Evolutionary Analysis of MIKCc-Type MADS-Box Genes in Gymnosperms and Angiosperms

Chen, Fei; Zhang, Xingtan; Liu, Xing; Zhang, Liangsheng

doi:10.3389/fpls.2017.00895

Cited by 55 publications

(48 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Phylogenetic analysis revealed that these ten genes were highly conserved evolutionarily. However, no AP1/FUL (A-type genes) subfamily genes were identi ed in this study, and the number of MIKC-type MADS-box genes was lower in L. chinense less than in A. thaliana, P. trichocarpa and Amborella trichopoda [94]. In actuality, L. chinense originated earlier than A. thaliana and P. trichocarpa but later than A. trichopoda, and in angiosperms, the number of ABCE-type genes has increased [7,94].…”

Section: Discussioncontrasting

confidence: 55%

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Tu¹,

Shen²,

Wen³

et al. 2020

Preprint

View full text Add to dashboard Cite

Background Liriodendron chinense (Hemsl.) Sarg. is an economically and ecologically important deciduous tree species that has been studied for many years. Although the complete L. chinense genome has been sequenced, the gene co-expression modules and tissue-specific genes of L. chinense remain unknown. Results Here, we used the bracts, petals, sepals, stamens, pistils, leaves, and the shoot apex of L. chinense as materials and analysed their gene co-expression modules and tissue-specific genes via hybrid sequencing. We identified 3,032 DEGs between the floral and vegetative tissues and 2,126 tissue-specific genes. By using WGCNA analysis, we identified 13 gene co-expression modules, and KEGG pathway enrichment analysis revealed that tissue-specific genes and genes from different modules were enriched in different pathways. Genes associated with plant defence were highly expressed in the bracts, genes participating in plant hormone signal transduction were highly expressed in the shoot apex, and genes participating in photosynthesis were highly expressed in the leaves, petals and sepals. Moreover, we identified 10 MIKC-type MADS-box genes that were classified as member of the AP3/PI, SVP, SEP, AG/SHP/STK, AGL12, SOC1 and TM8 subfamily. Phylogenetic analysis showed that the expression profiles of these ten genes were consistent with those reported in Arabidopsis and Populus , indicating that these genes are highly conserved evolutionarily and related to floral and vegetative tissue development. The small number of MIKC-type MADS-box genes in L. chinense was probably owing to its incomplete genome annotation. Conclusions In this work, we provided a reference transcriptome for L. chinense research by using hybrid sequencing. We identified 2,126 tissue-specific genes and 3,032 DEGs that contributed greatly to the functional differences between vegetative organs and floral organs. By using WGCNA analysis, 13 gene co-expression modules and 52 hub genes from six co-expression modules of interest were identified. Moreover, we identified 10 MIKC-type MADS-box genes that might be related to the development and growth regulation of floral and vegetative organs. These findings will improve our understanding of gene co-expression, tissue specific genes and flower development model of L. chinense .

show abstract

Section: Discussioncontrasting

confidence: 55%

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Tu¹,

Shen²,

Wen³

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Then, FastTree software was used to establish phylogenetic tree using 1,000 resamples, and constructed by maximum-likelihood using the JTT + CAT model. FastTree provides local support values by the Shimodaira-Hasegawa (SH) test, the resulting support values were closely correlated with the traditional bootstrap ( r = 0.975) ( Price et al, 2010 ; Chen et al, 2017 ). The local support values below 60 are hidden in the constructed tree.…”

Section: Methodsmentioning

confidence: 88%

Genome-Wide Identification and Expression Profiling of ATP-Binding Cassette (ABC) Transporter Gene Family in Pineapple (Ananas comosus (L.) Merr.) Reveal the Role of AcABCG38 in Pollen Development

Chen

Zhao

et al. 2017

Front. Plant Sci.

View full text Add to dashboard Cite

Pineapple (Ananas comosus L.) cultivation commonly relies on asexual reproduction which is easily impeded by many factors in agriculture production. Sexual reproduction might be a novel approach to improve the pineapple planting. However, genes controlling pineapple sexual reproduction are still remain elusive. In different organisms a conserved superfamily proteins known as ATP binding cassette (ABC) participate in various biological processes. Whereas, till today the ABC gene family has not been identified in pineapple. Here 100 ABC genes were identified in the pineapple genome and grouped into eight subfamilies (5 ABCAs, 20 ABCBs, 16 ABCCs, 2 ABCDs, one ABCEs, 5 ABCFs, 42 ABCGs and 9 ABCIs). Gene expression profiling revealed the dynamic expression pattern of ABC gene family in various tissues and different developmental stages. AcABCA5, AcABCB6, AcABCC4, AcABCC7, AcABCC9, AcABCG26, AcABCG38 and AcABCG42 exhibited preferential expression in ovule and stamen. Over-expression of AcABCG38 in the Arabidopsis double mutant abcg1-2abcg16-2 partially restored its pollen abortion defects, indicating that AcABCG38 plays important roles in pollen development. Our study on ABC gene family in pineapple provides useful information for developing sexual pineapple plantation which could be utilized to improve pineapple agricultural production.

show abstract

“…The recent genome comparisons indicate that male ‘BC’ and female ‘C’ systems already existed to specify reproductive cells in gymnosperm cones, and they were duplicated via the ε WGD, after which the C duplicates diversified into angiosperm C and D genes. An A/E gymnosperm pro-orthologue gave rise to angiosperm A and E genes, and further duplicated A genes were also retained after the ε WGD 19 , 21 – 24 . These duplicated and diversified gene sets organised to generate the first now-extinct flowers, and recent reconstructions suggest that these were bisexual with petal-like tepals and pollen-bearing stamens arranged in multiple concentric whorls, and female carpels in a central spiral 25 .…”

Section: Contributions Of Whole-genome Duplications To the Origin Andmentioning

confidence: 99%

Recent advances in understanding the roles of whole genome duplications in evolution

MacKintosh

Ferrier

2018

F1000Res

View full text Add to dashboard Cite

Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life.

show abstract

Evolutionary Analysis of MIKCc-Type MADS-Box Genes in Gymnosperms and Angiosperms

Cited by 55 publications

References 29 publications

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Genome-Wide Identification and Expression Profiling of ATP-Binding Cassette (ABC) Transporter Gene Family in Pineapple (Ananas comosus (L.) Merr.) Reveal the Role of AcABCG38 in Pollen Development

Recent advances in understanding the roles of whole genome duplications in evolution

Contact Info

Product

Resources

About