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Comparative Genomics and Functional Genomics Analysis of Horticulture Plants 2022

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (30 December 2023) | Viewed by 10119

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Prof. Dr. Enhua Xia

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Guest Editor

School of Tea and Food Science and Technology, Anhui Agricultural University, Hefei 230036, China
Interests: comparative genomics; functional genomics; cold resistance; tea quality; secondary metabolism

Prof. Dr. Xingtan Zhang

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Guest Editor

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics, Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Interests: assembly and typing of complex genomes; development of bioinformatic analysis techniques; functionally important genes based on big data in histology

Prof. Dr. Haifeng Wang

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Guest Editor

College of Agriculture, Guangxi University, Nanning 530004, China
Interests: polyploidy; epigenetics; bioinformatics; plant evolution
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Special Issue Information

Dear Colleagues,

Horticultural plants play essential and diverse roles in human lifestyles by providing fruits, vegetables, beverages, herbal medicines, and ornamentals, as well as by shaping human art, culture, and environments. With the advent of sequencing technologies, 200 more horticultural plant species have been genome-sequenced in the past decade. Horticultural plants have a highly diverse and complex genome, usually with a high degree of heterozygosity and high ploidy due to their long and complicated history of evolution and domestication. Along with the genome sequencing of horticultural plants, a large number of omics datasets have been released, such as pan-genomics, transcriptomics, proteomics, and metabolomics, which has greatly promoted the development of horticultural plant genetics and breeding. Nevertheless, challenges in the investigation of horticultural plant genomics to multi-omics comparative analyses, and especially how those comprehensive datasets contribute to horticultural plant functional genetics and molecular breeding programmes, are still underway.

Herein, we are pleased to invite you to participate in this Special Issue of IJMS on “Comparative Genomics and Functional Genomics Analysis in Horticulture Plant 2022”. In this Issue, a wide range of research aimed at comparative and functional genomics, plant breeding and the genetic improvement of horticultural plants is welcomed. The associated horticultural plants include, but are not limited to, flowers, fruits, vegetables, and beverages. Research articles and up-to-date review articles are welcome.

Prof. Dr. Enhua Xia
Prof. Dr. Xingtan Zhang
Prof. Dr. Haifeng Wang
Guest Editors

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Keywords

horticultural plant
comparative genomics
functional genomics
population genetics
plant breeding
genetic improvement
quality formation
stress resistance

Published Papers (5 papers)

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Research

20 pages, 7710 KiB

Open AccessArticle

Small RNA and Degradome Sequencing Reveal Roles of miRNAs in the Petal Color Fading of Malus Crabapple

by Hao Rong, Xin Han, Yue Xin, Zhouxian Ni, Wangxiang Zhang and Li’an Xu

Int. J. Mol. Sci. 2023, 24(14), 11384; https://doi.org/10.3390/ijms241411384 - 13 Jul 2023

Cited by 3 | Viewed by 1578

Abstract

The Malus crabapple is an important woody ornamental plant. The fading of petals during its development significantly affects their ornamental value. Petal color is related to anthocyanin content and miRNAs play an important role in the post-transcriptional regulation of anthocyanin synthesis. However, the mechanisms underlying miRNA regulation of petal fading have rarely been studied. Transcriptome and small RNA sequencing of petals from the blooming phases of Malus. ‘Indian Summer’ varieties S1 (small bud), S2 (initial-flowering), and S3 (late-flowering) allowed us to identify 230 known miRNAs and 17 novel miRNAs, including 52 differentially expressed miRNAs which targeted 494 genes and formed 823 miRNA–target pairs. Based on the target gene annotation results, miRNA–target pairs were screened that may be involved in the fading process of Malus crabapple petals through three different pathways: anthocyanin synthesis, transport, and degradation, involving mcr-miR858-MYB1\MYB5 and mcr-miR396-McCHI inhibiting anthocyanin synthesis; mcr-miR167, mcr-miR390, mcr-miR535, and mcr-miR858 inhibiting anthocyanin transport from the cytoplasm to the vacuole by targeting ABC transporter genes (ABCB, ABCC, ABCD, and ABCG); and mcr-miR398 targeting the superoxide dismutase genes (CZSOD2 and CCS) to accelerate anthocyanin degradation. These findings offer a novel approach to understanding the mechanism of petal fading and serve as a reference for other plants with floral fading. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis of Horticulture Plants 2022)

