Article
Plant Sciences
Jia-Yi Wu, Jia-Yu Xue, Yves Van de Peer
Summary: The evolution of NLR genes in magnoliids is mainly driven by tandem duplication, with most magnoliids showing a pattern of initial expansion followed by contraction and then further expansion. Transcriptome analysis revealed low expression of most NLR genes in Saururus chinensis, with some R genes showing relatively higher expression in roots and fruits.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Yun-Hai Lu, Intikhab Alam, Yan-Qing Yang, Ya-Cen Yu, Wen-Chao Chi, Song-Biao Chen, Boulos Chalhoub, Li-Xi Jiang
Summary: The YABBY gene family, present in all seed plants, plays crucial roles in plant growth and development, including polarity establishment, leaf and flower formation, and response to hormonal signals and environmental stress. Through identification of 364 YABBY genes in 37 Brassicaceae genomes, it was found that these genes are largely conserved across species but exhibit considerable functional divergence.
Article
Fisheries
Shang Geng, Tianjun Xu, Yuena Sun
Summary: In this study, we identified 27 ChemR genes in miiuy croaker and analyzed their characteristics, including gene structure, evolutionary mechanism, and expression levels upon bacterial infection. The results showed that these genes underwent tandem and segmental duplication events during evolution, and teleost fishes' ChemRs may have a higher evolutionary dynamic compared to vertebrates. Additionally, 21 positively selected codons were detected in vertebrate ChemRs under Model 8, and certain genes were significantly up-regulated upon Vibrio harveyi infection, providing valuable information for further functional analysis.
FISH & SHELLFISH IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xiaoming Song, Nan Li, Yingchao Zhang, Yi Liang, Rong Zhou, Tong Yu, Shaoqin Shen, Shuyan Feng, Yu Zhang, Xiuqing Li, Hao Lin, Xiyin Wang
Summary: Through transcriptomics and genomics analysis, this study identified and analyzed the genes related to chlorophyll and carotenoid in celery and other species. The study found that transcription factors play a role in regulating the expression of these genes. Expansion of carotenoid-related genes was observed in celery, while no notable expansion was found in chlorophyll biosynthesis genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agronomy
Xinhui Zhang, Weicheng Yuan, Yujie Zhao, Yuan Ren, Xueqing Zhao, Zhaohe Yuan
Summary: Gene duplication is the major resource for generating new genes and understanding the evolution of gene families after duplication events is crucial. AOMTs play a role in anthocyanin methylation, but detailed identification and analysis of the AOMT gene family in pomegranate have not been reported. The PgAOMT family evolved primarily through whole-genome duplication and tandem duplication.
Article
Biochemical Research Methods
Chaitanya Aluru, Mona Singh
Summary: The study introduces a reconciliation-based framework that considers the relative positions of protein domains within extant sequences to uncover tandem domain duplications accurately. By developing an integer linear programming approach and a heuristic algorithm, the researchers are able to identify single and tandem domain duplication events with high accuracy. Through extensive simulation studies and testing on an orthogroup with complex domain duplication patterns, the effectiveness of the approach is demonstrated.
Article
Plant Sciences
Leonardo Bruno, Matteo Ronchini, Giorgio Binelli, Antonella Muto, Adriana Chiappetta, Maria Beatrice Bitonti, Paolo Gerola
Summary: Gene duplication is a vital process in the evolution of eukaryotes, leading to the presence of multiple copies of a gene with differentiated expressions and functions. To test this hypothesis, the expression domains of three beta-glucuronidase genes (AtGUS) in Arabidopsis thaliana were compared with the GUS evolutionary tree in angiosperms. The study confirmed that the differentiation of gene copies can be indicated by their maintenance in all derived species. The results also revealed the presence of different clusters of gene copies originating from ancient duplication events.
