Origin, evolution, and molecular function of DELLA proteins in plants

Gibberellic acid(GA), a ubiquitous phytohormone, has various effects on regulators of plant growth and development. GAs promote growth by overcoming growth restraint mediated by DELLA proteins(DELLAs). DELLAs, in the GRAS family of plant-specific nuclear proteins, are nuclear transcriptional regulators harboring a unique N-terminal GA perception region for binding the GA receptor GIBBERELLIN INSENSITIVE DWARF1(GID1) and a C-terminal GRAS domain necessary for GA repression activity via interaction with multiple regulatory proteins. The N-terminal conserved region of DELLAs evolved to form a mode of GID1/DELLA-mediated GA signaling originating in bryophytes and ferns. Binding of GA to GID1 increases the affinity between DELLAs and a SCF E3 ubiquitin–ligase complex, thus promoting the eventual destruction of DELLAs by the 26 S proteasome. DELLAs negatively regulate GA response by releasing transcription factors to directly activate downstream genes and indirectly regulate GA biosynthesis genes increasing GA responsiveness and feedback control by promoting GID1 transcription. GA communicates extensively with other plant hormones and uses crosstalk to regulate plant growth and development. In this review, we summarize current understanding of evolutionary DELLA-mediated gibberellin signaling and functional diversification of DELLA, focusing primarily on interactions of DELLAs with diverse phytohormones.

Cotton BLH1 and KNOX6 antagonistically modulate fiber elongation via regulation of linolenic acid biosynthesis

BEL1-LIKE HOMEODOMAIN(BLH)proteins are known to function in various plant developmental processes.However,the role of BLHs in regulating plant cell elongation is still unknown.Here,we identify a BLH gene,GhBLH1,that positively regulates fiber cell elongation.Combined transcriptomic and biochemical analyses reveal that GhBLH1 enhances linolenic acid accumulation to promote cotton fiber cell elongation by activating the transcription of GhFAD7A-1 via binding of the POX domain of GhBLH1 to the TGGA cis-element in the GhFAD7A-1 promoter.Knockout of GhFAD7A-1 in cotton significantly reduces fiber length,whereas overexpression of GhFAD7A-1 results in longer fibers.The K2 domain of GhKNOX6 directly interacts with the POX domain of GhBLH1 to form a functional heterodimer,which interferes with the transcriptional activation of GhFAD7A-1 via the POX domain of GhBLH1.Overexpression of GhKNOX6 leads to a significant reduction in cotton fiber length,whereas knockout of GhKNOX6 results in longer cotton fibers.An examination of the hybrid progeny of GhBLH1 and GhKNOX6 transgenic cotton lines provides evidence that GhKNOX6 negatively regulates GhBLH1-mediated cotton fiber elongation.Our results show that the interplay between GhBLH1 and GhKNOX6 modulates regulation of linolenic acid synthesis and thus contributes to plant cell elongation.

Single-Nucleotide Resolution Mapping of the Gossypium raimondii Transcriptome Reveals a New Mechanism for Alternative Splicing of Introns

Alternative splicing （AS） is a vital genetic mechanism that enhances the diversity of eukaryotic transcriptomes. Here, we generated 8.3 Gb high-quality RNA-sequencing data from cotton （Gossypium raimondii） and performed a systematic, comparative analysis of AS events. We mapped 85% of the RNA-sequencing data onto the reference genome and identified 154 368 splice junctions with 16 437 as events in 10197 genes. I ntron retention constituted the majority （40%） of all AS events in G. raimondii. Comparison across 11 eukaryote species showed that intron retention is the most common AS type in higher plants. Although transposable elements （TEs） were found in only 2.9% of all G. raimondii introns, they are present in 43% of the retained introns, suggesting that TE-insertion may be an important mechanism for intron retention during AS. The majority of the TE insertions are concentrated 0-40 nt upstream of the 3＇-splice site, substantially altering the distribution of branch points from preferred positions and reducing the efficiency of intron splicing by decreasing RNA secondary structure flexibility. Our data suggest that TE-insertion-induced changes in branch point-site distribution are important for intron retention-type AS. Our findings may help explain the vast differences in intron-retention frequencies between vertebrates and higher plants.