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18 pages, 5214 KiB

Open AccessArticle

Combined Transcriptome and Metabolome Analysis Reveals Adaptive Defense Responses to DON Induction in Potato

by Biao Zhao, Hang Yu, Dan Liu, Jiaqi Wang, Xu Feng, Fumeng He, Tianshuai Qi, Chong Du, Linlin Wang, Haifeng Wang and Fenglan Li

Int. J. Mol. Sci. 2023, 24(9), 8054; https://doi.org/10.3390/ijms24098054 - 29 Apr 2023

Cited by 2 | Viewed by 1820

Abstract

Phytophthora infestans poses a serious threat to potato production, storage, and processing. Understanding plant immunity triggered by fungal elicitors is important for the effective control of plant diseases. However, the role of the potato stress response to Fusarium toxin deoxynivalenol (DON)-induced stress is still not fully understood. In this study, the metabolites of DON-treated potato tubers were studied for four time intervals using UPLC-MS/MS. We identified 676 metabolites, and differential accumulation metabolite analysis showed that alkaloids, phenolic acids, and flavonoids were the major differential metabolites that directly determined defense response. Transcriptome data showed that differentially expressed genes (DEGs) were significantly enriched in phenylpropane and flavonoid metabolic pathways. Weighted gene co-expression network analysis (WGCNA) identified many hub genes, some of which modulate plant immune responses. This study is important for understanding the metabolic changes, transcriptional regulation, and physiological responses of active and signaling substances during DON induction, and it will help to design defense strategies against Phytophthora infestans in potato. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis of Horticulture Plants 2022)

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18 pages, 3925 KiB

Open AccessArticle

Integrated Metabolomic and Transcriptomic Analysis Reveals That Amino Acid Biosynthesis May Determine Differences in Cold-Tolerant and Cold-Sensitive Tea Cultivars

by Yaohua Cheng, Qiuyan Ban, Junlin Mao, Mengling Lin, Xiangxiang Zhu, Yuhui Xia, Xiaojie Cao, Xianchen Zhang and Yeyun Li

Int. J. Mol. Sci. 2023, 24(3), 1907; https://doi.org/10.3390/ijms24031907 - 18 Jan 2023

Cited by 11 | Viewed by 2007

Abstract

Cold stress is one of the major abiotic stresses limiting tea production. The planting of cold-resistant tea cultivars is one of the most effective measures to prevent chilling injury. However, the differences in cold resistance between tea cultivars remain unclear. In the present study, we perform a transcriptomic and metabolomic profiling of Camellia sinensis var. “Shuchazao” (cold-tolerant, SCZ) and C. sinensis var. assamica “Yinghong 9” (cold-sensitive, YH9) during cold acclimation and analyze the correlation between gene expression and metabolite biosynthesis. Our results show that there were 51 differentially accumulated metabolites only up-regulated in SCZ in cold–acclimation (CA) and de–acclimation (DA) stages, of which amino acids accounted for 18%. The accumulation of L-arginine and lysine in SCZ in the CA stage was higher than that in YH9. A comparative transcriptomic analysis showed an enrichment of the amino acid biosynthesis pathway in SCZ in the CA stage, especially “arginine biosynthesis” pathways. In combining transcriptomic and metabolomic analyses, it was found that genes and metabolites associated with amino acid biosynthesis were significantly enriched in the CA stage of SCZ compared to CA stage of YH9. Under cold stress, arginine may improve the cold resistance of tea plants by activating the polyamine synthesis pathway and CBF (C-repeat-binding factor)–COR (cold-regulated genes) regulation pathway. Our results show that amino acid biosynthesis may play a positive regulatory role in the cold resistance of tea plants and assist in understanding the cold resistance mechanism differences among tea varieties. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis of Horticulture Plants 2022)

