Muhammad Aaqil Khan

Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species.

Nicotiana otophora is a wild parental species of Nicotiana tabacum, an interspecific hybrid of Nicotiana tomentosiformis and Nicotiana sylvestris. However, N. otophora is least understood as an alternative paternal donor. Here, we compared the fully assembled chloroplast (cp) genome of N. otophora and with those of closely related species. The analysis showed a cp genome size of 156,073 bp and exhibited a typical quadripartite structure, which contains a pair of inverted repeats separated by small and large single copies, containing 163 representative genes, with 165 microsatellites distributed unevenly throughout the genome. Comparative analysis of a gene with known function across Nicotiana species revealed 76 protein-coding sequences, 20 tRNA sequences, and 3 rRNA sequence shared between the cp genomes. The analysis revealed that N. otophora is a sister species to N. tomentosiformis within the Nicotiana genus, and Atropha belladonna and Datura stramonium are their closest relatives. These findings provide a valuable analysis of the complete N. otophora cp genome, which can identify species, elucidate taxonomy, and reconstruct the phylogeny of genus Nicotiana.

Bacterial endophytes from arid land plants regulate endogenous hormone content and promote growth in crop plants: an example of Sphingomonas sp. and Serratia marcescens

ABSTRACT The objective of the present study was to determine the potential plant growth-promoting action of bacterial endophytes isolated from arid land-dwelling plants under normal conditions. Overall, five bacterial endophytes LK11 (Sphingomonas sp. LK11), TP5 (Bacillus subtilis), MPB5.3 (B. subtilis subsp. Subtilis), S9 (B. subtilis subsp. Subtilis), and TP1 (Serratia marcescens) were evaluated based on morphological characteristics after isolation and purification. Phytohormonal analysis of these endophytes predicted indole acetic acid (IAA) production 12.31 ± 0.45 , 6.8 ± 0.59, and 10.5 ± 1.02 μM/mL in the culture broths of LK11, MPB5.3, and TP1, respectively. Under controlled greenhouse conditions, these endophytes were inoculated into soybean, and their growth-promoting characteristics were compared with those of non-phytohormone-producing endophytes. In terms of plant growth promotion, among IAA-producing endophytes, LK11 and TP1 greatly improved physiological characteristics such as shoot/root length, fresh/dry weight, and chlorophyll contents. However, the non-phytohormone-producing endophytes TP5 and S9 did not show a growth-promoting effect. Based on these results, plants inoculated with LK11 and TP1 along with a control were subjected to endogenous hormonal analysis and showed a significant increase in abscisic acid (457.30–398.55 vs. 205.93 ng/g D.W.) and a decrease in jasmonic acid content (50.07–85.07 vs. 93.90 ng/g D.W.), respectively. Total gibberellin content was found to significantly increase in endophyte-inoculated plants (155.43–146.94 ng/g D.W.) as compared to that in controls (113.76 ng/g D.W.). In summary, bacterial endophytes might be used to enhance crop plant physiological characteristics isolated from arid land-inhabiting plants under normal conditions.

The Complete Chloroplast Genome of Wild Rice (Oryza minuta) and Its Comparison to Related Species

Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the O. minuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata. Thus, the complete O. minuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny.

Mitochondrial Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species

Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. O. minuta has the potential to resist against various pathogenic diseases such as bacterial blight (BB), white backed planthopper (WBPH) and brown plant hopper (BPH). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. The mtDNA genome is 515,022 bp, containing 60 protein coding genes, 31 tRNA genes and two rRNA genes. The mitochondrial genome organization and the gene content at the nucleotide level are highly similar (89%) to that of O. rufipogon. Comparison with other related species revealed that most of the genes with known function are conserved among the Poaceae members. Similarly, O. minuta mt genome shared 24 protein-coding genes, 15 tRNA genes and 1 ribosomal RNA gene with other rice species (indica and japonica). The evolutionary relationship and phylogenetic analysis revealed that O. minuta is more closely related to O. rufipogon than to any other related species. Such studies are essential to understand the evolutionary divergence among species and analyze common gene pools to combat risks in the current scenario of a changing environment.

Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis

We investigated the complete chloroplast (cp) genomes of non-model Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea using Illumina paired-end sequencing to understand their genetic organization and structure. Detailed bioinformatics analysis revealed genome sizes of both subspecies ranging between 154.4~154.5 kbp, with a large single-copy region (84,197~84,158 bp), a small single-copy region (17,738~17,813 bp) and pair of inverted repeats (IRa/IRb; 26,264~26,259 bp). Both cp genomes encode 130 genes, including 85 protein-coding genes, eight ribosomal RNA genes and 37 transfer RNA genes. Whole cp genome comparison of A. halleri ssp. gemmifera and A. lyrata ssp. petraea, along with ten other Arabidopsis species, showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. The location and distribution of repeat sequences were determined, and sequence divergences of shared genes were calculated among related species. Comparative phylogenetic analysis of the entire genomic data set and 70 shared genes between both cp genomes confirmed the previous phylogeny and generated phylogenetic trees with the same topologies. The sister species of A. halleri ssp. gemmifera is A. umezawana, whereas the closest relative of A. lyrata spp. petraea is A. arenicola.

