Physicochemical and Thermal Characteristics of Onion Skin from Fifteen Indian Cultivars for Possible Food Applications

Every year tons of onion waste is produced worldwide. The dried outer onion skin contributed up to 70% of this waste. Outer-dried skins of fifteen prominent onion cultivars from India were selected for the study. A comparative study was done for proximate profiling, thermal characteristics, functional grouping, and mineral contents. Skin of cv. “NHRDF Red” contained the highest amount of crude protein (5.97 ± 0.15 g/100 g), ash (12.24 ± 0.59 g/100 g), and fiber (8.28 ± 0.20 g/100 g), whereas cv. “Pusa Red” possessed the highest amount of total fat (0.47 ± 0.02 g/100 g) and the maximum carbohydrates (76.66 ± 0.56 g/100 g) were found in “Pusa Riddhi.” Mineral analysis showed that cv. “NHRDF Red” had the maximum concentration of all 9 minerals along with sulphur content. Fourier transform infrared spectroscopy analysis explored the various metabolites present in each cultivar. The thermal analysis explored cv. “Agri Found Dark Red” as highly thermally stable having 70.98% residual mass. The lowest Tg temperature range was found between 64.4°C and 90.6°C for “Agri Found Dark Red.” Skin of cv. “NHRDF Red” was reported as the best source of protein, fiber, and minerals, which may be utilized for developing a food product.

The Taxus genome provides insights into paclitaxel biosynthesis

The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We have completed a chromosome-level genome of Taxus chinensis var. mairei with a total length of 10.23 gigabases. Taxus shared an ancestral whole-genome duplication with the coniferophyte lineage and underwent distinct transposon evolution. We discovered a unique physical and functional grouping of CYP725As (cytochrome P450) in the Taxus genome for paclitaxel biosynthesis. We also identified a gene cluster for taxadiene biosynthesis, which was formed mainly by gene duplications. This study will facilitate the elucidation of paclitaxel biosynthesis and unleash the biotechnological potential of Taxus.

The Taxus genome provides insights into paclitaxel biosynthesis

The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We have completed a chromosome-level genome of Taxus chinensis var. mairei with a total length of 10.23 Gb. Taxus shared an ancestral whole-genome duplication with the coniferophyte lineage and underwent distinct transposon evolution. We discovered a unique physical and functional grouping of CYP725As (cytochrome P450) in the Taxus genome for paclitaxel biosynthesis. We also identified a gene cluster in the taxadiene biosynthesis, which was mainly formed by gene duplications. This study will facilitate the elucidation of paclitaxel biosynthesis and unleash the biotechnological potential of Taxus.One Sentence SummaryA chromosome-level genome assembly of Taxus chinensis var. mairei uncovers its unique genome evolution process and genetic architectures for the paclitaxel biosynthesis pathway.

FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts

Summary Typical RNA sequencing (RNA-Seq) analyses are performed either at the gene level by summing all reads from the same locus, assuming that all transcripts from a gene make a protein or at the transcript level, assuming that each transcript displays unique function. However, these assumptions are flawed, as a gene can code for different types of transcripts and different transcripts are capable of synthesizing similar, different or no protein. As a consequence, functional changes are not well illustrated by either gene or transcript analyses. We propose to improve RNA-Seq analyses by grouping the transcripts based on their similar functions. We developed FuSe to predict functional similarities using the primary and secondary structure of proteins. To estimate the likelihood of proteins with similar functions, FuSe computes two confidence scores: knowledge (KS) and discovery (DS) for protein pairs. Overlapping protein pairs exhibiting high confidence are grouped to form ‘similar function protein groups’ and expression is calculated for each functional group. The impact of using FuSe is demonstrated on in vitro cells exposed to paracetamol, which highlight genes responsible for cell adhesion and glycogen regulation which were earlier shown to be not differentially expressed with traditional analysis methods. Availability and implementation The source code is available at https://github.com/rajinder4489/FuSe. Data for APAP exposure are available in the BioStudies database (http://www.ebi.ac.uk/biostudies) under accession numbers S-HECA143, S-HECA(158) and S-HECA139. Supplementary information Supplementary data are available at Bioinformatics online.

A weapons–testes trade-off in males is amplified in female traits

Sexually selected weapons are assumed to trade off with traits related to ejaculates, such as testes. However, remarkably little is known about what governs resource allocation and why trade-offs are found in some cases and not others. Often-used models depict competitive allocation occurring within the functional grouping of traits (e.g. reproduction); however, other factors including tissue expense and developmental timing may influence allocation. Experimental comparisons of investment across the sexes have the potential to illuminate allocation rules, because the sexes do not always use traits for the same functions. Here, we capitalize upon a species where females have weapons–testes homologues. We report that a documented trade-off in investment between hind-limb weapons and testes in leaf-footed cactus bugs, Narnia femorata , is even more pronounced in female hind limbs and ovaries. Female hind limbs in this species do not share the clear reproductive function of male hind limbs; therefore, this trade-off spans trait functional groups. Such patterns of investment suggest that future studies of reproductive trade-offs should consider factors such as tissue expense and developmental timing.