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14 pages, 1554 KiB

Open AccessArticle

Evolutionary Landscape of Tea Circular RNAs and Its Contribution to Chilling Tolerance of Tea Plant

by Jin Huang, Yanli Wang, Jie Yu, Fangdong Li, Lianghui Yi, Yunze Li, Na Xie, Qiong Wu, Lidiia Samarina, Wei Tong and Enhua Xia

Int. J. Mol. Sci. 2023, 24(2), 1478; https://doi.org/10.3390/ijms24021478 - 12 Jan 2023

Cited by 7 | Viewed by 1847

Abstract

Chilling stress threatens the yield and distribution pattern of global crops, including the tea plant (Camellia sinensis), one of the most important cash crops around the world. Circular RNA (circRNA) plays roles in regulating plant growth and biotic/abiotic stress responses. Understanding the evolutionary characteristics of circRNA and its feedbacks to chilling stress in the tea plant will help to elucidate the vital roles of circRNAs. In the current report, we systematically identified 2702 high-confidence circRNAs under chilling stress in the tea plant, and interestingly found that the generation of tea plant circRNAs was associated with the length of their flanking introns. Repetitive sequences annotation and DNA methylation analysis revealed that the longer flanking introns of circRNAs present more repetitive sequences and higher methylation levels, which suggested that repeat-elements-mediated DNA methylation might promote the circRNAs biogenesis in the tea plant. We further detected 250 differentially expressed circRNAs under chilling stress, which were functionally enriched in GO terms related to cold/stress responses. Constructing a circRNA-miRNA-mRNA interaction network discovered 139 differentially expressed circRNAs harboring potential miRNA binding sites, which further identified 14 circRNAs that might contribute to tea plant chilling responses. We further characterized a key circRNA, CSS-circFAB1, which was significantly induced under chilling stress. FISH and silencing experiments revealed that CSS-circFAB1 was potentially involved in chilling tolerance of the tea plant. Our study emphasizes the importance of circRNA and its preliminary role against low-temperature stress, providing new insights for tea plant cold tolerance breeding. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis of Horticulture Plants 2022)

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15 pages, 5497 KiB

Open AccessArticle

Genome-Wide Characterization and Evolutionary Expansion of Poplar NAC Transcription Factors and Their Tissue-Specific Expression Profiles under Drought

by Lu Meng, Siyuan Chen, Dawei Li, Minren Huang and Sheng Zhu

Int. J. Mol. Sci. 2023, 24(1), 253; https://doi.org/10.3390/ijms24010253 - 23 Dec 2022

Cited by 4 | Viewed by 2010

Abstract

The NAC (NAM, ATAF1/2 and CUC2) is a large gene family of plant-specific transcription factors that play a pivotal role in various physiological processes and abiotic stresses. Due to the lack of genome-wide characterization, intraspecific and interspecific synteny, and drought-responsive expression pattern of NAC genes in poplar, the functional characterization of drought-related NAC genes have been scarcely reported in Populus species. Here, we identified a total of 170 NAC domain-containing genes in the P. trichocarpa genome, 169 of which were unevenly distributed on its nineteen chromosomes. These NAC genes were phylogenetically divided into twenty subgroups, some of which exhibited a similar pattern of exon–intron architecture. The synteny and Ka/Ks analysis indicated that the expansion of NAC genes in poplar was mainly due to gene duplication events occurring before and after the divergence of Populus and Salix. Ten PdNAC (P. deltoids × P. euramericana cv.’Nanlin895’) genes were randomly selected and cloned. Their drought-responsive expression profiles showed a tissue-specific pattern. The transcription factor PdNAC013 was verified to be localized in the nucleus. Our research results provide genomic information for the expansion of NAC genes in the poplar genome, and for further characterizing putative poplar NAC genes associated with water-deficit. Full article

(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis of Horticulture Plants 2022)

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