scholarly journals In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack LEC2, one of the key regulators of initiation of the process

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sonali Sachin Ranade ◽  
Ulrika Egertsdotter
Keyword(s):  
Arabidopsis Thaliana ◽  
Somatic Embryogenesis ◽  
Picea Abies ◽  
Pinus Taeda ◽  
In Silico ◽  
Somatic Embryos ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Conifer Species ◽  
Putative Gene

Abstract Background Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation. Results Current work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g. BBM, LEC1, LEC1-LIKE, LEC2 and FUSCA3, based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes from Arabidopsis thaliana were used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genus Picea (Picea abies) and Pinus (Pinus taeda), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences of Arabidopsis thaliana proteins and phylogenetic analysis (Phylogeny.fr). Conclusions This in silico analysis suggests absence of LEC2 in Picea abies and Pinus taeda, the conifer species whose genomes have been sequenced. Based on available sequence data to date, LEC2 was also not detected in the other conifer species included in the study. LEC2 is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. Potential alternative mechanisms that might be functional in conifers to compensate the lack of LEC2 are discussed.

scholarly journals Identifikasi famili gen putatif penyandi protease inhibitor dengan pendekatan in silico komparatif pada genom Hevea brasiliensis Muell. Arg (Identification of putative gene family encoding protease inhibitors by in silico comparative analysis in Hevea brasiliensis Muell. Arg genome)

2017 ◽  
Vol 85 (2) ◽  
Author(s):  
Irfan MARTIANSYAH ◽  
Riza Arief PUTRANTO ◽  
Nurul KHUMAIDA
Keyword(s):  
Arabidopsis Thaliana ◽  
Protease Inhibitor ◽  
Hevea Brasiliensis ◽  
In Silico ◽  
Functional Characterization ◽  
Rubber Tree ◽  
Whole Genome Sequence ◽  
Putative Gene ◽  
Small Proteins ◽  
Genome Wide

AbstractProtease inhibitors (PIs) are small proteins that form complexes with proteases and inhibits their proteolytic activity. Its potential application as an antimicrobial agent has been studied. Most of PIs' molecule size is around 8-22 kDa depending on their protein families.To date, on the basis of sequence homologies of inhibitor domains, PIs have been classified into 48 families in all organisms. In plant, more than 13 families of PIs have been identified but they were not widely identified in the rubber tree (Hevea brasiliensis Muell.Arg). In the present study, 40 putative HbPI genes, designated as HbPI01 to HbPI36, were identified from whole-genome sequence of rubber tree clone Reyan 7-33-97 using 7453 scaffolds available online in NCBI with the accession code: LVXX01000000. Multiple sequence alignment using MUSCLE algorithm discovered seven conserved motifs (Motifs I-VII) among HbPIs. Phylogenetic analysis of 50 and 36 PI amino acid residues of 32 scaffolds containing putative PI genes from Arabidopsis thaliana and H. brasiliensis showed three clusters (families): LTP-I, SERPIN and LTP-II. LTP-I has 23 putative HbPI genes (HbPI05 to HbPI27) and 12 AtPI genes. SERPIN, a family member of serine protease inhibitor group, has 11 putative HbPI genes (HbPI01 to HbPI04 and HbPI28 to HbPI34) and 22 AtPI genes. LTP-II has 2 putative HbPI genes (HbPI35 to HbPI36) and 16 AtPI genes. In conclusion, this work provides valuable information for further functional characterization of HbPI genes in H. brasiliensis.[Key words: protease inhibitor, genome-wide, scaffold, in silico, Hevea brasiliensis]. AbstrakProtease inhibitor (PI) merupakan protein yang membentuk kompleks dengan protease dan menghambat aktivitas proteolitik dari enzim tersebut. Potensi penggunaan protease inhibitor sebagai agensia antimikroba telah diketahui. Kebanyakan PI memiliki ukuran molekul sekitar 8-22 kDa bergantung pada familinya. Saat ini, PI dapat diklasifikasikan menjadi 48 famili di seluruh organisme berdasarkan kemiripan sekuen dari domain inhibitornya. Pada tanaman, lebih dari 13 famili PI telah diketahui tetapi pada tanaman karet (Hevea brasiliensis Muell.Arg) belum diidentifikasi. Pada penelitian ini, sebanyak 40 gen putatif penyandi PI (HbPI01 hingga HbPI36) telah berhasil diidentifikasi dari 7453 scaffold genom utuh tanaman karet klon Reyan 7-33-97 yang tersedia secara daring dengan kode aksesi LVXX01000000. Penjajaran sekuen menggunakan algoritma MUSCLE memper-lihatkan tujuh konservasi motif (Motif I-VIII) pada famili gen putatif HbPIs. Analisis pohon filogenetik dari tanaman Arabidopsis thaliana dan H. brasiliensis sebanyak 50 dan 36 sekuen residu asam amino dari 32 scaffold yang mengandung gen putatif PI menunjukkan adanya tiga klaster besar, yaitu famili LTP-I, SERPIN dan LTP-II. LTP-I terdiri dari 23 gen putatif HbPI (HbPI05 hingga HbPI27) dan 12 gen AtPI. SERPIN yang merupakan anggota kelas protease inhibitor serin terdiri dari 11 gen putatif HbPI (HbPI01hingga HbPI04 dan HbPI28 hingga HbPI34) dan 22 gen AtPI. LTP-II terdiri dari 2 gen putatif HbPI (HbPI35 hingga HbPI36) dan 16 gen AtPIs. Penelitian ini menghasilkan informasi penting untuk melakukan karakterisasi fungsional lebih mendalam pada gen HbPI tanaman karet ke depannya.[Kata kunci: protease inhibitor, genome-wide,scaffold, in silico, Hevea brasiliensis].