Comparative analysis of complete plastid genomes from wild soybean (Glycine soja) and nine other Glycine species

The plastid genomes of different plant species exhibit significant variation, thereby providing valuable markers for exploring evolutionary relationships and population genetics. Glycine soja (wild soybean) is recognized as the wild ancestor of cultivated soybean (G. max), representing a valuable genetic resource for soybean breeding programmes. In the present study, the complete plastid genome of G. soja was sequenced using Illumina paired-end sequencing and then compared it for the first time with previously reported plastid genome sequences from nine other Glycine species. The G. soja plastid genome was 152,224 bp in length and possessed a typical quadripartite structure, consisting of a pair of inverted repeats (IRa/IRb; 25,574 bp) separated by small (178,963 bp) and large (83,181 bp) single-copy regions, with a 51-kb inversion in the large single-copy region. The genome encoded 134 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 39 transfer RNA genes, and possessed 204 randomly distributed microsatellites, including 15 forward, 25 tandem, and 34 palindromic repeats. Whole-plastid genome comparisons revealed an overall high degree of sequence similarity between G. max and G. gracilis and some divergence in the intergenic spacers of other species. Greater numbers of indels and SNP substitutions were observed compared with G. cyrtoloba. The sequence of the accD gene from G. soja was highly divergent from those of the other species except for G. max and G. gracilis. Phylogenomic analyses of the complete plastid genomes and 76 shared genes yielded an identical topology and indicated that G. soja is closely related to G. max and G. gracilis. The complete G. soja genome sequenced in the present study is a valuable resource for investigating the population and evolutionary genetics of Glycine species and can be used to identify related species.

Isolation and characterization of a novel silicate-solubilizing bacterial strain Burkholderia eburnea CS4-2 that promotes growth of japonica rice (Oryza sativa L. cv. Dongjin)

ABSTRACT The current study aimed to isolate and identify japonica rice (Oryza sativa L. cv. Dongjin) root-associated rhizobacteria and to investigate their ability to solubilize silicate, produce indole acetic acid (IAA), promote plant growth, and encourage silicon (Si) uptake and deposit in plants. A single bacterial isolate was selected on the basis of its silica-solubilizing ability and IAA production. The 16S rRNA gene sequence of the isolate identified it as Burkholderia eburnea CS4-2. Burkholderia eburnea CS4-2 produced high amounts of IAA at pH 8. When combined with silica fertilization, soil inoculation with CS4-2 promoted all growth attributes over those of the water-treated (control) and insoluble silica-fertilized plants. Microscopic observations also demonstrated a significant difference in the Si deposits on the leaf epidermis of rice plants under different treatments, indicating that more Si was deposited in plants fertilized with both B. eburnea CS4-2 and insoluble silica than in either insoluble silica-fertilized or water-treated plants. Inductively coupled plasma spectrometry analysis confirmed the same trend of Si concentration in whole-plant biomass of the rice that received the same treatments, respectively. Therefore, we conclude that B. eburnea CS4-2 has the ability to produce IAA under high-pH conditions, solubilize silicate, and promote plant growth. Graphical Abstract

Additive effects due to biochar and endophyte application enable soybean to enhance nutrient uptake and modulate nutritional parameters

