Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume

Abstract Background Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. Though PEBP family genes have been well studied in Arabidopsis and other model species, less is known about these genes in perennial trees. Results To understand the evolution of PEBP genes and their functional roles in flowering control, we identified 56 PEBP members belonging to three gene clades (MFT-like, FT-like, and TFL1-like) and five lineages (FT, BFT, CEN, TFL1, and MFT) across nine Rosaceae perennial species. Structural analysis revealed highly conserved gene structure and protein motifs among Rosaceae PEBP proteins. Codon usage analysis showed slightly biased codon usage across five gene lineages. With selection pressure analysis, we detected strong purifying selection constraining divergence within most lineages, while positive selection driving the divergence of FT-like and TFL1-like genes from the MFT-like gene clade. Spatial and temporal expression analyses revealed the essential role of FT in regulating floral bud breaking and blooming in P. mume. By employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module required for dormancy release and blooming in P. mume. Conclusions We have characterized the PEBP family genes in nine Rosaceae species and examined their phylogeny, genomic syntenic relationship, duplication pattern, and expression profiles during flowering process. These results revealed the evolutionary history of PEBP genes and their functions in regulating floral bud development and blooming among Rosaceae tree species.

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Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

10.21203/rs.2.10527/v3 ◽

2019 ◽

Author(s):

Licao Cui ◽

Guang Yang ◽

Jali Yan ◽

Yan Pan ◽

Xiaojun Nie

Keyword(s):

Regulatory Network ◽

Expression Profiles ◽

Purifying Selection ◽

Mapk Cascade ◽

Mitogen Activated Protein Kinase ◽

Functional Study ◽

Systematic Analysis ◽

Protein Motifs ◽

Genome Wide ◽

A Genome

Abstract Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been conducted in barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs in barley through a genome-wide search against the updated reference genome. Then, phylogenetic relationship, gene structure and conserved protein motifs organization of them were systematically analyzed and results supported the predictions. Gene duplication analysis revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of them were further investigated in different organs and under diverse abiotic stresses using the available 173 RNA-seq datasets, and then the tissue-specific and stress-responsive candidates were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs. Conclusion This study provides the targets for further functional study and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

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Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus

BMC Genomics ◽

10.1186/s12864-021-08106-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Panpan Wang ◽

Yong Mao ◽

Yongquan Su ◽

Jun Wang

Keyword(s):

Gene Expression ◽

Codon Usage ◽

Codon Bias ◽

Purifying Selection ◽

Marsupenaeus Japonicus ◽

Bias Analysis ◽

Codon Preference ◽

Optimal Codons ◽

Usage Patterns ◽

Usage Analysis

Abstract Background Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. Results Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω < 1). Parity Rule 2 (PR2) and effective number of codons (ENc) plot analysis showed that the codon usage patterns of both species were influenced by both mutations and selection. Moreover, the average observed ENc value was lower than the expected value for both species, suggesting that factors other than GC may play roles in these phenomena. The results of multispecies clustering based on codon preference were consistent with traditional classification. Conclusions This study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species.

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Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

BMC Genomics ◽

10.1186/s12864-019-6144-9 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 5

Author(s):

Licao Cui ◽

Guang Yang ◽

Jiali Yan ◽

Yan Pan ◽

Xiaojun Nie

Keyword(s):

Regulatory Network ◽

Expression Profiles ◽

Purifying Selection ◽

Mapk Cascade ◽

Mitogen Activated Protein Kinase ◽

Functional Study ◽

Systematic Analysis ◽

Protein Motifs ◽

Genome Wide ◽

A Genome

Abstract Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been conducted in barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs in barley through a genome-wide search against the updated reference genome. Then, phylogenetic relationship, gene structure and conserved protein motifs organization of them were systematically analyzed and results supported the predictions. Gene duplication analysis revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of them were further investigated in different organs and under diverse abiotic stresses using the available 173 RNA-seq datasets, and then the tissue-specific and stress-responsive candidates were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs. Conclusion This study provides the targets for further functional study and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

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Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

10.21203/rs.2.10527/v2 ◽

2019 ◽

Author(s):

Licao Cui ◽

Guang Yang ◽

Jali Yan ◽

Yan Pan ◽

Xiaojun Nie

Keyword(s):

Regulatory Network ◽

Expression Profiles ◽

Purifying Selection ◽

Mapk Cascade ◽

Mitogen Activated Protein Kinase ◽

Functional Study ◽

Systematic Analysis ◽

Protein Motifs ◽

Genome Wide ◽

A Genome

Abstract Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been conducted in barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs in barley through a genome-wide search against the updated reference genome. Then, phylogenetic relationship, gene structure and conserved protein motifs organization of them were systematically analyzed and results supported the predictions. Gene duplication analysis revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of them were further investigated in different organs and under diverse abiotic stresses using the available 173 RNA-seq datasets, and then the tissue-specific and stress-responsive candidates were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs. Conclusion This study provides the targets for further functional study and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

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Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity

International Journal of Molecular Sciences ◽

10.3390/ijms22126556 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6556

Author(s):

Junjun Huang ◽

Xiaoyu Li ◽

Xin Chen ◽

Yaru Guo ◽

Weihong Liang ◽

...

