated with different physiological processes. Expression patterns of eighteen SmPPOs were significantly altered under MeJA treatment, and twelve were yeast extract and Ag+-responsive, suggesting the majority of SmPPOs are stress-responsive. Analysis of high-throughput small RNA sequences and degradome data showed that miR1444-mediated regulation of PPOs existing in P. trichocarpa is absent from S. miltiorrhiza. Instead, a subset of SmPPOs was posttranscriptionally regulated by a novel miRNA, termed Smi-miR12112. It indicates the specificity and significance of miRNA-mediated regulation of PPOs. The results shed light on the regulation of SmPPO expression and suggest the complexity of SmPPO-associated phenolic acid biosynthesis and metabolism.

Genome-wide analysis of calcium-dependent protein kinases and their expression patterns in response to herbivore and wounding stresses in soybean.

Calcium-dependent protein kinases (CDPKs) play important roles in various aspects of plant physiology and involve in many cellular processes. However, genome-wide analysis of CDPK family in plant species is limited and few studies have been reported in soybean. In this study, a total of 39 genes encoding CDPKs were identified from the whole-genome sequence of soybean (Glycine max), which were denominated as GmCPK1-GmCPK39. These 39 CDPK genes could be classified into four subfamilies, and most genes showed tissue-specific expression patterns. Eight soybean CDPKs clustered together with the previously reported CDPKs related to pathogen, wounding, or herbivore stress were further analyzed. Differential gene expression analysis of these eight CDPK genes in response to herbivore and wounding stresses helps us identify GmCPK3 and GmCPK31 as the candidate genes for herbivore resistance in soybean, whose relative transcript abundance rapidly increased after wound and herbivore attacks. Sub-cellular localization revealed that GmCPK3 and GmCPK31 were localized in plasma membranes, which is consistent with previously reported plant defense related CDPKs. These results may suggest that GmCPK3 and GmCPK31 play important roles in the plant response to biotic stress. Simultaneously, our study will provide an important foundation for further functional characterization of the soybean CDPK gene family.

Genome-wide analysis of MATE transporters and expression patterns of a subgroup of MATE genes in response to aluminum toxicity in soybean.

BackgroundMultidrug and toxic compound extrusion (MATE) family is an important group of the multidrug efflux transporters that extrude organic compounds, transporting a broad range of substrates such as organic acids, plant hormones and secondary metabolites. However, genome-wide analysis of MATE family in plant species is limited and no such studies have been reported in soybean.ResultsA total of 117 genes encoding MATE transporters were identified from the whole genome sequence of soybean (Glycine max), which were denominated as GmMATE1 - GmMATE117. These 117 GmMATE genes were unevenly localized on soybean chromosomes 1 to 20, with both tandem and segmental duplication events detected, and most genes showed tissue-specific expression patterns. Soybean MATE family could be classified into four subfamilies comprising ten smaller subgroups, with diverse potential functions such as transport and accumulation of flavonoids or alkaloids, extrusion of plant-derived or xenobiotic compounds, regulation of disease resistance, and response to abiotic stresses. Eight soybean MATE transporters clustered together with the previously reported MATE proteins related to aluminum (Al) detoxification and iron translocation were further analyzed. Seven stress-responsive cis-elements such as ABRE, ARE, HSE, LTR, MBS, as well as a cis-element of ART1 (Al resistance transcription factor 1), GGNVS, were identified in the upstream region of these eight GmMATE genes. Differential gene expression analysis of these eight GmMATE genes in response to Al stress helps us identify GmMATE75 as the candidate gene for Al tolerance in soybean, whose relative transcript abundance increased at 6, 12 and 24 h after Al treatment, with more fold changes in Al-tolerant than Al-sensitive cultivar, which is consistent with previously reported Al-tolerance related MATE genes.ConclusionsA total of 117 MATE transporters were identified in soybean and their potential functions were proposed by phylogenetic analysis with known plant MATE transporters. The cis-elements and expression patterns of eight soybean MATE genes related to Al detoxification/iron translocation were analyzed, and GmMATE75 was identified as a candidate gene for Al tolerance in soybean. This study provides a first insight on soybean MATE family and their potential roles in soybean response to abiotic stresses especially Al toxicity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2559-8) contains supplementary material, which is available to authorized users.

Confamiliar transferability of simple sequence repeat (SSR) markers from cotton (Gossypium hirsutum L.) and jute (Corchorus olitorius L.) to twenty two Malvaceous species.

