Mengqin Hu’s research while affiliated with Guangdong Ocean University and other places

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Publications (4)


Phylogenetic analysis of Ipomoea species and Arabidopsis LEA proteins. The proteins were classed into LEA_1, LEA_2, LEA_3, LEA_4, LEA_5, LEA_6, SMP, and Dehydrin, represented by colors such as green, orange, yellow-green, blue, dark blue, red, purple, and pink, respectively. The red star icons, yellow check marks, blue check marks, green triangles, orange stars, blue triangles, purple triangles, and red check marks indicated IbLEAs in sweet potato, I. trifida, I. triloba, I. nil, I. purpurea, I. aquatica, I. cairica, and A. thaliana, respectively
Distribution of LEA genes across the chromosomes of the seven Ipomoea species. A Distribution in sweet potato (I. batatas). B Distribution in I. trifida. C Distribution in I. triloba. D Distribution in I. nil. E Distribution in I. purpurea. F Distribution in I. cairica. G Distribution in I. aquatica
Gene location and collinearity analysis of the LEA genes in Ipomoea species. The genes were located on different chromosomes. Duplicated gene pairs are linked with a colored line
Schematic representation of syntenic genes among sweet potato (I. batatas), I. trifida, I. triloba, I. nil, I. purpurea, I. cairica, and I. aquatica. The chromosomes of the seven Ipomoea species were reordered. Grey lines in the background indicate the collinear blocks within Ipomoea genomes, with LEA gene pairs highlighted in chromatic color
Phylogenetic tree, gene structure and motif compositions of LEA genes in Ipomoea species. The phylogenetic tree was constructed using IQtree. Different colors represent protein motif analysis, and a number represents each motif

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Comparative analysis of the LEA gene family in seven Ipomoea species, focuses on sweet potato (Ipomoea batatas L.)
  • Article
  • Full-text available

December 2024

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22 Reads

BMC Plant Biology

Mengqin Hu

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Zhenqin Li

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Xiongjian Lin

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[...]

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Hongbo Zhu

Late Embryogenesis Abundant (LEA) proteins are extensively distributed among higher plants and are crucial for regulating growth, development, and abiotic stress resistance. However, comprehensive data regarding the LEA gene family in Ipomoea species remains limited. In this study, we conducted a genome-wide comparative analysis across seven Ipomoea species, including sweet potato (I. batatas), I. trifida, I. triloba, I. nil, I. purpurea, I. cairica, and I. aquatica, identifying 73, 64, 77, 62, 70, 70, and 74 LEA genes, respectively. The LEA genes were divided into eight subgroups: LEA_1, LEA_2, LEA_3, LEA_4, LEA_5, LEA_6, SMP, and Dehydrin according to the classification of the LEA family in Arabidopsis. Gene structure and protein motif analyses revealed that genes within the same phylogenetic group exhibited comparable exon/intron structures and motif patterns. The distribution of LEA genes across chromosomes varied among the different Ipomoea species. Duplication analysis indicated that segmental and tandem duplications significantly contributed to the expansion of the LEA gene family, with segmental duplications being the predominant mechanism. The analysis of the non-synonymous (Ka) to synonymous (Ks) ratio (Ka/Ks) indicated that the duplicated Ipomoea LEA genes predominantly underwent purifying selection. Extensive cis-regulatory elements associated with stress responses were identified in the promoters of LEA genes. Expression analysis revealed that the LEA gene exhibited widespread expression across diverse tissues and showed responsive modulation to various abiotic stressors. Furthermore, we selected 15 LEA genes from sweet potatoes for RT-qPCR analysis, demonstrating that five genes responded to salt stress in roots, while three genes were responsive to drought stress in leaves. Additionally, expression changes of seven genes varied at different stages of sweet potato tuber development. These findings enhanced our understanding of the evolutionary dynamics of LEA genes within the Ipomoea genome and may inform future molecular breeding strategies for sweet potatoes.

