Functional differentiation and spatial-temporal co-expression networks of the NBS-encoding gene family in Jilin ginseng, Panax ginseng C.A. Meyer

AbstractThe APETALA2/Ethylene Responsive Factor (AP2/ERF) gene family has been shown to play a crucial role in plant growth and development, stress responses and secondary metabolite biosynthesis. Nevertheless, little is known about the gene family in ginseng (Panax ginseng), an important traditional medicinal herb in Asia and North America. Here, we report the systematic analysis of the gene family present in ginseng using several transcriptomic databases. A total of 189 putative AP2/ERF genes, defined as PgERF001 through PgERF189. The 93 PgERF genes that have the complete AP2 domain in their open reading frames were classified into five subfamilies, DREB, ERF, AP2, RAV and Soloist. The DREB subfamily and ERF subfamily were further clustered four and six groups, respectively, compared to the 12 groups of these subfamilies found in Arabidopsis. Gene ontology categorized these 397 transcripts of the 189 PgERF genes into eight functional subcategories, suggesting their functional differentiation and they have been especially enriched for the nucleic acid binding transcription factor activity subcategory. The expression activity and networks of the 397 PgERF transcripts have substantially diversified across tissues, developmental stages and genotypes. Then, the expression change of six PgERF genes randomly selected from DREB subfamily, i.e., PgERF073, PgERF079, PgERF110, PgERF115, PgERF120 and PgERF128 responding to cold stress suggesting that DREB subfamily genes played an important role in cold resistance of ginseng. Finally, we studied the responses of the PgERF genes to methyl jasmonate (MeJA). 288 (72.5%) of the 397 PgERF gene transcripts responded to the MeJA treatment, with 136 up-regulated and 152 down-regulated, indicating that most members of the PgERF gene family are responsive to MeJA. These results provide resources and knowledge necessary for family-wide functional analysis of the PgERF genes in ginseng and related species.

Download Full-text

Molecular signatures of selection associated with host-plant differences in Pieris butterflies

10.1101/627182 ◽

2019 ◽

Author(s):

Yu Okamura ◽

Ai Sato ◽

Natsumi Tsuzuki ◽

Masashi Murakami ◽

Hanna Heidel-Fischer ◽

...

Keyword(s):

Gene Family ◽

Host Plant ◽

Host Plants ◽

Protein A ◽

Functional Differentiation ◽

Major Allergen ◽

Arms Race ◽

Defense System ◽

Evolutionary Forces ◽

Key Innovation

AbstractAdaptive traits that enable organisms to conquer novel niches and experience subsequent diversification are ecologically and evolutionarily important. The larvae of Pieris butterflies express nitrile-specifier proteins (NSPs), a key innovation for overcoming the glucosinolate (GLS)-myrosinase-based defense system of their Brassicales host-plants. NSPs are a member of the NSP-like gene family, which includes the major allergen (MA) protein, a paralog of NSP with a GLS-disarming function, and a single domain major allergen (SDMA) protein, whose function is unknown. The arms-race between a highly variable host-plant defense system and members of the NSP-like gene family is suggested to mediate diversification in both Pierid butterflies and Brassicales plants. Here, we combined feeding experiments using 25 Brassicaceae plants and five Pieris species with larval transcriptome data to investigate the evolutionary forces acting on NSP-like gene family members associated with patterns of host-plant usage. Although we observed significantly elevated nonsynonymous to synonymous substitution ratios in NSPs, no such pattern was observed in MAs or SDMAs. Furthermore, we found a signature of positive selection of NSP at a phylogenetic branch which reflects different host-plant preferences. Our data indicate that NSPs have evolved in response to shifting preferences for host plants among five Pieris butterflies, whereas MAs and SDMAs appear to have more conserved functions. Our results show that the evolution and functional differentiation of key genes used in host-plant adaptation play a crucial role in the chemical arms-race between Pieris butterflies and their Brassicales host-plants.