Cross-species transferability is a quick and economic method to enrich SSR database, particularly for minor crops where little genomic information is available. However, transferability of SSR markers varies greatly between species, genera and families of plant species. We assessed confamiliar transferability of SSR markers from cotton (Gossypium hirsutum) and jute (Corchorus olitorius) to 22 species distributed in different taxonomic groups of Malvaceae. All the species selected were potential industrial crop species having little or no genomic resources or SSR database. Of the 14 cotton SSR loci tested, 13 (92.86 %) amplified in G. arboreum and 71.43 % exhibited cross-genera transferability. Nine out of 11 jute SSRs (81.81 %) showed cross-transferability across genera. SSRs from both the species exhibited high polymorphism and resolving power in other species. The correlation between transferability of cotton and jute SSRs were highly significant (r = 0.813). The difference in transferability among species was also significant for both the marker groups. High transferability was observed at genus, tribe and subfamily level. At tribe level, transferability of jute SSRs (41.04 %) was higher than that of cotton SSRs (33.74 %). The tribe Byttnerieae exhibited highest SSR transferability (48.7 %). The high level of cross-genera transferability (>50 %) in ten species of Malvaceae, where no SSR resource is available, calls for large scale transferability testing from the enriched SSR databases of cotton and jute.

Identification of potential miRNAs and their targets in Vriesea carinata (Poales, Bromeliaceae)

The miRNAs play important roles in regulation of gene expression at the post-transcriptional level. A small RNA and RNA-seq of libraries were constructed to identify miRNAs in Vriesea carinata, a native bromeliad species from Brazilian Atlantic Rainforest. Illumina technology was used to perform high throughput sequencing and data was analyzed using bioinformatics tools. We obtained 2,191,509 mature miRNAs sequences representing 54 conserved families in plant species. Further analysis allowed the prediction of secondary structures for 19 conserved and 16 novel miRNAs. Potential targets were predicted from pre-miRNAs by sequence homology and validated using RTqPCR approach. This study provides the first identification of miRNAs and their potential targets of a bromeliad species.

Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis.

BackgroundGDSL esterases/lipases are a newly discovered subclass of lipolytic enzymes that are very important and attractive research subjects because of their multifunctional properties, such as broad substrate specificity and regiospecificity. Compared with the current knowledge regarding these enzymes in bacteria, our understanding of the plant GDSL enzymes is very limited, although the GDSL gene family in plant species include numerous members in many fully sequenced plant genomes. Only two genes from a large rice GDSL esterase/lipase gene family were previously characterised, and the majority of the members remain unknown. In the present study, we describe the rice OsGELP (Oryza sativa GDSL esterase/lipase protein) gene family at the genomic and proteomic levels, and use this knowledge to provide insights into the multifunctionality of the rice OsGELP enzymes.ResultsIn this study, an extensive bioinformatics analysis identified 114 genes in the rice OsGELP gene family. A complete overview of this family in rice is presented, including the chromosome locations, gene structures, phylogeny, and protein motifs. Among the OsGELPs and the plant GDSL esterase/lipase proteins of known functions, 41 motifs were found that represent the core secondary structure elements or appear specifically in different phylogenetic subclades. The specification and distribution of identified putative conserved clade-common and -specific peptide motifs, and their location on the predicted protein three dimensional structure may possibly signify their functional roles. Potentially important regions for substrate specificity are highlighted, in accordance with protein three-dimensional model and location of the phylogenetic specific conserved motifs. The differential expression of some representative genes were confirmed by quantitative real-time PCR. The phylogenetic analysis, together with protein motif architectures, and the expression profiling were analysed to predict the possible biological functions of the rice OsGELP genes.ConclusionsOur current genomic analysis, for the first time, presents fundamental information on the organization of the rice OsGELP gene family. With combination of the genomic, phylogenetic, microarray expression, protein motif distribution, and protein structure analyses, we were able to create supported basis for the functional prediction of many members in the rice GDSL esterase/lipase family. The present study provides a platform for the selection of candidate genes for further detailed functional study.

Detecting adaptive evolution and functional divergence in aminocyclopropane-1-carboxylate synthase (ACS) gene family

Ethylene is an essential plant gaseous hormone that controls many aspects of plant growth and development, especially the fruit ripening. It is important to know how this hormone is synthesized and how its production is regulated to understand the roles of ethylene in plant development. The aminocyclopropane-1-carboxylate synthase (ACS) gene is a rate-limiting enzyme in the ethylene biosynthesis pathway, which is encoded by a highly divergent multi-gene family in plant species. Although many ACS genes have been cloned from a wide variety of plant species previously, their origin and evolutionary process are still not clear. In this study, we conducted a phylogenetic analysis based on an updated dataset including 107 members of plant ACS genes and eight ACS-like genes from animal as well as six AATase genes. The motifs were identified and the positive selection and functional divergence in the ACS gene family were detected. The results obtained from these analyses are consistent with previous division of the ACS gene family in angiosperm, i.e., three distinct clades, and show that the duplications of three subclades (I, II and III) ACS genes have occurred after the divergence of gymnosperm and angiosperm. We conclude that the ACS genes could have experienced three times significant positive selection as they underwent expansion in land plants and gain the full-scale ethylene biosynthesis and regulatory functions, and all plant ACS genes originated from plant-ACS-like genes which come from AATase genes.