Using Genome-Referenced Expressed Sequence Tag Assembly to Analyze the Origin and Expression Patterns of Gossypium hirsutum Transcripts

We assembled a total of 297,239 Gossypium hirsutum （Gh, a tetraploid cotton, AADD） expressed sequence tag （EST） sequences that were available in the National Center for Biotechnology Information database, with reference to the recently published G. raimondii （Gr, a diploid cotton, DD） genome, and obtained 49,125 UniGenes. The average lengths of the U niGenes were increased from 804 and 791 bp in two previous EST assemblies to 1,019 bp in the current analysis. The number of putative cotton UniGenes with lengths of 3 kb or more increased from 25 or 34 to 1,223. As a result, thousands of originally independent G. hirsutum ESTs were aligned to produce large contigs encoding transcripts with very long open reading frames, indicating that the G. raimondii genome sequence provided remarkable advantages to assemble the tetraploid cotton transcriptome. Significant different distribution patterns within several GO terms, including transcription factor activity, were observed between D- and A-derived assemblies. Tran- scriptome analysis showed that, in a tetraploid cotton cell, 29,547 UniGenes were possibly derived from the D subgenome while another 19,578 may come from the A subgenome. Finally, some of the in silico data were confirmed by reverse transcription polymerase chain reaction experiments to show the changes in transcript levels for several gene families known to play key role in cotton fiber development. We believe that our work provides a useful platform for functional and evolutionary genomic studies in cotton.

In vivo immunomodulatory alleviating effects of animal milk oligosaccharides on murine NEC:A study

Human milk oligosaccharides may mediate prebiotic and anti-inflammatory effects on newborns.It is essential for preterm infants susceptible to intestinal dysfunction and necrotizing enterocolitis(NEC).However,the infant breastfeeding rate remains low,and there is still a great demand for suitable substitutes for HMOs prebiotic effect.In this paper,we study the new molecular insights of the protective mechanism of four animal milk ol-igosaccharides against developing experimental NEC from the perspective of intestinal flora balance and immunomodulatory mechanism.Studies have found that milk oligosaccharides(MOs),especially yak milk oli-gosaccharides,can directly affect the intestinal barrier by inhibiting the expression of inflammatory factors,restoring the abundance of Bifidobacteria,Bacteroidetes and Lactobacilli,improving the intestinal function,bac-terial colonization and NEC resistance of premature infants after birth.These results emphasize that MOs,a substitute for breastfeeding,have specific preventive and alleviating effects on neonatal NEC.

Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species

Cotton(Gossypium spp.)is one of the most important economic crops in the world and also a major source of natural fiber,oil,and protein.The morphology of cotton species varies from trailing herbaceous perennials to trees<10 m.Like other important crops,modern cotton cultivars are polyploids and have gone through polyploidization,evolution,and domestication.The cotton genus comprises approximately 45 diploid(2n=2x=26)and seven tetraploid species(2n=4x=52)(Guan et al.,2014).

Patterns of presence-absence variants in Upland cotton

Dear Editor,Sources of genetic variations in genomes include small-scale sources(such as single-nucleotide polymorphisms(SNPs),insertions/deletions(InDels),and simple sequence repeats and larger-scale structural variations(mainly presence-absence variants(PAVs))and copy number variants).PAVs are sequences that are either inserted or missing in genomes in comparison with a reference sequence or genome.PAVs can have a much longer sequence than SNPs and InDels,as illustrated in the human genome(Conrad et al.,2010).PAVs are important genomic structural variations that can directly affect genomic structure and key functional genes in the genome(Kumar et al.,2007).Moreover,the use of PAVs for studying quantitative traits has been valuable(Lam et al.,2010).