Download Full-text

Genome-wide analysis of chloride channel-encoding gene family members and identification of CLC genes that respond to Cl−/salt stress in upland cotton

Molecular Biology Reports ◽

10.1007/s11033-020-06023-z ◽

2020 ◽

Vol 47 (12) ◽

pp. 9361-9371

Author(s):

Xun Liu ◽

Boyi Pi ◽

Jianwei Pu ◽

Cong Cheng ◽

Jiajia Fang ◽

...

Keyword(s):

Salt Stress ◽

Gene Family ◽

Chloride Channel ◽

Upland Cotton ◽

Family Members ◽

Genome Wide Analysis ◽

Genome Wide ◽

Encoding Gene

Download Full-text

A new cysteine-rich protein-encoding gene family in Giardia duodenalis

Gene ◽

10.1016/0378-1119(95)00759-8 ◽

1996 ◽

Vol 169 (1) ◽

pp. 33-38 ◽

Cited By ~ 20

Author(s):

Nanhua Chen ◽

Jacqueline A. Upcroft ◽

Peter Upcroft

Keyword(s):

Gene Family ◽

Giardia Duodenalis ◽

Cysteine Rich Protein ◽

Protein Encoding ◽

Encoding Gene

Download Full-text

Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

BMC Genomics ◽

10.1186/s12864-020-07226-1 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Manyi Sun ◽

Mingyue Zhang ◽

Jugpreet Singh ◽

Bobo Song ◽

Zikai Tang ◽

...

Keyword(s):

Genetic Variation ◽

Disease Resistance ◽

Positive Selection ◽

Gene Family ◽

Selection Pressure ◽

Black Spot ◽

Orthologous Gene ◽

European Pear ◽

Encoding Gene ◽

Encoding Genes

Abstract Background The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’, an Asian pear) and Pyrus communis (‘Bartlett’, a European pear) genomes, but the patterns of genetic variation and selection pressure on these genes during pear domestication have remained unsolved. Results In this study, 338 and 412 NBS-encoding genes were identified from Asian and European pear genomes. This difference between the two pear species was the result of proximal duplications. About 15.79% orthologous gene pairs had Ka/Ks ratio more than one, indicating two pear species undergo strong positive selection after the divergence of Asian and European pear. We identified 21 and 15 NBS-encoding genes under fire blight and black spot disease-related QTL, respectively, suggesting their importance in disease resistance. Domestication caused decreased nucleotide diversity across NBS genes in Asian cultivars (cultivated 6.23E-03; wild 6.47E-03), but opposite trend (cultivated 6.48E-03; wild 5.91E-03) appeared in European pears. Many NBS-encoding coding regions showed Ka/Ks ratio of greater than 1, indicating the role of positive selection in shaping diversity of NBS-encoding genes in pear. Furthermore, we detected 295 and 122 significantly different SNPs between wild and domesticated accessions in Asian and European pear populations. Two NBS genes (Pbr025269.1 and Pbr019876.1) with significantly different SNPs showed >5x upregulation between wild and cultivated pear accessions, and > 2x upregulation in Pyrus calleryana after inoculation with Alternaria alternata. We propose that positively selected and significantly different SNPs of an NBS-encoding gene (Pbr025269.1) regulate gene expression differences in the wild and cultivated groups, which may affect resistance in pear against A. alternata. Conclusion Proximal duplication mainly led to the different number of NBS-encoding genes in P. bretschneideri and P. communis genomes. The patterns of genetic diversity and positive selection pressure differed between Asian and European pear populations, most likely due to their independent domestication events. This analysis helps us understand the evolution, diversity, and selection pressure in the NBS-encoding gene family in Asian and European populations, and provides opportunities to study mechanisms of disease resistance in pear.

