| 1. |
- Akhter, Shirin, et al.
(author)
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Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway
- 2022
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In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 236:5, s. 1951-1963
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Journal article (peer-reviewed)abstract
- Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.
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| 2. |
- Akhter, Shirin, et al.
(author)
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Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies
- 2018
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In: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 9
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Journal article (peer-reviewed)abstract
- Recent efforts to sequence the genomes and transcriptomes of several gymnosperm species have revealed an increased complexity in certain gene families in gymnosperms as compared to angiosperms. One example of this is the gymnosperm sister Glade to angiosperm TM3-like MADS-box genes, which at least in the conifer lineage has expanded in number of genes. We have previously identified a member of this subclade, the conifer gene DEFICIENS AGAMOUS LIKE 19 (DAL19), as being specifically upregulated in cone-setting shoots. Here, we show through Sanger sequencing of mRNA-derived cDNA and mapping to assembled conifer genomic sequences that DAL19 produces six mature mRNA splice variants in Picea abies. These splice variants use alternate first and last exons, while their four central exons constitute a core region present in all six transcripts. Thus, they are likely to be transcript isoforms. Quantitative Real-Time PCR revealed that two mutually exclusive first DAL19 exons are differentially expressed across meristems that will form either male or female cones, or vegetative shoots. Furthermore, mRNA in situ hybridization revealed that two mutually exclusive last DAL19 exons were expressed in a cell-specific pattern within bud meristems. Based on these findings in DAL19, we developed a sensitive approach to transcript isoform assembly from short-read sequencing of mRNA. We applied this method to 42 putative MADS-box core regions in P abies, from which we assembled 1084 putative transcripts. We manually curated these transcripts to arrive at 933 assembled transcript isoforms of 38 putative MADS-box genes. 152 of these isoforms, which we assign to 28 putative MADS-box genes, were differentially expressed across eight female, male, and vegetative buds. We further provide evidence of the expression of 16 out of the 38 putative MADS-box genes by mapping PacBio Iso-Seq circular consensus reads derived from pooled sample sequencing to assembled transcripts. In summary, our analyses reveal the use of mutually exclusive exons of MADS-box gene isoforms during early bud development in P. abies, and we find that the large number of identified MADS-box transcripts in P. abies results not only from expansion of the gene family through gene duplication events but also from the generation of numerous splice variants.
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| 3. |
- Akhter, Shirin
(author)
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Molecular mechanisms regulating early cone development in Norway spruce Picea abies (Karst)
- 2019
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Doctoral thesis (other academic/artistic)abstract
- Flower development progress through distinct phases that are controlled by complex genetic networks, which in turn are regulated by both endogenous and exogenous factors. A large number of functional studies have been conducted over the past decades to understand the genetic networks that regulate flower development in angiosperm model species. In gymnosperms, however, the gene regulatory networks behind distinct phases of cone development are largely unknown due to the lack of functional studies. In a morphological study of early cone development in Picea abies, three distinct growth phases were defined. Transcriptome comparisons of female and vegetative buds in the three growth phases identified members of the MADS-box gene family, LEAFY-orthologs, bZIP- , AP2-, and SBP-domain proteins as being highly expressed in the different phases of female cone development. In a separate study different isoform of the MADS-box gene, DAL19 were identified. Isoforms specific expression in male, female and vegetative bud meristems provided evidence that alternative splicing may influence cone formation in a bud identity specific manner. In the early cone-setting acrocona mutant, P. abies var. acrocona, leading shoots often have needles at the base, but ovuliferous scale-like structures in the top. Hence, during shoot development, the leading shoots make a morphological shift and produce transition shoots. RNA sequencing of acrocona transition shoots demonstrated that the MADS-box genes DAL10 and DAL21, which previously have been associated with reproductive shoot identity were expressed at high levels in transition shoot meristems before the morphological shift. In addition, genes encoding FT/TFL-like, bZIP-, SOC1-like and gymnosperm specific MADS-domain proteins co-expressed with DAL10 and DAL21, suggesting at a putative role for these genes in the early development of reproductive meristems. In addition, genes encoding F-box protein and ubiquitin were expressed at high levels in late acrocona transition shoots, which possibly reflects an involvement of hormonal signalling in the acrocona transition shoot phenotype.
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| 4. |
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| 5. |
- Akhter, Shirin, et al.
(author)
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Transcriptome studies of the early cone-setting acrocona mutant provide evidence for a functional conservation of the age-dependent flowering pathway between angiosperms and gymnosperms.
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Other publication (other academic/artistic)abstract
- All seed plants go through a juvenile period before they initiate seed- and pollen-bearing organs and reproduce. Reproductive phase-change is well characterized in angiosperm model species, but much less well described in gymnosperms. Here, we utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies; a representative of the gymnosperm lineage. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. By sequence analysis of mRNA and microRNA transcripts, we demonstrate that orthologous components of the Age-dependent flowering pathway are active at the time of cone initiation. We show that a member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL7, is active in reproductive meristems, whereas a putative negative regulator of PaSPL7, microRNA156 is upregulated in vegetative meristem. By allele-specific assembly, we also identify a short nucleotide polymorphism (SNP) in the miRNA156 binding of PaSPL7. By genotyping a segregating population of inbred acrocona trees, we show a clear co-segregation between the early cone-setting phenotype and trees homozygous for the SNP. Hence, the data presented demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating cone-setting in the conifer P. abies.
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| 6. |
- Uddenberg, Daniel, et al.
(author)
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Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology
- 2015
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In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 6
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Research review (peer-reviewed)abstract
- Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right.
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