The Relational Bottleneck as an Inductive Bias for Efficient Abstraction

A central challenge for cognitive science is to explain how abstract concepts are acquired from limited experience. This effort has often been framed in terms of a dichotomy between empiricist and nativist approaches, most recently embodied by debates concerning deep neural networks and symbolic cognitive models. Here, we highlight a recently emerging line of work that suggests a novel reconciliation of these approaches, by exploiting an inductive bias that we term the relational bottleneck. We review a family of models that employ this approach to induce abstractions in a data-efficient manner, emphasizing their potential as candidate models for the acquisition of abstract concepts in the human mind and brain

The Coordinated Action of MYB Activators and Repressors Controls Proanthocyanidin and Anthocyanin Biosynthesis in Vaccinium

Vaccinium berries are regarded as “superfoods” owing to their high concentrations of anthocyanins, flavonoid metabolites that provide pigmentation and positively affect human health. Anthocyanin localization differs between the fruit of cultivated highbush blueberry (V. corymbosum) and wild bilberry (V. myrtillus), with the latter having deep red flesh coloration. Analysis of comparative transcriptomics across a developmental series of blueberry and bilberry fruit skin and flesh identified candidate anthocyanin regulators responsible for this distinction. This included multiple activator and repressor transcription factors (TFs) that correlated strongly with anthocyanin production and had minimal expression in blueberry (non-pigmented) flesh. R2R3 MYB TFs appeared key to the presence and absence of anthocyanin-based pigmentation; MYBA1 and MYBPA1.1 co-activated the pathway while MYBC2.1 repressed it. Transient overexpression of MYBA1 in Nicotiana benthamiana strongly induced anthocyanins, but this was substantially reduced when co-infiltrated with MYBC2.1. Co-infiltration of MYBC2.1 with MYBA1 also reduced activation of DFR and UFGT, key anthocyanin biosynthesis genes, in promoter activation studies. We demonstrated that these TFs operate within a regulatory hierarchy where MYBA1 activated the promoters of MYBC2.1 and bHLH2. Stable overexpression of VcMYBA1 in blueberry elevated anthocyanin content in transgenic plants, indicating that MYBA1 is sufficient to upregulate the TF module and activate the pathway. Our findings identify TF activators and repressors that are hierarchically regulated by SG6 MYBA1, and fine-tune anthocyanin production in Vaccinium. The lack of this TF module in blueberry flesh results in an absence of anthocyanins.publishedVersio

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164\ua0Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models

MYBA and MYBPA transcription factors co-regulate anthocyanin biosynthesis in blue-coloured berries

The regulatory network of R2R3 MYB transcription factors in anthocyanin biosynthesis is not fully understood in blue-coloured berries containing delphinidin compounds. We used blue berries of bilberry (Vaccinium myrtillus) to comprehensively characterise flavonoid-regulating R2R3 MYBs, which revealed a new type of co-regulation in anthocyanin biosynthesis between members of MYBA-, MYBPA1- and MYBPA2-subgroups. VmMYBA1, VmMYBPA1.1 and VmMYBPA2.2 expression was elevated at berry ripening and by abscisic acid treatment. Additionally, VmMYBA1 and VmMYBPA1.1 expression was strongly downregulated in a white berry mutant. Complementation and transient overexpression assays confirmed VmMYBA1 and VmMYBA2 to induce anthocyanin accumulation. Promoter activation assays showed that VmMYBA1, VmMYBPA1.1 and VmMYBPA2.2 had similar activity towards dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS), but differential regulation activity for UDP-glucose flavonoid 3-O-glucosyltransferase (UFGT) and flavonoid 3′5′-hydroxylase (F3′5′H) promoters. Silencing of VmMYBPA1.1 in berries led to the downregulation of key anthocyanin and delphinidin biosynthesis genes. Functional analyses of other MYBPA regulators, and a member of novel MYBPA3 subgroup, associated them with proanthocyanidin biosynthesis and F3′5′H expression. The existence of 18 flavonoid-regulating MYBs indicated gene duplication, which may have enabled functional diversification among MYBA, MYBPA1 and MYBPA2 subgroups. Our results provide new insights into the intricate regulation of the complex anthocyanin profile found in blue-coloured berries involving regulation of both cyanidin and delphinidin branches

Spatiotemporal modulation of flavonoid metabolism in blueberries

Blueberries are distinguished by their purple-blue fruit color, which develops during ripening and is derived from a characteristic composition of flavonoid-derived anthocyanin pigments. The production of anthocyanins is confined to fruit skin, leaving the colorless fruit flesh devoid of these compounds. By linking accumulation patterns of phenolic metabolites with gene transcription in Northern Highbush (Vaccinium corymbosum) and Rabbiteye (Vaccinium virgatum) blueberry, we investigated factors limiting anthocyanin production in berry flesh. We find that flavonoid production was generally lower in fruit flesh compared with skin and concentrations further declined during maturation. A common set of structural genes was identified across both species, indicating that tissue-specific flavonoid biosynthesis was dependent on co-expression of multiple pathway genes and limited by the phenylpropanoid pathway in combination with CHS, F3H, and ANS as potential pathway bottlenecks. While metabolite concentrations were comparable between the blueberry genotypes when fully ripe, the anthocyanin composition was distinct and depended on the degree of hydroxylation/methoxylation of the anthocyanidin moiety in combination with genotype-specific glycosylation patterns. Co-correlation analysis of phenolic metabolites with pathway structural genes revealed characteristic isoforms of O-methyltransferases and UDP-glucose:flavonoid-3-O-glycosyltransferase that were likely to modulate anthocyanin composition. Finally, we identified candidate transcriptional regulators that were co-expressed with structural genes, including the activators MYBA, MYBPA1, and bHLH2 together with the repressor MYBC2, which suggested an interdependent role in anthocyanin regulation