Keyword(s):

Gene Expression ◽

Abc Transporters ◽

Developmental Stages ◽

Aluminum Toxicity ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Purifying Selection ◽

Biotic Stresses ◽

Genome Wide ◽

New Germplasm

ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.

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CONCUR: quick and robust calculation of codon usage from ribosome profiling data

Bioinformatics ◽

10.1093/bioinformatics/btaa733 ◽

2020 ◽

Author(s):

Michaela Frye ◽

Susanne Bornelöv

Keyword(s):

Codon Usage ◽

Ribosome Profiling ◽

Supplementary Information ◽

Supplementary Data ◽

Usage Analysis

Abstract Summary CONCUR is a standalone tool for codon usage analysis in ribosome profiling experiments. CONCUR uses the aligned reads in BAM format to estimate codon counts at the ribosome E-, P- and A-sites and at flanking positions. Availability and implementation CONCUR is written in Perl and is freely available at https://github.com/susbo/concur. Supplementary information Supplementary data are available at Bioinformatics online.

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Genotype and transcriptome effects on somatic embryogenesis in Cryptomeria japonica

PLoS ONE ◽

10.1371/journal.pone.0244634 ◽

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.

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Host Adaptation of Codon Usage in SARS-CoV-2 From Mammals Indicate Natural Selection

10.21203/rs.3.rs-1125942/v1 ◽

2021 ◽

Author(s):

Yanan Fu ◽

Yanping Huang ◽

Jingjing Rao ◽

Feng Zeng ◽

Ruiping Yang ◽

...

Keyword(s):

Natural Selection ◽

Codon Usage ◽

Binding Affinity ◽

Codon Bias ◽

Synonymous Codon ◽

Host Adaptation ◽

Synonymous Codon Usage ◽

Mutation Pressure ◽

Usage Analysis ◽

Human Receptor

Abstract The outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, spread across hosts from humans to animals, transmitting particularly effectively in mink. How SARS-CoV-2 selects and evolves in the host, and the differences in the evolution of different animals are still unclear. To analysis the mutation and codon usage bias of SARS-CoV-2 in infected humans and animals. The SARS-CoV-2 sequence in mink (Mink-SARS2) and binding energy with receptor were calculated compared with human. The relative synonymous codon usage of viral encoded gene was analyzed to characterize the differences and the evolutionary characteristics. A synonymous codon usage analysis showed that SARS-CoV-2 is optimized to adapt in the animals in which it is currently reported, and all of the animals showed decreased adaptability relative to that of humans, except for mink. The neutrality plot showed that the effect of natural selection on different SARS-CoV-2 sequences is stronger than mutation pressure. A binding affinity analysis indicated that the spike protein of the SARS-CoV-2 variant in mink showed a greater preference for binding with the mink receptor ACE2 than with the human receptor, especially as the mutation Y453F and N501T in Mink-SARS2 lead to improvement of binding affinity for mink receptor. In summary, mutations Y453F and N501T in Mink-SARS2 lead to improvement of binding affinity with mink receptor, indicating possible natural selection and current host adaptation. Monitoring the variation and codon bias of SARS-CoV-2 provides a theoretical basis for tracing the epidemic, evolution and cross-species spread of SARS-CoV-2.

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Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control

Nature Communications ◽

10.1038/s41467-019-12987-9 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Fredrik Barrenas ◽

Kevin Raehtz ◽

Cuiling Xu ◽

Lynn Law ◽

Richard R. Green ◽

...

Keyword(s):

Wound Healing ◽

Expression Profiles ◽

Healing Process ◽

Gene Expression Profiles ◽

Gene Signature ◽

African Green Monkey ◽

Wound Healing Process ◽

Sequencing Data ◽

Green Monkey ◽

Conserved Gene

Abstract Natural hosts of simian immunodeficiency virus (SIV) avoid AIDS despite lifelong infection. Here, we examined how this outcome is achieved by comparing a natural SIV host, African green monkey (AGM) to an AIDS susceptible species, rhesus macaque (RM). To asses gene expression profiles from acutely SIV infected AGMs and RMs, we developed a systems biology approach termed Conserved Gene Signature Analysis (CGSA), which compared RNA sequencing data from rectal AGM and RM tissues to various other species. We found that AGMs rapidly activate, and then maintain, evolutionarily conserved regenerative wound healing mechanisms in mucosal tissue. The wound healing protein fibronectin shows distinct tissue distribution and abundance kinetics in AGMs. Furthermore, AGM monocytes exhibit an embryonic development and repair/regeneration signature featuring TGF-β and concomitant reduced expression of inflammatory genes compared to RMs. This regenerative wound healing process likely preserves mucosal integrity and prevents inflammatory insults that underlie immune exhaustion in RMs.

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