scholarly journals Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

2020 ◽  
Author(s):  
Zheng Liu ◽  
Xiao-Xia Ge ◽  
Xiao-Meng Wu ◽  
Qiang Xu ◽  
Ross G. Atkinson ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Sweet Orange ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionary Features ◽  
Duplication Events

Abstract Background: In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few B3 transcription factors are reported to regulate embryogenesis, little is known about the B3 superfamily in citrus, and which members might be involved in SE.Results: Genome-wide sequence analysis identified 72 (CsB3) and 69 (CgB3) putative B3 superfamily members in the genomes of sweet orange (Citrus sinensis, polyembryonic) and pummelo (C. grandis, monoembryonic), respectively. Genome duplication analysis indicated that segmental and tandem duplication events contributed to the expansion of the B3 superfamily in citrus, and that the B3 superfamily evolved under the effect of purifying selection. Phylogenetic relationships were well supported by conserved gene structure and motifs outside the B3 domain, which allowed possible functions to be inferred by comparison with homologous genes from Arabidopsis. Expression analysis identified 23 B3 superfamily members that were expressed during SE in citrus and 17 that may play functional roles at late SE stages. Eight B3 genes were identified that were specific to the genome of polyembryonic sweet orange compared to monoembryonic pummelo. Of these eight B3 genes, CsARF19 was found to be specifically expressed at higher levels in embryogenic callus (EC), implying its possible involvement in EC initiation. Conclusions: This study provides a genome-wide analysis of the citrus B3 superfamily, including its genome organization, evolutionary features and expression profiles, and identifies specific family members that may be associated with SE.

scholarly journals Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

2019 ◽  
Author(s):  
Zheng Liu ◽  
Xiao-Xia Ge ◽  
Xiao-Meng Wu ◽  
Ross G. Atkinson ◽  
Wen-Wu Guo
Keyword(s):  
Somatic Embryogenesis ◽  
Sweet Orange ◽  
Expression Profiles ◽  
In Vitro Regeneration ◽  
Purifying Selection ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionary Features

Abstract Background In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few B3 transcription factors are reported to regulate embryogenesis, little is known about the B3 superfamily in citrus, and which members might be involved in SE.Results Genome-wide sequence analysis identified 72 ( CsB3 ) and 69 ( CgB3 ) putative B3 superfamily members in the genomes of sweet orange ( Citrus sinensis , polyembryonic) and pummelo ( C. grandis , monoembryonic), respectively. Genome duplication analysis indicated that segmental and tandem duplication events contributed to the expansion of the B3 superfamily in citrus, and that the B3 superfamily evolved under the effect of purifying selection. Phylogenetic relationships were well supported by conserved gene structure and motifs outside the B3 domain, which allowed possible functions to be inferred by comparison with homologous genes from Arabidopsis . Expression analysis identified 23 B3 superfamily members that were expressed during SE in citrus and 17 that may play functional roles at late SE stages. Eight B3 genes were identified that were specific to the genome of polyembryonic sweet orange compared to monoembryonic pummelo. Of these eight, CsARF19 was found to be specifically expressed at higher levels in embryogenic callus (EC), implying its possible involvement in EC initiation.Conclusions This study provides a genome-wide analysis of the citrus B3 superfamily, including its genome organization, evolutionary features and expression profiles, and identifies specific family members that may be associated with SE.

scholarly journals Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

2019 ◽  
Author(s):  
Zheng Liu ◽  
Xiao-Xia Ge ◽  
Xiao-Meng Wu ◽  
Wen-Wu Guo
Keyword(s):  
Somatic Embryogenesis ◽  
Sweet Orange ◽  
Expression Profiles ◽  
In Vitro Regeneration ◽  
Gene Families ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionary Features