Download Full-text

SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family: TRANSCRIPTOME-Wide Identification, Phylogenetic Relationship, Expression Patterns and Network Interaction Analysis in Panax ginseng C. A. Meyer

Plants ◽

10.3390/plants9030354 ◽

2020 ◽

Vol 9 (3) ◽

pp. 354

Author(s):

Shaokun Li ◽

Li Li ◽

Yang Jiang ◽

Jun Wu ◽

Honghua Sun ◽

...

Keyword(s):

Gene Family ◽

Panax Ginseng ◽

Interaction Analysis ◽

Binding Protein ◽

Expression Patterns ◽

Evolutionary Analysis ◽

Main Function ◽

Squamosa Promoter Binding Protein ◽

Expression Characteristics ◽

Spl Gene

SPL (SQUAMOSA promoter binding protein-like) gene family is specific transcription factor in the plant that have an important function for plant growth and development. Although the SPL gene family has been widely studied and reported in many various plant species from gymnosperm to angiosperm, there are no systematic studies and reports about the SPL gene family in Panax ginseng C. A. Meyer. In this study, we conducted transcriptome-wide identification, evolutionary analysis, structure analysis, and expression characteristics analysis of SPL gene family in Panax ginseng by bioinformatics. We annotated the PgSPL gene family and found that they might involve in multiple functions including encoding structural proteins, but the main function were still focused on the binding function. The result showed that 106 PgSPL transcripts were classified into two clades - A and B, both of which respectively consisted of three groups. Besides, we profiled PgSPL transcripts’ genotypic, temporal, and spatial expression characteristics. Furthermore, we calculated the correlation of PgSPL transcripts in the 14 tissues of a 4 years old ginseng and 42 farmers’ cultivars farmers’ cultivars of 4 years old ginsengs’ roots with both results showing that SPL transcripts formed a single network, which indicated that PgSPLs inter-coordinated when performing their functions. What’s more, we found that most PgSPL transcripts tended to express in older ginseng instead of younger ginseng, which was not only reflected in the expression of more types of SPL transcripts in older ginseng, but also in the higher expression of SPL transcripts in older ginseng. Additionally, we found that four PgSPL transcripts were only massively expressed in roots. According to PgSPL transcripts’ expression characteristics, we found that PgSPL23-35 and PgSPL24-09 were most proper two transcripts to further study as ginseng age’s molecular marker. These results provide the basis for further elucidation of the PgSPL transcripts’ biological function in ginseng and ginseng genetics improvement and gene breeding in the future.

Download Full-text

Variability among members of the Hor-2 multigene family

Genome ◽

10.1139/g93-055 ◽

1993 ◽

Vol 36 (3) ◽

pp. 397-403 ◽

Cited By ~ 17

Author(s):

Vladimir Kanazin ◽

Evgeny Ananiev ◽

Tom Blake

Keyword(s):

Polymerase Chain Reaction ◽

Gene Family ◽

Storage Proteins ◽

Gene Families ◽

Reaction Sequence ◽

Chain Reaction ◽

Genes Encoding ◽

Polymerase Chain ◽

Encoding Gene ◽

Barley Genotypes

The hordeins comprise the major prolamin storage proteins of barley. Two major and one minor gene families encode these alcohol-soluble proteins. The Hor-2 gene family encoding the B-hordeins has been estimated to contain 15–30 copies. Although several genes encoding B-hordeins have been cloned and sequenced, little is known about the mechanisms responsible for the generation of the enormous genetic variability at this locus. Polymerase chain reaction sequence amplification provided a simple technique that permitted the amplification of the Hor-2 gene family members from the genomes of several barley genotypes. Sequence analysis of clones permitted the identification of a region within the Hor-2 structural gene that appears to undergo recombinational and slippage-like gene conversion events. In this report we describe variability of the B-hordein genes, possible mechanisms responsible for it, and implications this may have on the evolution of prolamin-encoding gene families.Key words: barley, hordeins, polymerase chain reaction, polymorphism.

Download Full-text