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Expansion and evolutionary patterns of GDSL-type esterases/lipases in Rosaceae genomes

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Abstract

GDSL-type esterase/lipase (GELP) is mainly characterized by a conserved GDSL domain at N terminus, and is widely found in all living species, both prokaryotes and eukaryotes. GELP gene family consists of a wide range of members playing important roles in plant physiological processes, such as development, stress responses, and functional divergences. In our study, 597 GELP genes were identified from six Rosaceae genomes (i.e., Fragaria vesca, Prunus persica, Prunus avium, Prunus mume, Pyrus bretschneideri, and Malus domestica) by a comprehensive analysis. All GELP genes were further divided into ten subfamilies based on phylogenetic tree analysis. Subfamily D and subfamily E are the two largest subfamilies. Microcollinearity analysis suggested that WGD/segmental events contribute to the expansion of the GELP gene family in M. domestica and P. bretschneideri compared to F. vesca, P. persica, P. avium, and P. mume. Some PbGELPs were expressed during the fruit development of P. bretschneideri and pollen tubes, indicating their activity in these tissues. The expression divergence of PbGELP duplication gene pairs suggests that many mutations were allowed during evolution, although the structure of GELP genes was highly conserved. The current study results provided the feasibility to understand the expansion and evolution patterns of GELP in Rosaceae genomes, and highlight the function during P. bretschneideri fruits and pollen tubes development.

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Acknowledgments

We extend our thanks to the reviewers and editors for their careful reading and helpful comments on this manuscript.

Funding

This study was supported by The National Natural Science Foundation of China (grant 31640068).

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Authors and Affiliations

  1. School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China

    Yunpeng Cao, Dandan Meng, Muhammad Abdullah, Jiangliu Yu, Dahui Li, Qing Jin, Yi Lin & Yongping Cai

  2. State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China

    Yahui Han

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  1. Yunpeng Cao
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  2. Yahui Han
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  3. Dandan Meng
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  4. Muhammad Abdullah
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  7. Qing Jin
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Contributions

YCao designed and performed the experiments. YCao, DM, and YH analyzed the data. YH, DM, YL, QJ, DL, JY, YCao, AM, and YCai contributed reagents/materials/analysis tools. YCao and YH wrote the paper. All authors reviewed and approved this submission.

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Correspondence to Yongping Cai.

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Figure S1

The Maximum Likelihood tree for GELP genes identified among the six Rosaceae genomes. Totally, 597 GELP genes were divided into ten subfamilies (A-J), and were indicated by different colors. (PNG 699 kb)

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Figure S2

The phylogenetic tree for GELP genes identified in six Rosaceae genomes. Subfamilies are numbered at the right part of the ML tree and marked with alternating tones to facilitate subfamily identification. (PNG 4633 kb)

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(TIF 6556 kb)

Figure S3

Motif logo of four conserved blocks found in Rosaceae GELP proteins: I (a), II (b), III (c), and V (d). The red triangles indicate conserved residues Ser-Gly-Asn-His in blocks. In the present study, the full-length GELP protein sequences were submitted to MEME website to scan conserved motifs in these proteins, based on previous research manuscripts (Dong et al. 2016). (PNG 1060 kb)

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Figure S4

Exon–intron structure analysis of Rosaceae GELP genes. The scale represents the length of the DNA sequence. Legend is at the top right of the Figure. (PNG 3048 kb)

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(TIF 4507 kb)

Figure S5

Heat map of P. bretschneideri GELP genes in different tissues, including MP (Mature pollen grains), HP (Hydrated pollen grains), PT (Pollen tube), SPT (Stop-growth pollen tube), fruit_stage1 (15 days after full blooming (DAB)), fruit_stage2 (30 DAB), fruit_stage3 (55 DAB), fruit_stage4 (85 DAB), fruit_stage5 (115 DAB), fruit_stage6 (mature stage), and fruit_stage7 (fruit senescence stage), and PbGELP gene expression levels in different conditions, including pear leaf with inoculated distilled water (Leaf_CK), pear leaf with inoculated black spot (Alternarlia alternate) 2 (Leaf_T2), pear leaf with inoculated black spot (Alternarlia alternate) 3 (Leaf_T3), pear fruit with no any treatment (Fruit_CK), pear fruit with Gibberellins treatment (Fruit_GA), pear with salt treatment (Leaf_Salt), pear fruit pericarp-russet (pericarp-russet), and pear fruit pericarp-green (pericarp-green). Blue and red colors correspond to down-regulation and up-regulation, respectively. (PNG 210 kb)

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Figure S6

The Maximum likelihood tree of GELP genes in six Rosaceae species, Arabidopsis and rice. (PDF 87 kb)

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Cao, Y., Han, Y., Meng, D. et al. Expansion and evolutionary patterns of GDSL-type esterases/lipases in Rosaceae genomes. Funct Integr Genomics 18, 673–684 (2018). https://doi.org/10.1007/s10142-018-0620-1

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