Abstract Background In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few of B3 transcription factors are reported to regulate embryogenesis, little is known about the possible roles of B3 superfamily during SE especially in citrus. Results In this study, a total of 72 (CsB3) and 69 (CgB3) putative B3 superfamily members were identified in the sweet orange (Citrus sinensis) and pummelo (C. grandis) genomes, respectively, each comprised four gene families and 14 phylogenetic classes. The B3 genes were unevenly distributed over citrus chromosomes and other non-anchored scaffolds. Genome duplication analysis indicated that the segmental and tandem duplication events have significantly contributed to the expansion of the citrus B3 superfamily. The evolutionary relationships among the B3 family members and their putative functions were deduced based on the results of phylogenetic analysis. Furthermore, transcriptomic analysis showed that citrus B3 genes have differential expression levels in various tissues, suggesting distinct biological roles of different members. Expression analysis revealed that the B3 superfamily members showed four types of expression profiles during SE in citrus and may play functional roles during SE, especially at late SE stages. Of them, CsARF19 is specifically expressed in sweet orange and at markedly higher levels in the embryogenic callus (EC), implying its possible involvement in EC initiation. Conclusions This study provides a genome-wide analysis of citrus B3 superfamily, including its genome organization, evolutionary features and expression profiles, which contributes to a better understanding of the B3 genes in citrus and their association with SE.

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

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 ◽  
Systematic Analysis ◽  
Functional Studies ◽  
Genome Wide ◽  
A Genome ◽  
Duplication Events

Abstract Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organism. Although it has been well characterized in many plants, no systematic analysis has been conducted in the model cereal crop barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs through a genome-wide search method using the latest published barley genomic data. Phylogenetic analysis assigned all the MAPK cascade genes into three groups in accordance to MAPK, MAPKK and MAPKKK family. Gene duplication 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 the HvMAPK, HvMAPKK and HvMAPKKKs were then investigated in different organs and under diverse stresses using the available 132 RNA-seq datasets, and then the tissue-specific and stress-responsive ones 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 candidates for further functional studies and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

scholarly journals A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1072 ◽  
Author(s):  
Cailin Qiao ◽  
Jing Yang ◽  
Yuanyuan Wan ◽  
Sirou Xiang ◽  
Mingwei Guan ◽  
...  
Keyword(s):  
Differential Expression ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Purifying Selection ◽  
High Similarity ◽  
Genome Wide ◽  
A Genome ◽  
Duplication Events ◽  
Group 2 ◽  
Genome Wide Survey

The multidrug and toxic compound extrusion (MATE) protein family is important in the export of toxins and other substrates, but detailed information on this family in the Brassicaceae has not yet been reported compared to Arabidopsis thaliana. In this study, we identified 57, 124, 81, 85, 130, and 79 MATE genes in A. thaliana, Brassica napus, Brassica oleracea, Brassica rapa, Brassica juncea, and Brassica nigra, respectively, which were unevenly distributed on chromosomes owing to both tandem and segmental duplication events. Phylogenetic analysis showed that these genes could be classified into four subgroups, shared high similarity and conservation within each group, and have evolved mainly through purifying selection. Furthermore, numerous B. napusMATE genes showed differential expression between tissues and developmental stages and between plants treated with heavy metals or hormones and untreated control plants. This differential expression was especially pronounced for the Group 2 and 3 BnaMATE genes, indicating that they may play important roles in stress tolerance and hormone induction. Our results provide a valuable foundation for the functional dissection of the different BnaMATE homologs in B. napus and its parental lines, as well as for the breeding of more stress-tolerant B. napus genotypes.

scholarly journals Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.)

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Yuzhu Huo ◽  
Wangdan Xiong ◽  
Kunlong Su ◽  
Yu Li ◽  
Yawen Yang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Panicum Virgatum ◽  
Expression Profiles ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass (Panicum virgatum L.). In this study, 42 PvTCP genes (PvTCPs) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 (miR319) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains. Members in the same clade have the similar gene structure and motif localization. Although all PvTCPs were expressed in tested tissues, their expression profiles were different under normal condition. The specific expression may indicate their different roles in plant growth and development. In addition, approximately 20 cis-acting elements were detected in the promoters of PvTCPs, and 40% were related to stress response. Moreover, the expression profiles of PvTCPs under salt stress were also analyzed and 29 PvTCPs were regulated after NaCl treatment. Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.

