scholarly journals Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit (Passiflora edulis Sims)

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Zhiqiang Xia ◽  
Dongmei Huang ◽  
Shengkui Zhang ◽  
Wenquan Wang ◽  
Funing Ma ◽  
...  
Keyword(s):  
Gene Family ◽  
Genome Assembly ◽  
Metabolic Pathways ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Passion Fruit ◽  
Integrated Analysis ◽  
Alpha Linolenic Acid ◽  
Passiflora Edulis ◽  
Duplication Events

AbstractPassion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7 Mb chromosome-scale genome assembly of passion fruit, with 98.91% (~1327.18 Mb) of the assembly assigned to nine pseudochromosomes. The genome includes 23,171 protein-coding genes, and most of the assembled sequences are repetitive sequences, with long-terminal repeats (LTRs) being the most abundant. Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae. Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA, which may have contributed to its large genome size. An integrated analysis of genomic, transcriptomic, and metabolomic data showed that ‘alpha-linolenic acid metabolism’, ‘metabolic pathways’, and ‘secondary metabolic pathways’ were the main pathways involved in the synthesis of important volatile organic compounds (VOCs) in passion fruit, and this analysis identified some candidate genes, including GDP-fucose Transporter 1-like, Tetratricopeptide repeat protein 33, protein NETWORKED 4B isoform X1, and Golgin Subfamily A member 6-like protein 22. In addition, we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways. Gene family analysis showed that the ACX, ADH, ALDH, and HPL gene families, especially ACX13/14/15/20, ADH13/26/33, ALDH1/4/21, and HPL4/6, were the key genes for ester synthesis, while the TPS gene family, especially PeTPS2/3/4/24, was the key gene family for terpene synthesis. This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.

scholarly journals Expansion, retention and loss in the Acyl-CoA Synthetase “Bubblegum” (Acsbg) gene family in vertebrate history

2018 ◽  
Author(s):  
Mónica Lopes-Marques ◽  
André M. Machado ◽  
Raquel Ruivo ◽  
Elza Fonseca ◽  
Estela Carvalho ◽  
...  
Keyword(s):  
Gene Family ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Gene Families ◽  
Gene Repertoire ◽  
Physiological Processes ◽  
Complex Lipid ◽  
History Of ◽  
Enzyme Families ◽  
Rate Limiting

AbstractFatty acids (FAs) constitute a considerable fraction of all lipid molecules with a fundamental role in numerous physiological processes. In animals, the majority of complex lipid molecules are derived from the transformation of FAs through several biochemical pathways. Yet, for FAs to enroll in these pathways they require an activation step. FA activation is catalyzed by the rate limiting action of Acyl-CoA synthases. Several Acyl-CoA enzyme families have been previously described and classified according to the chain length of FA they process. Here, we address the evolutionary history of the ACSBG gene family which activates, FA with more than 16 carbons. Currently, two different ACSBG gene families, ACSBG1 and ACSBG2, are recognized in vertebrates. We provide evidence that a wider and unequal ACSBG gene repertoire is present in vertebrate lineages. We identify a novel ACSBG-like gene lineage which occurs specifically in amphibians, ray finned fish, coelacanths and chondrichthyes named ACSBG3. Also, we show that the ACSBG2 gene lineage duplicated in the Theria ancestor. Our findings, thus offer a far richer understanding on FA activation in vertebrates and provide key insights into the relevance of comparative and functional analysis to perceive physiological differences, namely those related with lipid metabolic pathways.

scholarly journals Identification of Raf-Like Kinases B Subfamily Genes in Gossypium Species Revealed GhRAF42 Enhanced Salt Tolerance in Cotton

2021 ◽  
Vol 22 (23) ◽  
pp. 12649
Author(s):  
Zhen Peng ◽  
Xuran Jiang ◽  
Zhenzhen Wang ◽  
Xiaoyang Wang ◽  
Hongge Li ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Gene Family ◽  
Purifying Selection ◽  
Integrated Analysis ◽  
Abiotic Factor ◽  
Virus Induced Gene Silencing ◽  
Salt Stress Response ◽  
Suitable Candidate ◽  
Duplication Events