scholarly journals Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

2021 ◽  
Author(s):  
Viola Kurm ◽  
Ilse Houwers ◽  
Claudia E. Coipan ◽  
Peter Bonants ◽  
Cees Waalwijk ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
In Silico ◽  
Species Complex ◽  
Sequence Data ◽  
In Silico Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

scholarly journals Genotype and transcriptome effects on somatic embryogenesis in Cryptomeria japonica

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244634
Author(s):  
Ayako Izuno ◽  
Tsuyoshi E. Maruyama ◽  
Saneyoshi Ueno ◽  
Tokuko Ujino-Ihara ◽  
Yoshinari Moriguchi
Keyword(s):  
Gene Expression ◽  
Somatic Embryogenesis ◽  
Tree Species ◽  
Somatic Embryos ◽  
Cryptomeria Japonica ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Normal Embryo ◽  
Conifer Species ◽  
Embryogenic Potential

Somatic embryogenesis (SE), which is in vitro regeneration of plant bodies from somatic cells, represents a useful means of clonal propagation and genetic engineering of forest trees. While protocols to obtain calluses and induce regeneration in somatic embryos have been reported for many tree species, the knowledge of molecular mechanisms of SE development is still insufficient to achieve an efficient supply of somatic embryos required for the industrial application. Cryptomeria japonica, a conifer species widely used for plantation forestry in Japan, is one of the tree species waiting for a secure SE protocol; the probability of normal embryo development appears to depend on genotype. To discriminate the embryogenic potential of embryonal masses (EMs) and efficiently obtain normal somatic embryos of C. japonica, we investigated the effects of genotype and transcriptome on the variation in embryogenic potential. Using an induction experiment with 12 EMs each from six genotypes, we showed that embryogenic potential differs between/within genotypes. Comparisons of gene expression profiles among EMs with different embryogenic potentials revealed that 742 differently expressed genes were mainly associated with pattern forming and metabolism. Thus, we suggest that not only genotype but also gene expression profiles can determine success in SE development. Consistent with previous findings for other conifer species, genes encoding leafy cotyledon, wuschel, germin-like proteins, and glutathione-S-transferases are likely to be involved in SE development in C. japonica and indeed highly expressed in EMs with high-embryogenic potential; therefore, these proteins represent candidate markers for distinguishing embryogenic potential.

scholarly journals Mycobacterium tuberculosis whole genome sequence data support repurposing antileprosy antibiotic as antituberculosis

2020 ◽  
Author(s):  
Jamal SAAD ◽  
Jenny GALLOU ◽  
Nathalie BERIRU ◽  
Michel DRANCOURT ◽  
Sophie BARON
Keyword(s):  
Pulmonary Tuberculosis ◽  
In Silico ◽  
Antibiotic Susceptibility ◽  
Sequence Data ◽  
Multidrug Resistant ◽  
Whole Genome Sequence ◽  
Drug Resistant ◽  
Routine Method ◽  
Extensively Drug Resistant ◽  
Sequence Variations

Background We implanted WGS as the routine method to profile the antibiotic susceptibility of M. tuberculosis isolates focusing on in silico resistance to antileprosy drugs that we recently proposed to reposition for the treatment of pulmonary tuberculosis. Methods We prospectively performed WGS of 112 M. tuberculosis isolates recovered from respiratory tract samples of 106 patients diagnosed with pulmonary tuberculosis between 2017 and 2019 and defined their antibiotic susceptibility profile to 17 antibiotics including antileprotics drugs. Results We incidentally observed 08 sequence variations in 07 genes, specific to seven sublineages. Altogether, we observed 09 (8%) rifampicin-resistant, 05 (4.4%) multidrug-resistant and 02 (1.7%) extensively-drug resistant isolates; whereas only one isolate exhibited in silico resistance to clofazimine. Conclusion These results support repurposing of antileprosis antibiotics as antituberculosis; and offer new targets for genotyping M. tuberculosis.

