A transcriptomics investigation into pine reproductive organ development

Niu, Shihui; Yuan, Huwei; Sun, Xinrui; Porth, Ilga; Li, Yue; El‐Kassaby, Yousry A.; Li, Wei

doi:10.1111/nph.13680

Cited by 40 publications

(44 citation statements)

References 65 publications

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“…Likewise, SOC1 and SOC1‐like annotated P. glauca genes, WS0056_A03 and WS00922_C06, respectively, are homologs of P. abies DAL3 (PaMADS7_DAL3; Melzer et al ., ). Functional analysis of CjMADS14 , the Cryptomeria japonica ortholog of P. abies DAL1 , and CjMADS15 , the C. japonica ortholog of P. abies DAL3 , indicated that expression of DAL1 is specific to the reproductive organs (and its function is related to suppressing reproductive repressors), whereas expression of DAL3 is more ubiquitous but included male and female strobili (Katahata et al ., ; Niu et al ., ).…”

Section: Discussionmentioning

confidence: 97%

Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce

et al. 2018

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In plants, there can be a trade-off between resource allocations to growth vs defense. Here, we use partial correlation analysis of gene expression to make inferences about the nature of this interaction. We studied segregating progenies of Interior spruce subject to weevil attack. In a controlled experiment, we measured pre-attack plant growth and post-attack damage with several morphological measures, and profiled transcriptomes of 188 progeny. We used partial correlations of individual transcripts (expressed sequence tags, ESTs) with pairs of growth/defense traits to identify important nodes and edges in the inferred underlying gene network, for example, those pairs of growth/defense traits with high mutual correlation with a single EST transcript. We give a method to identify such ESTs. A terpenoid ABC transporter gene showed strongest correlations (P = 0.019); its transcript represented a hub within the compact 166-member gene-gene interaction network (P = 0.004) of the negative genetic correlations between growth and subsequent pest attack. A small 21-member interaction network (P = 0.004) represented the uncovered positive correlations. Our study demonstrates partial correlation analysis identifies important gene networks underlying growth and susceptibility to the weevil in spruce. In particular, we found transcripts that strongly modify the trade-off between growth and defense, and allow identification of networks more central to the trade-off.

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Section: Discussionmentioning

confidence: 97%

Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce

et al. 2018

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“…Wang et al (2001Wang et al ( , 2004, Li et al (2008), and Zhang and Liu (2015) conducted partial studies on the external morphological, reproductive and reproductive biology characteristics of P. massoniana polycone. Niu et al (2016) studied the gene expression of the unisexual and heterotypic bisexual flowers on polycone type P. tabuliformis. Using the male flowers which were gradually changing into the female flowers as experimental material, they found that the transcription of the male flower part of the bisexual flower was more similar to the normal female flower.…”

Section: Discussionmentioning

confidence: 99%

“…Franco (Pullman et al, 2005), Pinus tabuliformis Carr. (Niu et al, 2013(Niu et al, , 2016; Pinus thunbergii Parl. (Kong et al, 2012), Pinus bungeana Zucc.…”

Section: Introductionmentioning

confidence: 99%

Initiation and Development of Sex Reversal and Ovule Abortion Process of Pinus massoniana Polycone Strobilu

Zhao¹

2018

IJAB

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This paper describes the morphological and microstructure of Pinus massoniana strobilus. The result revealed two distinct development processes of the polycone. The first process was seen during the strobilus differentiation stage of P. massoniana. It occurred from August and synchronized with the starting time of the normal microstrobili development to the end of December, with strings of reproductive primordia on the terminal buds. During this period, not only the visible microstrobili were shown, but also the megastrobilum, characterized bracts and ovuliferous scales appeared. Even strings of megastrobilum primordia grew at the base of the terminal buds. The second process was seen during the sex reversal of the development of the microstrobilus. The terminal buds differentiated and developed in the form of microstrobilus till mid-March next year. In the next 10 days or so, the microsporangia changed into bracts and ovuliferous scales of the megastrobilus basipetally. By the end of March, the microstrobili were entirely converted to megastrobili and the female "polycone" formed. Besides, ovule abortion was observed during the development of female gametophyte of the polycone. In mid-April, the number of free nuclei of ovules in the female gametophyte of polycone began to decrease and the center gradually became empty. At the beginning of May, the free nuclei of the normal ovules began to cellize, but the free nuclei of the aborted ovules in the polycone virtually disappeared and only the cavity was visible.

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“…Yet until now few studies have focused on the development of Pinus reproductive organs. In Pinus tabuliformis, unusual bisexual cones were found; here, the gene expression pattern of MADS-box transcription factors, FT/TFL1-like and LFY/NDLY genes was compared between unisexual and bisexual cones [52]. In Pinus bungeana, 39.62 Gb of RNA sequencing data was analyzed from two kinds of sexual cones, obtaining 85,305 unigenes, 53,944 (63.23%) of which were annotated in public databases [53].…”

Section: Gymnosperm Gene Annotation Using Transcriptome Datamentioning

confidence: 99%

Pinus massoniana Introgression Hybrids Display Differential Expression of Reproductive Genes

Cao

et al. 2019

Forests

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Pinus massoniana and P. hwangshanensis are two conifer species located in southern China, which are of both economic and ornamental value. Around the middle and lower reaches of the Yangtze River, P. massoniana occurs mainly at altitudes below 700 m, while P. hwangshanensis can be found above 900 m. At altitudes where the distribution of both pines overlaps, a natural introgression hybrid exists, which we will further refer to as the Z pine. This pine has a morphological character that shares attributes of both P. massoniana and P. hwangshanensis. However, compared to the other two pines, its reproductive structure, the pinecone, has an ultra-low ripening rate with seeds that germinate poorly. In this study, we aimed to find the reason for the impaired cone maturation by comparing transcriptome libraries of P. massoniana and Z pine cones at seven successive growth stages. After sequencing and assembly, we obtained unigenes and then annotated them against NCBI’s non-redundant nucleotide and protein sequences, Swiss-Prot, Clusters of Orthologous Groups, Gene Ontology and KEGG Orthology databases. Gene expression levels were estimated and differentially expressed genes (DEGs) of the two pines were mined and analyzed. We found that several of them indeed relate to reproductive process. At every growth stage, these genes are expressed at a higher level in P. massoniana than in the Z pine. These data provide insight into understanding which molecular mechanisms are altered between P. massoniana and the Z pine that might cause changes in the reproductive process.

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A transcriptomics investigation into pine reproductive organ development

Cited by 40 publications

References 65 publications

Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce

Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce

Initiation and Development of Sex Reversal and Ovule Abortion Process of Pinus massoniana Polycone Strobilu

Pinus massoniana Introgression Hybrids Display Differential Expression of Reproductive Genes

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