Salinity is a critical abiotic factor that significantly reduces agricultural production. Cotton is an important fiber crop and a pioneer on saline soil, hence genetic architecture that underpins salt tolerance should be thoroughly investigated. The Raf-like kinase B-subfamily (RAF) genes were discovered to regulate the salt stress response in cotton plants. However, understanding the RAFs in cotton, such as Enhanced Disease Resistance 1 and Constitutive Triple Response 1 kinase, remains a mystery. This study obtained 29, 28, 56, and 54 RAF genes from G. arboreum, G. raimondii, G. hirsutum, and G. barbadense, respectively. The RAF gene family described allopolyploidy and hybridization events in allotetraploid cotton evolutionary connections. Ka/Ks analysis advocates that cotton evolution was subjected to an intense purifying selection of the RAF gene family. Interestingly, integrated analysis of synteny and gene collinearity suggested dispersed and segmental duplication events involved in the extension of RAFs in cotton. Transcriptome studies, functional validation, and virus-induced gene silencing on salt treatments revealed that GhRAF42 is engaged in salt tolerance in upland cotton. This research might lead to a better understanding of the role of RAFs in plants and the identification of suitable candidate salt-tolerant genes for cotton breeding.

scholarly journals Genome-Wide Analysis of WRKY Gene Family and the Dynamic Responses of Key WRKY Genes Involved in Ostrinia furnacalis Attack in Zea mays

2021 ◽  
Vol 22 (23) ◽  
pp. 13045
Author(s):  
Yin Tang ◽  
Jingfei Guo ◽  
Tiantao Zhang ◽  
Shuxiong Bai ◽  
Kanglai He ◽  
...  
Keyword(s):  
Gene Family ◽  
Target Genes ◽  
Gene Families ◽  
Dynamic Responses ◽  
Phylogenomic Analysis ◽  
Maize Genome ◽  
Wrky Gene ◽  
Ostrinia Furnacalis ◽  
Corn Borer ◽  
Duplication Events

WRKY transcription factors comprise one of the largest gene families and serve as key regulators of plant defenses against herbivore attack. However, studies related to the roles of WRKY genes in response to herbivory are limited in maize. In this study, a total of 128 putative maize WRKY genes (ZmWRKYs) were identified from the new maize genome (v4). These genes were divided into seven subgroups (groups I, IIa–e, and III) based on phylogenomic analysis, with distinct motif compositions in each subgroup. Syntenic analysis revealed that 72 (56.3%) of the genes were derived from either segmental or tandem duplication events (69 and 3, respectively), suggesting a pivotal role of segmental duplication in the expansion of the ZmWRKY family. Importantly, transcriptional regulation prediction showed that six key WRKY genes contribute to four major defense-related pathways: L-phenylalanine biosynthesis II and flavonoid, benzoxazinoid, and jasmonic acid (JA) biosynthesis. These key WRKY genes were strongly induced in commercial maize (Jingke968) infested with the Asian corn borer, Ostrinia furnacalis, for 0, 2, 4, 12 and 24 h in the field, and their expression levels were highly correlated with predicted target genes, suggesting that these genes have important functions in the response to O. furnacalis. Our results provide a comprehensive understanding of the WRKY gene family based on the new assembly of the maize genome and lay the foundation for further studies into functional characteristics of ZmWRKY genes in commercial maize defenses against O. furnacalis in the field.

scholarly journals Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii

2021 ◽  
Vol 12 ◽  
Author(s):  
Jielong Zhou ◽  
Peifu Wu ◽  
Zhongping Xiong ◽  
Naiyong Liu ◽  
Ning Zhao ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Phylogenetic Analyses ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Thaumetopoea Pityocampa ◽  
High Quality ◽  
Protein Coding ◽  
Peptidoglycan Recognition Protein ◽  
Recognition Protein ◽  
Chromosome Level

A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.

scholarly journals A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Qingzhen Wei ◽  
Jinglei Wang ◽  
Wuhong Wang ◽  
Tianhua Hu ◽  
Haijiao Hu ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Specific Gene ◽  
High Quality ◽  
Total Size ◽  
Protein Coding ◽  
Fruit Length ◽  
Protein Coding Genes