Somatic embryogenesis in conifers—A case study of induction and development of somatic embryos in Picea abies

1996 ◽  
Vol 20 (1) ◽  
pp. 3-9 ◽  
Author(s):  
S. von Arnold ◽  
D. Clapham ◽  
U. Egertsdotter ◽  
L. H. Mo
Keyword(s):  
Somatic Embryogenesis ◽  
Picea Abies ◽  
Somatic Embryos

scholarly journals Somaclonal Variation During Picea abies and P. omorika Somatic Embryogenesis and Cryopreservation

2017 ◽  
Vol 59 (1) ◽  
pp. 93-103 ◽  
Author(s):  
Teresa Hazubska-Przybył ◽  
Monika Dering
Keyword(s):  
Somatic Embryogenesis ◽  
Picea Abies ◽  
Somaclonal Variation ◽  
Genetic Stability ◽  
Somatic Embryos ◽  
Plant Material ◽  
Stress Factors ◽  
Embryogenic Cultures ◽  
Embryogenic Lines

AbstractEmbryogenic cultures of plants are exposed to various stress factors bothin vitroand during cryostorage. In order to safely include the plant material obtained by somatic embryogenesis in combination with cryopreservation for breeding programs, it is necessary to monitor its genetic stability. The aim of the present study was the assessment of somaclonal variation in plant material obtained from embryogenic cultures ofPicea abies(L.) Karst. andP. omorika(Pančić) Purk. maintainedin vitroor stored in liquid nitrogen by the pregrowth-dehydration method. The analysis of genetic conformity with using microsatellite markers was performed on cotyledonary somatic embryos (CSE), germinating somatic embryos (GSE) and somatic seedlings (SS), obtained from tissues maintainedin vitroor from recovered embryogenic tissues (ETc) and CSE obtained after cryopreservation. The analysis revealed changes in the DNA of somatic embryogenesis-derived plant material of bothPiceaspp. They were found in plant material from 8 out of 10 tested embryogenic lines ofP. abiesand in 10 out of 19 embryogenic lines ofP. omorikaafterin vitroculture. Changes were also detected in plant material obtained after cryopreservation. Somaclonal variation was observed in ETc and CSE ofP. omorikaand at ETv stage ofP. abies. However, most of the changes were induced at the stage of somatic embryogenesis initiation. These results confirm the need for monitoring the genetic stability of plants obtained by somatic embryogenesis and after cryopreservation for both spruce species.

scholarly journals Fungal Genomic Resources for Strain Identification and Diversity Analysis of 1900 Fungal Species

2021 ◽  
Vol 7 (4) ◽  
pp. 288
Author(s):  
Mir Asif Iquebal ◽  
Sarika Jaiswal ◽  
Vineet Kumar Mishra ◽  
Rahul Singh Jasrotia ◽  
Ulavappa B. Angadi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
In Silico ◽  
Sequence Data ◽  
Fungal Species ◽  
Genomic Research ◽  
Whole Genome Sequence ◽  
Strain Identification ◽  
Diversity Analysis ◽  
Whole Genome

Identification and diversity analysis of fungi is greatly challenging. Though internal transcribed spacer (ITS), region-based DNA fingerprinting works as a “gold standard” for most of the fungal species group, it cannot differentiate between all the groups and cryptic species. Therefore, it is of paramount importance to find an alternative approach for strain differentiation. Availability of whole genome sequence data of nearly 2000 fungal species are a promising solution to such requirement. We present whole genome sequence-based world’s largest microsatellite database, FungSatDB having >19M loci obtained from >1900 fungal species/strains using >4000 assemblies across globe. Genotyping efficacy of FungSatDB has been evaluated by both in-silico and in-vitro PCR. By in silico PCR, 66 strains of 8 countries representing four continents were successfully differentiated. Genotyping efficacy was also evaluated by in vitro PCR in four fungal species. This approach overcomes limitation of ITS in species, strain signature, and diversity analysis. It can accelerate fungal genomic research endeavors in agriculture, industrial, and environmental management.

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