Author Correction:The complexity of the Fragaria x ananassa(octoploid)transcriptome by single-molecule long-read sequencing

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The complexity of the Fragaria x ananassa(octoploid)transcriptome by singlemolecule long-read sequencing

Strawberry(Fragaria x ananassa)is an allopolyploid species with diverse and complex transcripts.The regulatory mechanisms of fruit development and maturation have been extensively studied;however,little is known about the signaling mechanisms that direct this process in octoploid strawberry(Fragaria x ananassa).Here,we used long-read sequencing(LRS)technology and RNA-seq analysis to investigate the diversity and complexity of the polyploid transcriptome and differentially expressed transcripts along four successive fruit developmental stages of cultivated strawberry.We obtained a reference transcriptome with 119,897 unique full-length isoforms,including 2017 new isoforms and 2510 long noncoding RNAs.Based on the genome of the plausible progenitor(Fragaria vesca),20,229 alternative splicing(AS)events were identified.Using this transcriptome,we found 17,485 differentially expressed transcripts during strawberry fruit development,including 527 transcription factors(TFs)belonging to 41 families.The expression profiles of all members of the auxin,ABA pathway,and anthocyanin biosynthesis gene families were also examined,and many of them were highly expressed at the ripe fruit stage,strongly indicating that the role of those genes is in the regulation of fruit ripening.We produce a high-quality reference transcriptome for octoploid strawberry,including much of the full-length transcript diversity,to help understand the regulatory mechanisms of fruit development and maturation of polyploid species,particularly via elucidation of the biochemical pathways involved in auxin,ABA,and anthocyanin biosynthesis.

Characterization of circRNAs associated with resistance to defoliating insects in soybean

Circular RNAs (circRNAs) are new type of non-coding endogenous RNA characterized by presence of covalent bond linking 3′ and 5′ ends recently. Various endogenous circRNAs with potential biological functions have been identified in animals and plants.However, little is known regarding circRNAs in soybean. In this study, we have performed genome-wide profiling of circRNAs that associate with insect resistance in soybean through bulk segregant RNA-seq and bioinformatics analysis. In total, 5,367 circRNAs were identified,of which 3,377 and 3,457 ones were detected from resistant and susceptible bulks respectively. These circRNAs showed diverse expression patterns, and 199 circRNAs were found to be differentially expressed between resistant and susceptible samples under stress of defoliation-damage by cotton bollworm feeding. Functional categorization of circRNA-hostgenes revealed that various biology processes were triggered to be active during chewing injury. Intriguingly, some circRNAs were predicted to involve in insect resistance processes,such as tropane, piperidine and pyridine alkaloid biosynthesis, and monoterpenoid biosynthesis.Furthermore, 1,118 circRNAs were predicted to have enrichened miRNA binding sites in soybean. This research provid not only circRNAs resources, but also useful clues about their biological insights in response to defense biotic stress in plant.

Soaking seed with paclobutrazol increased tolerance of juvenile oilseed rape to waterlogging

Global increase in demand for edible plant oil along with changing climates has led to a greater need to grow oilseed rape even in wet and humid environments.To find effective measures to increase tolerance of juvenile oilseed rape to waterlogging is vitally important.A pot experiment was conducted to investigate effects of soaking seed in paclobutrazol(PBZ)solution(0(W),0.1(P1),0.3(P2)or 0.5(P3)g/L)on the growth of juvenile oilseed rape(Brassica napus L.cv.‘Zhongshuang 11’).Seed soaking with water without waterlogging was used as a control.Results showed that waterlogging decreased oilseed rape growth significantly;however,soaking seed with lower doses of PBZ(P1 and P2)significantly ameliorated the decrease in plant dry weight caused by waterlogging.Compared with W,both root dry weights and shoot dry weights of P1 and P2 treatments were significantly increased at 5 d and 10 d after waterlogging,and photosynthetic pigment contents and antioxidative enzyme activities were increased by P2 treatment at both 2 samples.Since it is labor saving and economical,soaking seed with an optimal dose(0.3 g/L)of PBZ might be an efficient way to improve waterlogging tolerance of oilseed rape.

Genome-wide analysis of GH3 gene family in soybean( Glycine max)

Auxin, as an important phytohormone, regulates plant growth and development by regula-ting the expression of diverse genes. GH3 is one of the main auxin - responsive genes, and has crucial roles in many biology processes. Studies have demonstrated GH3 gene family in various plants, but no ge-nome -wide analysis of the GH3 gene family has been conducted for a legume species. Here we performed a comprehensive genome mining and identified a total of 24 GH3 genes, located on 13 different chromo-somes in the soybean genome （ GmGH3. 1 to GmGH3. 24） . Most of the predicted GmGH3s clustered to-gether in pairs, reflecting the ancient genome duplication event. Analysis of gene structure revealed the presence of introns in protein - coding regions, and that their size, abundance and distribution varied within the gene family. Expression analysis of GmGH3 genes in soybean various tissues of different devel-opmental stages displayed their temporally and spatially expression patterns. We have identified 24 GH3 genes in the soybean genome. The expansion of GmGH3 genes and their distribution pattern on the chro-mosomes revealed genome - wide segmental duplications of soybean. Diverse expression of GmGH3s dur-ing soybean growth and development indicated their important function roles.

Comparative genomic study of a wild soybean by whole genome re-sequencing

Wild soybean resources, which are progenitor of cultivated soybean with selected agronomic characters, have rich genetic diversity. Here we used genome re-sequencing technology to analyze genetic variations between the wild soybean ＇ED059’ and cultivar ＇Tianlong 2＇. In genome level, 3,214,319 and 1,519,765 single nucleotide polymorphisms （SNPs）, 553,141 and 314,430 insertion/deletion polymorphisms （InDels）, and 471,063 and 334,412 structural variations （SVs） were identified between ＇ED0595＇ and ＇Tianlong 2＇ respec-tively based on soybean （Glycine max L. Merr） reference genome. Base on gene annotation of reference genome, 68,830 （2.14%） and 34,570 （2.27%） non-synonymous SNPs, 8,478 and 4,826 frameshift substitution were detected in CDS regions of ＇ED0595＇ and ＇Tianlong 2＇. ＇ED059’ harbored much more specific genetic variations of jasmonic acid （JA）, salicylic acid （SA） and ethylene （ET） biosynthesis and signal pathway genes than those in ＇Tianlong 2＇ indicating its unique strong insect defense activity. This work provides important information allowing better understanding of the soybean genome and being helpful for dissecting the genetic basis of important traits such as insect defense in soybean.