Abstract Eggplant (Solanum melongena L.) is an economically important vegetable crop in the Solanaceae family, with extensive diversity among landraces and close relatives. Here, we report a high-quality reference genome for the eggplant inbred line HQ-1315 (S. melongena-HQ) using a combination of Illumina, Nanopore and 10X genomics sequencing technologies and Hi-C technology for genome assembly. The assembled genome has a total size of ~1.17 Gb and 12 chromosomes, with a contig N50 of 5.26 Mb, consisting of 36,582 protein-coding genes. Repetitive sequences comprise 70.09% (811.14 Mb) of the eggplant genome, most of which are long terminal repeat (LTR) retrotransposons (65.80%), followed by long interspersed nuclear elements (LINEs, 1.54%) and DNA transposons (0.85%). The S. melongena-HQ eggplant genome carries a total of 563 accession-specific gene families containing 1009 genes. In total, 73 expanded gene families (892 genes) and 34 contraction gene families (114 genes) were functionally annotated. Comparative analysis of different eggplant genomes identified three types of variations, including single-nucleotide polymorphisms (SNPs), insertions/deletions (indels) and structural variants (SVs). Asymmetric SV accumulation was found in potential regulatory regions of protein-coding genes among the different eggplant genomes. Furthermore, we performed QTL-seq for eggplant fruit length using the S. melongena-HQ reference genome and detected a QTL interval of 71.29–78.26 Mb on chromosome E03. The gene Smechr0301963, which belongs to the SUN gene family, is predicted to be a key candidate gene for eggplant fruit length regulation. Moreover, we anchored a total of 210 linkage markers associated with 71 traits to the eggplant chromosomes and finally obtained 26 QTL hotspots. The eggplant HQ-1315 genome assembly can be accessed at http://eggplant-hq.cn. In conclusion, the eggplant genome presented herein provides a global view of genomic divergence at the whole-genome level and powerful tools for the identification of candidate genes for important traits in eggplant.

scholarly journals Comparative Genomic Insights into the Longhorned Tick, Haemaphysalis Longicornis

2020 ◽  
Author(s):  
Rui-Ling Zhang ◽  
Qian Zhang ◽  
Zhong Zhang
Keyword(s):  
Gene Family ◽  
Genome Assembly ◽  
Animal Health ◽  
Gene Families ◽  
High Ratio ◽  
Gene Family Evolution ◽  
Comparative Genomic ◽  
Haemaphysalis Longicornis ◽  
Gene Set ◽  
Terrestrial Vertebrates

Abstract Background: The longhorned tick, Haemaphysalis longicornis Neumann, is widely distributed across temperate regions. It can parasitize terrestrial vertebrates, including birds and a large number of mammals. They are a concern in human and animal health notably for their potential to transmit infectious agents. Methods: Genome survey was investigated using GenomeScope v1.0.0 with a maximum k-mer coverage cutoff of 1,000. Non-redundant assembly was polished with Illumina short reads using two rounds of NextPolish v1.1.0. Genome completeness was assessed using BUSCO v3.0.2 pipeline analyses against arthropod gene set (n = 1, 066). Ab initio predictions were generated using BRAKER v2.1.5. Transcriptomic reads were mapped to the genome with HISAT2 v2.2.0 and assembled with StringTie v2.1.2. Gene functions were assigned against UniProtKB database using Diamond v0.9.24. Orthogroups of 16 Chelicerata species were inferred using OrthoFinder v2.3.8 and gene family evolution was estimated using CAFÉ v4.2.1. Gene families related to digestion and detoxification, i.e. cytochrome P450 (CYP), carboxyl/cholinesterase (CCE), glutathione-S-transferase (GST), ATP-binding cassette (ABC) transporter were annotated by searching in the genome assembly. Results: The final genome assembly has a size of 3.12 Gb, a scaffold N50 of 1.09 Mb, and captured 92.4% of the BUSCO gene set (n=1,066). Genome architecture pattern of the longhorned tick resembles another tick, Ixodes scapularis (Say), particularly in large size, highly repetitive DNA (~65%) and protein-coding genes (21,550). We also identified 5,601 non-coding RNAs with a high ratio of tRNAs (4,271). Gene family evolution revealed 350 rapidly evolving gene families. Combining function enrichment analyses of gene ontology (GO) and KEGG pathway, 255 families experiencing significant expansions mainly involves in cuticle synthesis, digestion and detoxification. Conclusions: The new genome assembly, annotation and comparative genomic analyses provide a valuable resource for insights into parasitic life mode of the longhorned tick.

scholarly journals High-quality genome assembly, annotation and evolutionary analysis of the mungbean (Vigna radiata) genome

2020 ◽  
Author(s):  
Qiang Yan ◽  
Qiong Wang ◽  
Cheng Xuzhen ◽  
Lixia Wang ◽  
Prakit Somta ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Vigna Radiata ◽  
Crop Improvement ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Close Relative ◽  
Specific Gene ◽  
Evolutionary Analysis ◽  
High Quality ◽  
High Quality Genome