Article
Genetics & Heredity
Xiaohui Liang, Junming Dong
Summary: This study investigates the evolutionary patterns of NLR genes in the Apiaceae family by performing comparative genomic analysis on four species. The results reveal different NLR gene numbers and patterns of gene loss and gain in these species. The ancestral NLR genes in Daucus carota show a contraction pattern, while A. sinensis, C. sativum, and A. graveolens display a different contraction pattern after an initial expansion of NLR genes.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Qiaoying Pei, Tong Yu, Tong Wu, Qihang Yang, Ke Gong, Rong Zhou, Chunlin Cui, Ying Yu, Wei Zhao, Xi Kang, Rui Cao, Xiaoming Song
Summary: The study identified a total of 73 Hsf genes in three representative Apiaceae species and revealed the role of whole-genome duplication in the expansion of the Hsf gene family within Apiaceae. Coriander was found to have more Hsf genes than celery and carrot, with considerable positive selection identified in 27 branches of the phylogenetic tree in these Apiaceae species. This research will guide future comparative and functional genomic studies on the Hsf gene family and others in Apiaceae.
HORTICULTURAL PLANT JOURNAL
(2021)
Article
Plant Sciences
Tao Tong, Yun-xia Fang, Ziling Zhang, Junjun Zheng, Xian Zhang, Jia Li, Chunyu Niu, Dawei Xue, Xiaoqin Zhang
Summary: This study characterized the KCS gene family in barley using genome sequences, identifying 33 KCS genes unevenly distributed in the genome. These genes were divided into 12 subgroups with diverse tissue expression patterns and overlapping functions. Barley KCS genes exhibited different response characteristics under drought stress.
PLANT GROWTH REGULATION
(2021)
Article
Biochemistry & Molecular Biology
Colin J. Shew, Paulina Carmona-Mora, Daniela C. Soto, Mira Mastoras, Elizabeth Roberts, Joseph Rosas, Dhriti Jagannathan, Gulhan Kaya, Henriette O'Geen, Megan Y. Dennis
Summary: Evidence shows that in humans, paralogous segmental duplication genes exhibit different expression patterns, possibly due to relaxed selection or neofunctionalization. While ancestral paralogs show greater expression conservation with chimpanzee orthologs, certain derived paralogs may retain or supplant ancestral functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Ivan Rodrigo Wolf, Rafael Plana Simoes, Guilherme Targino Valente
Summary: The study reveals that K-nn, page rank, and degree are the most relevant topological features in GRNs, significantly influencing the control of life-essential subsystems. The importance of transcription factors in biological systems depends mainly on K-nn and page rank or degree. Gene/genome duplication is a crucial evolutionary process that enhances K-nn as the most relevant feature.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Xiaowen Shang, Zhaolan Han, Dayan Zhang, Ya Wang, Hao Qin, Zhongwei Zou, Lin Zhou, Xujun Zhu, Wanping Fang, Yuanchun Ma
Summary: TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors are important for controlling cell growth and proliferation in plants. The CsTCP genes in tea plants can be divided into two classes, with different structures and functions. The expansion of the gene family is mainly caused by gene duplication and repetitive events. CsTCP genes in different groups show differences in response to external stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Wenjing Tao, Ruiying Li, Tingting Li, Zhimin Li, Yihan Li, Licao Cui
Summary: Gene duplication, resulting from various mechanisms, plays a crucial role in expanding gene families and can contribute to species formation and adaptive evolution. This study focused on barley and identified 214 significantly expanded gene families. The expanded genes showed faster evolutionary rates, smaller sizes, lower selection pressure, and distinct expression patterns compared to non-expanded genes. Several stress-response-related genes/gene families were discovered, offering potential for breeding stress-resistant barley plants.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Dongna Ma, Qiansu Ding, Zejun Guo, Zhizhu Zhao, Liufeng Wei, Yiying Li, Shiwei Song, Hai-Lei Zheng
Summary: This study systematically analyzed the aegiceras-specific genes (ASGs) in Aegiceras corniculatum, revealing their origin mainly from gene duplication and characteristics in gene structure and expression patterns. ASGs are mainly involved in pathways related to adversity stress, including plant hormone signal transduction and photosynthesis, and exhibit co-expression relationships in gene modules.
MOLECULAR GENETICS AND GENOMICS
(2021)