Spatiotemporal modulation of flavonoid metabolism in blueberries

Blueberries are distinguished by their purple-blue fruit color, which develops during ripening and is derived from a characteristic composition of flavonoid-derived anthocyanin pigments. The production of anthocyanins is confined to fruit skin, leaving the colorless fruit flesh devoid of these compounds. By linking accumulation patterns of phenolic metabolites with gene transcription in Northern Highbush (Vaccinium corymbosum) and Rabbiteye (Vaccinium virgatum) blueberry, we investigated factors limiting anthocyanin production in berry flesh. We find that flavonoid production was generally lower in fruit flesh compared with skin and concentrations further declined during maturation. A common set of structural genes was identified across both species, indicating that tissue-specific flavonoid biosynthesis was dependent on co-expression of multiple pathway genes and limited by the phenylpropanoid pathway in combination with CHS, F3H, and ANS as potential pathway bottlenecks. While metabolite concentrations were comparable between the blueberry genotypes when fully ripe, the anthocyanin composition was distinct and depended on the degree of hydroxylation/methoxylation of the anthocyanidin moiety in combination with genotype-specific glycosylation patterns. Co-correlation analysis of phenolic metabolites with pathway structural genes revealed characteristic isoforms of O-methyltransferases and UDP-glucose:flavonoid-3-O-glycosyltransferase that were likely to modulate anthocyanin composition. Finally, we identified candidate transcriptional regulators that were co-expressed with structural genes, including the activators MYBA, MYBPA1, and bHLH2 together with the repressor MYBC2, which suggested an interdependent role in anthocyanin regulation

MYBA and MYBPA transcription factors co-regulate anthocyanin biosynthesis in blue-coloured berries

Abstract The regulatory network of R2R3 MYB transcription factors in anthocyanin biosynthesis is not fully understood in blue-coloured berries containing delphinidin compounds. We used blue berries of bilberry (Vaccinium myrtillus) to comprehensively characterise flavonoid-regulating R2R3 MYBs, which revealed a new type of co-regulation in anthocyanin biosynthesis between members of MYBA-, MYBPA1- and MYBPA2-subgroups. VmMYBA1, VmMYBPA1.1 and VmMYBPA2.2 expression was elevated at berry ripening and by abscisic acid treatment. Additionally, VmMYBA1 and VmMYBPA1.1 expression was strongly downregulated in a white berry mutant. Complementation and transient overexpression assays confirmed VmMYBA1 and VmMYBA2 to induce anthocyanin accumulation. Promoter activation assays showed that VmMYBA1, VmMYBPA1.1 and VmMYBPA2.2 had similar activity towards dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS), but differential regulation activity for UDP-glucose flavonoid 3-O-glucosyltransferase (UFGT) and flavonoid 3′5′-hydroxylase (F3′5′H) promoters. Silencing of VmMYBPA1.1 in berries led to the downregulation of key anthocyanin and delphinidin biosynthesis genes. Functional analyses of other MYBPA regulators, and a member of novel MYBPA3 subgroup, associated them with proanthocyanidin biosynthesis and F3′5′H expression. The existence of 18 flavonoid-regulating MYBs indicated gene duplication, which may have enabled functional diversification among MYBA, MYBPA1 and MYBPA2 subgroups. Our results provide new insights into the intricate regulation of the complex anthocyanin profile found in blue-coloured berries involving regulation of both cyanidin and delphinidin branches

Additional file 4: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

BLASTP comparison of manually edited gene models to the revised ‘Hongyang’ gene models. List of best reciprocal BLASTp matches between the revised Actinidia chinensis ‘Hongyang’ genes [18]and the Red5 gene set (XLSX 436 kb

Additional file 3: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Comparison of predicted paired end distance to genome.Heatmaps of alignment distance scores for the alignment of the read pairs from the 9Kb long-insert mate-paired-end (LIMP) library to each of the 29 chromosomes within the Red5 whole genome assembly and. Individual chromosome plots were prepared using hagfish_blockplot from the software program ‘hagfish’ ( https://github.com/mfiers/hagfish/ ). Individual images were cropped for height (not length) then cut and pasted into a table format for easier viewing. Each image depicted the entire length of the chromosome but all images are of standard length irrespective of chromosome length. Green regions indicate mate pairs aligning to the whole genome sequence within the expected distance of the library. Black indicates regions without mate pair alignment. Pinkish-red indicates regions where the distance between mated paired end reads is shorter (assembly compression relative to physical genome) or longer (assembly expansion relative to physical genome). (PPTX 432 kb

Additional file 7: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Details of sequenced cDNA’s generated. Fasta formatted sequences of 812 bidirectionally sequenced expressed sequence tag clones from A. chinensis var. chinensis used in evaluating manually annotated gene models of Red5. (FASTA 1204 kb