scholarly journals Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 730 ◽  
Author(s):  
Sun ◽  
Wang ◽  
Ma ◽  
Li ◽  
Liu
Keyword(s):  
Somatic Embryogenesis ◽  
Upland Cotton ◽  
Expression Profiles ◽  
Gene Families ◽  
Early Response ◽  
Auxin Signaling ◽  
Evolutionary Divergence ◽  
Genome Wide ◽  
A Genome ◽  
Early Response Genes

Auxin is well known to regulate growth and development processes. Auxin early response genes serve as a critical component of auxin signaling and mediate auxin regulation of diverse physiological processes. In the present study, a genome-wide identification and comprehensive analysis of auxin early response genes were conducted in upland cotton. A total of 71 auxin response factor (ARF), 86 Auxin/Indole-3-Acetic Acid (Aux/IAA), 63 Gretchen Hagen3 (GH3), and 194 small auxin upregulated RNA (SAUR) genes were identified in upland cotton, respectively. Phylogenetic analysis revealed that the ARF, GH3, and SAUR families were likely subject to extensive evolutionary divergence between Arabidopsis and upland cotton, while the Aux/IAA family was evolutionary conserved. Expression profiles showed that the ARF, Aux/IAA, GH3, and SAUR family genes were extensively involved in embryogenic competence acquisition of upland cotton callus. The Aux/IAA family genes generally showed a higher expression level in the non-embryogenic callus (NEC) of highly embryogenic cultivar CCRI24 than that of recalcitrant cultivar CCRI12, which may be conducive to initializing the embryogenic transformation. Auxin early response genes were tightly co-expressed with most of the known somatic embryogenesis (SE) related genes, indicating that these genes may regulate upland cotton SE by interacting with auxin early response genes.

scholarly journals Genome-wide identification and expression analysis of the JAZ gene family in turnip

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kai Jia ◽  
Cunyao Yan ◽  
Jing Zhang ◽  
Yunxia Cheng ◽  
Wenwen Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Tandem Duplication ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Specific Protein ◽  
Gene Pairs ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structure And Expression

AbstractJAZ is a plant-specific protein family involved in the regulation of plant development, abiotic stresses, and responses to phytohormone treatments. In this study, we carried out a bioinformatics analysis of JAZ genes in turnip by determining the phylogenetic relationship, chromosomal location, gene structure and expression profiles analysis under stresses. The 36 JAZ genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The JAZ genes were located on 10 chromosomes. Two gene pairs were involved in tandem duplication events. We identified 44 collinear JAZ gene pairs in the turnip genome. Analysis of the Ka/Ks ratios indicated that the paralogs of the BrrJAZ family principally underwent purifying selection. Expression analysis suggested JAZ genes may be involved in the formation of turnip tuberous root, and they also participated in the response to ABA, SA, MeJA, salt stress and low-temperature stress. The results of this study provided valuable information for further exploration of the JAZ gene family in turnip.

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

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.

Identification of putative markers of triclabendazole resistance by a genome-wide analysis of genetically recombinant Fasciola hepatica

Parasitology ◽  
2013 ◽  
Vol 140 (12) ◽  
pp. 1523-1533 ◽  
Author(s):  
J. HODGKINSON ◽  
K. CWIKLINSKI ◽  
N. J. BEESLEY ◽  
S. PATERSON ◽  
D. J. L. WILLIAMS
Keyword(s):  
Genetic Resources ◽  
Fasciola Hepatica ◽  
Genome Wide Analysis ◽  
Extensive Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms ◽  
Triclabendazole Resistance

SUMMARYDespite years of investigation into triclabendazole (TCBZ) resistance in Fasciola hepatica, the genetic mechanisms responsible remain unknown. Extensive analysis of multiple triclabendazole-susceptible and -resistant isolates using a combination of experimental in vivo and in vitro approaches has been carried out, yet few, if any, genes have been demonstrated experimentally to be associated with resistance phenotypes in the field. In this review we summarize the current understanding of TCBZ resistance from the approaches employed to date. We report the current genomic and genetic resources for F. hepatica that are available to facilitate novel functional genomics and genetic experiments for this parasite in the future. Finally, we describe our own non-biased approach to mapping the major genetic loci involved in conferring TCBZ resistance in F. hepatica.

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