We studied the effects of hardwood-derived biochar (BC) and the phytohormone-producing endophyte Galactomyces geotrichum WLL1 in soybean (Glycine max (L.) Merr.) with respect to basic, macro- and micronutrient uptakes and assimilations, and their subsequent effects on the regulation of functional amino acids, isoflavones, fatty acid composition, total sugar contents, total phenolic contents, and 1,1-diphenyl-2-picrylhydrazyl (DPPH)-scavenging activity. The assimilation of basic nutrients such as nitrogen was up-regulated, leaving carbon, oxygen, and hydrogen unaffected in BC+G. geotrichum-treated soybean plants. In comparison, the uptakes of macro- and micronutrients fluctuated in the individual or co-application of BC and G. geotrichum in soybean plant organs and rhizospheric substrate. Moreover, the same attribute was recorded for the regulation of functional amino acids, isoflavones, fatty acid composition, total sugar contents, total phenolic contents, and DPPH-scavenging activity. Collectively, these results showed that BC+G. geotrichum-treated soybean yielded better results than did the plants treated with individual applications. It was concluded that BC is an additional nutriment source and that the G. geotrichum acts as a plant biostimulating source and the effects of both are additive towards plant growth promotion. Strategies involving the incorporation of BC and endophytic symbiosis may help achieve eco-friendly agricultural production, thus reducing the excessive use of chemical agents.摘要目的探讨提高大豆作物品质的方法。创新点研究了生物炭和植物内生菌联合使用对大豆营养 吸收和营养品质的叠加作用。方法采用硬木生物炭和半乳糖霉菌(Galactomyces geotrichum WLL1)对大豆进行处理,按照处理 方式的不同分成四组,包括对照组(无处理)、 G. geotrichum 处理组、生物炭处理组和生物炭与 G. geotrichum 联合处理组。通过对比研究生物炭和内生菌对大豆宏量营养素和微量营养素的吸 收和同化的作用,并观察其对功能性氨基酸、异 黄酮、脂肪酸组成、总糖含量、总酚含量和1,1- 二苯基苦基苯肼(DPPH)自由基清除能力的影 响。结论研究结果发现生物炭和内生菌单独或联合处理均 能增加大豆养分的吸收,促进功能性氨基酸的合 成,并提升大豆营养品质。同时,生物炭是一种 额外的营养源,而内生菌能产生生物刺激效应, 两者联合使用具有叠加作用,比单独使用更加有 效。

Osmoprotective functions conferred to soybean plants via inoculation with Sphingomonas sp. LK11 and exogenous trehalose

Osmotic stress induced by drought can hinder the growth and yield of crop plants. To understand the eco-physiological role of osmoprotectants, the combined utilization of endophytes and osmolytes (trehalose) can be an ideal strategy used to overcome the adverse effects of drought. Hence, in the present study, we aimed to investigate the role of Sphingomonas sp. LK11, which produces phytohormones and synthesizes trehalose, in improving soybean plant growth under drought-induced osmotic stress (-0.4, -0.9, and -1.2MPa). The results showed that the inoculation of soybean plants with Sphingomonas sp. LK11 significantly increased plant length, dry biomass, photosynthetic pigments, glutathione, amino acids (proline, glycine, and glutamate), and primary sugars as compared to control plants under varying drought stresses. Trehalose applied to the plant with or without endophyte-inoculation also showed similar plant growth-promoting attributes under stress. Stress exposure significantly enhanced endogenous jasmonic (JA) and abscisic (ABA) acid contents in control plants. In contrast, Sphingomonas sp. LK11-inoculation significantly lowered ABA and JA levels in soybean plants, but these phytohormones increased in response to combined treatments during stress. The drought-induced osmotic stress resistance associated with Sphingomonas sp. LK11 and trehalose was also evidenced by increased mRNA gene expression of soybean dehydration responsive element binding protein (DREB)-type transcription factors (GmDREBa and GmDREB2) and the MYB (myeloblastosis) transcription factor (GmMYBJ1) as compared to the control. In conclusion, our findings demonstrated that inoculation with this endophyte and trehalose improved the negative effects of drought-induced osmotic stress, and it enhanced soybean plant growth and tolerance.

Salt tolerance of Glycine max.L induced by endophytic fungus Aspergillus flavus CSH1, via regulating its endogenous hormones and antioxidative system

Abiotic stress resistance strategies are powerful approaches to sustainable agriculture because they reduce chemical input and enhance plant productivity. In current study, an endophytic fungus, Aspergillus flavus CHS1 was isolated from Chenopodium album Roots. CHS1 was initially screened for growth promoting activities like siderphore, phosphate solubilization, and the production of indole acetic acid and gibberellins and were further assayed for its ability to promote the growth of mutant Waito-C rice. The results revealed that different plant growth characteristic such as chlorophyll content, root-shoot length, and biomass production were significantly promoted during CHS1 treatment. This growth promotion action was due to the presence of various types of GAs and IAA in the endophyte culture filtrate. Significant up regulation with respect to levels in the control was observed in all endogenous plant GAs, after treatment with CHS1. Furthermore, to evaluate the potential of CHS1 against NaCl stress up to 400 mM, it was tested for its ability to improve soybean plant growth under NaCl stress. In endophyte-soybean interaction, CHS1 association significantly increased plant growth and attenuated the NaCl stress by down regulating ABA and JA synthesis. Similarly, it significantly elevated antioxidant activities of enzymes catalase, polyphenoloxidase, superoxide dismutase and peroxidase as compared to non-inoculated salt stress plants. Thus, CHS1 ameliorated the adverse effect of high NaCl stress and rescued soybean plant growth by regulating the endogenous plant hormones and antioxidative system. We conclude that CHS1 isolate could be exploited to increase salt resistant and yield in crop plants.