Mungbean (Vigna radiata [L.]) is an important economic crop grown in South, and East Asia. The low contiguity of the current assembly of V. radiata genome has limited its application. Here, we report a high-quality chromosome-scale assembled genome of V. radiata to facilitate the investigation of its genome characteristics and evolution. By combination of Nanopore long reads, Illumina short reads and Hi-C data, we generated a high-quality genome assembly of V. radiata, with 473.67 megabases assembled into 11 chromosomes with contig N50 and scaffold N50 of 11.3 and 42.4 megabases, respectively. A total of 52.8% of the genome was annotated as repetitive sequences, among which LTRs (long terminal repeats) were predominant (33.9%). The genome of V. radiata was predicted to contain 33,924 genes, 32,470 (95.7%) of which could be functionally annotated. Evolutionary analysis revealed an estimated divergence time of V. radiata from its close relative V. angularis of ~11.66 million years ago. In addition, 277 V. radiata specific gene families, 18 positively selected genes were detected and functionally annotated. This high-quality mungbean genome will provide valuable resources for further genetic analysis and crop improvement of mungbean and other legume species.

scholarly journals Identification of the WUSCHEL-Related Homeobox (WOX) Gene Family, and Interaction and Functional Analysis of TaWOX9 and TaWUS in Wheat

2020 ◽  
Vol 21 (5) ◽  
pp. 1581 ◽  
Author(s):  
Zheng Li ◽  
Dan Liu ◽  
Yu Xia ◽  
Ziliang Li ◽  
Doudou Jing ◽  
...  
Keyword(s):  
Gene Family ◽  
Oryza Sativa L ◽  
Dynamic Balance ◽  
Functional Characterization ◽  
Gene Families ◽  
Triticum Aestivum L ◽  
Genome Wide ◽  
A Genome ◽  
Paralogous Copy ◽  
Duplication Events

The WUSCHEL-related homeobox (WOX) is a family of plant-specific transcription factors, with important functions, such as regulating the dynamic balance of division and differentiation of plant stem cells and plant organ development. We identified 14 distinct TaWOX genes in the wheat (Triticum aestivum L.) genome, based on a genome-wide scan approach. All of the genes under evaluation had positional homoeologs on subgenomes A, B and D except TaWUS and TaWOX14. Both TaWOX14a and TaWOX14d had a paralogous copy on the same genome due to tandem duplication events. A phylogenetic analysis revealed that TaWOX genes could be divided into three groups. We performed functional characterization of TaWOX genes based on the evolutionary relationships among the WOX gene families of wheat, rice (Oryza sativa L.), and Arabidopsis. An overexpression analysis of TaWUS in Arabidopsis revealed that it affected the development of outer floral whorl organs. The overexpression analysis of TaWOX9 in Arabidopsis revealed that it promoted the root development. In addition, we identified some interaction between the TaWUS and TaWOX9 proteins by screening wheat cDNA expression libraries, which informed directions for further research to determine the functions of TaWUS and TaWOX9. This study represents the first comprehensive data on members of the WOX gene family in wheat.

scholarly journals A high-quality genome assembly of Morinda officinalis, a famous native southern herb in the Lingnan region of southern China

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Jihua Wang ◽  
Shiqiang Xu ◽  
Yu Mei ◽  
Shike Cai ◽  
Yan Gu ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Genome Assembly ◽  
Large Scale ◽  
Active Component ◽  
Southern China ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Comparative Genomic ◽  
Edible Plant ◽  
High Quality

AbstractMorinda officinalis is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of southern China. Its dried roots (called bajitian in traditional Chinese medicine) are broadly used to treat various diseases, such as impotence and rheumatism. Here, we report a high-quality chromosome-scale genome assembly of M. officinalis using Nanopore single-molecule sequencing and Hi-C technology. The assembled genome size was 484.85 Mb with a scaffold N50 of 40.97 Mb, and 90.77% of the assembled sequences were anchored on eleven pseudochromosomes. The genome includes 27,698 protein-coding genes, and most of the assemblies are repetitive sequences. Genome evolution analysis revealed that M. officinalis underwent core eudicot γ genome triplication events but no recent whole-genome duplication (WGD). Likewise, comparative genomic analysis showed no large-scale structural variation after species divergence between M. officinalis and Coffea canephora. Moreover, gene family analysis indicated that gene families associated with plant–pathogen interactions and sugar metabolism were significantly expanded in M. officinalis. Furthermore, we identified many candidate genes involved in the biosynthesis of major active components such as anthraquinones, iridoids and polysaccharides. In addition, we also found that the DHQS, GGPPS, TPS-Clin, TPS04, sacA, and UGDH gene families—which include the critical genes for active component biosynthesis—were expanded in M. officinalis. This study provides a valuable resource for understanding M. officinalis genome evolution and active component biosynthesis. This work will facilitate genetic improvement and molecular breeding of this commercially important plant.

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