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Comparative analysis of the LEA gene family in seven Ipomoea species focuses on sweet potato (Ipomoea batatas)

October 2024

·

23 Reads

Late Embryogenesis Abundant (LEA) proteins are extensively distributed among higher plants and are crucial for regulating growth, development, and abiotic stress resistance. However, comprehensive data regarding the LEA gene family in Ipomoea species remains limited. In this study, we conducted a genome-wide comparative analysis across seven Ipomoea species, including sweet potato ( I. batatas ), I. trifida , I. triloba , I. nil , I. purpurea , I. cairica , and I. aquatica , identifying 73, 64, 77, 62, 70, 70, and 74 LEA genes, respectively. The LEA genes were divided into eight subgroups: LEA_1, LEA_2, LEA_3, LEA_4, LEA_5, LEA_6, SMP, and Dehydrin according to the classification of the LEA family in Arabidopsis. Gene structure and protein motif analyses revealed that genes within the same phylogenetic group exhibited comparable exon/intron structures and motif patterns. The distribution of LEA genes across chromosomes varied among the different Ipomoea species. Duplication analysis indicated that segmental and tandem duplications significantly contributed to the expansion of the LEA gene family, with segmental duplications being the predominant mechanism. The analysis of the non-synonymous (Ka) to synonymous (Ks) ratio (Ka/Ks) indicated that the duplicated Ipomoea LEA genes predominantly underwent purifying selection. Extensive cis-regulatory elements associated with stress responses were identified in the promoters of LEA genes. Expression analysis revealed that the LEA gene exhibited widespread expression across diverse tissues and showed responsive modulation to various abiotic stressors. Furthermore, we selected 15 LEA genes from sweet potatoes for RT-qPCR analysis, demonstrating that five genes responded to salt stress in roots, while three genes were responsive to drought stress in leaves. Additionally, expression levels of seven genes varied at different stages of sweet potato tuber development. These findings enhanced our understanding of the evolutionary dynamics of LEA genes within the Ipomoea genome and may inform future molecular breeding strategies for sweet potatoes.


Figure 1. Chromosomal localization and distribution of I. batatas (a), I. trifida (b) and I. triloba (c). The bars represent chromosomes, with chromosome numbers on the left and gene names on the right. The number line on the left gives a visual view of chromosome length, and the number line on the left indicates species. Blue, yellow, and red represent the size of the gene density on the chromosome, from small to large, respectively.
Figure 5. Analysis of conserved motif, conserved domain, and exon-intron structure of GRF genes in I. batatas, I. trifida, and I. triloba. (a) The phylogenetic tree of IbGRFs, ItfGRFs, and ItbGRFs was constructed by the neighbor-joining method based on MEGA7.0 with 1000 bootstrap replicates. (b) The ten conserved motifs were shown in different colors. (c) The conserved domains were shown in 34 GRFs; the green and yellow boxes represent WRC and QLQ domains, respectively. (d) Exonintron structures of GRFs. The green boxes, yellow boxes, and black lines represent UTRs, exons, and introns, respectively.
Identification of IbGRFs and analysis of physicochemical properties of proteins in sweet potato.
Genome-Wide Identification and Expression Analysis of Growth-Regulating Factor Family in Sweet Potato and Its Two Relatives

August 2024

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20 Reads

Genes

Growth-regulating factor (GRF) is a multi-gene family that plays an important role in plant growth and development and is widely present in plants. Currently, GRF gene members have been reported in many plants, but the GRF gene family has not been found in sweet potato. In this study, ten GRF genes were identified in sweet potato (Ipomoea batatas), twelve and twelve were identified in its two diploid relatives (Ipomoea trifida) and (Ipomoea triloba), which were unevenly distributed on nine different chromosomes. Subcellular localization analysis showed that GRF genes of sweet potato, I. trifida, and I. triloba were all located in the nucleus. The expression analysis showed that the expression of IbGRFs was diverse in different sweet potato parts, and most of the genes were upregulated and even had the highest expression in the vigorous growth buds. These findings provide molecular characterization of sweet potato and its two diploid relatives, the GRF families, further supporting functional characterization.