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RNA alternative splicing, a post-transcriptional stage in eukaryotes, is crucial in cellular homeostasis and disease processes. Due to the rapid development of the next-generation sequencing (NGS) technology and the flood of NGS data, the detection of differential splicing from RNA-seq data has become mainstream. A range of bioinformatic tools has been developed. However, until now, an independent and comprehensive comparison of available algorithms/tools at the event level is still lacking. Here, 21 different tools are subjected to systematic evaluation, based on simulated RNA-seq data where exact differential splicing events are introduced. We observe immense discrepancies among these tools. SUPPA, DARTS, rMATS and LeafCutter outperforme other event-based tools. We also examine the abilities of the tools to identify novel splicing events, which shows that most event-based tools are unsuitable for discovering novel splice sites. To improve the overall performance, we present two methodological approaches i.e. low-expression transcript filtering and tool-pair combination. Finally, a new protocol of selecting tools to perform differential splicing analysis for different analytical tasks (e.g. precision and recall rate) is proposed. Under this protocol, we analyze the distinct splicing landscape in the DUX4/IGH subgroup of B-cell acute lymphoblastic leukemia and uncover the differential splicing of TCF12. All codes needed to reproduce the results are available at https://github.com/mhjiang97/Benchmarking_DS.

Here, the complete mitogenome of Petalonia binghamiae (J. Agardh) K. L. Vinogradova was determined and analyzed. The length of the complete P. binghamiae mitogenome was determined to be 37,460 bp. The mitogenome contains a set of 68 genes, including 35 protein-coding genes, 3 rRNA genes, 24 tRNA genes, 1 tRNA pseudogene, and 5 unidentified open reading frames (ORFs). The noncoding sequence constitutes 7.03% of the P. binghamiae mtDNA. Twenty-seven of the 35 (77.14%) protein-coding genes ended with a TAA stop codon, 6 (17.14%) with TAG, and 2 (5.71%) with TGA. All protein-coding genes in P. binghamiae were inferred to use the start codon ATG, except for nad11. The mitogenome phylogenetic analysis, based on 35 protein-coding genes, reveals that P. binghamia showed that P. binghamiae was clustered together with P. fascia. The complete mitochondrial genome sequence provided here would be useful for further understanding the evolution of Petalonia.

Betaphycus Doty, Eucheuma J. Agardh, and Kappaphycus Doty (Solieriaceae, Gigartinales) are the three most commercially important seaweed genera that produce carrageenan. In the present study we provide mitogenomes of Betaphycus gelatinus, Eucheuma denticulatum and Kappaphycus alvarezii. The mitogenomes of these three species contain a set of 50 genes, including 24 protein-coding genes, 2 rRNA genes, and 24 tRNA genes. The mitogenome length ranges from 25,198 bp (Kappaphycus alvarezii) to 25,327 bp (Eucheuma denticulatum). As compared with the previous published mitogenomes of Florideophyceae species, only the species in Gelidiaceae and Pterocladiaceae have smaller mitochondrial genome size than these reported here. At the junction of two transcription units, we identified a stem-loop structure in six representative Gigartinales species, which is presumed to play an important role in the replication and transcription of mitochondrial genes. In Gigartinales the difference in gene order among the four Solieriaceae (B. gelatinus, E. denticulatum, K. alvarezii, K. striatus) and other two Gigartinales species (Chondrus crispus and Mastocarpus papillatus) can be explained by inversion of two tRNA genes. Collinearity analysis of the 12 mitochondrial genomes of Florideophyceae showed considerable sequence synteny across all the species compared, with the exception of a highly variable region between atp6 and rpl20 genes. Phylogenetic analyses based on 21 shared mitochondrial genes showed that the four Solieriaceae species form one clade (Solieriaceae clade). Within this clade, B. gelatinae is basal relative to the other three species. The genus Kappaphycus is more closely related to Eucheuma than Betaphycus.

Herein, the complete Gracilaria edulis mitogenome was determined and analysed. The complete G. edulis mitogenome length was 25,708 bp. The mitogenome contains 50 genes, including 24 protein-coding,...

As a unique photosynthetic product in brown algae, mannitol exhibits high synthesis and accumulation in Saccharina japonica. Mannitol acts as a carbon-storage compound and is an osmoprotectant, imparting increased tolerance to osmotic stress. However, the underlying biochemical and molecular mechanisms in macroalgae have not been studied. Analysis of genomic and transcriptomic data has shown that mannitol metabolism in S. japonica is a circular pathway composed of four steps. In this study, one S. japonica mannitol-1-phosphate dehydrogenase (M1PDH2) and two mannitol-1-phosphatase (M1Pase) proteins were recombinantly expressed to analysis enzyme biochemical properties. RNA sequencing and droplet digital polymerase chain reaction were used to analyze the gene expression patterns of mannitol metabolism in different generations, tissues, sexes, and abiotic stresses. Our findings revealed insights into the mannitol synthesis pathways in brown algae. All genes were constitutively expressed in all samples, allowing maintenance of basic mannitol anabolism and dynamic maintenance of the “saccharide pool” in vivo as the main storage and antistress mechanism. Enzyme assays confirmed that the recombinant proteins produced mannitol, with the specific activity of SjaM1Pase1 being 1.8–4831 times that of other algal enzymes. Combined with the transcriptional analysis, SjaM1Pase1 was shown to be the dominant gene of mannitol metabolism. Mannitol metabolism genes in multicellular filamentous (gametophyte) and large parenchyma thallus (sporophyte) generations had different expression levels and responded differently under environmental stresses (hyposaline and hyperthermia) in gametophytes and sporophytes. The considerable variation in enzyme characteristics and expression of mannitol synthesis genes suggest their important ecophysiological significance in the evolution of complex systems (filamentous and thallus) and environmental adaptation of Laminariales.

Marine algae have an extraordinary ability to absorb halogens which provide algae with an inorganic antioxidant impacting atmospheric chemistry. Although brown algal Laminariales species are the most efficient iodine accumulators among all living systems, andSaccharina japonicais the primary material used for iodine extraction, the functions and regulatory mechanisms of these species have not been fully documented. In this study, a functional genomics analysis of the algal vanadium-dependent haloperoxidase (vHPO) gene family was conducted; there genes can introduce halogen atoms into organic compounds. The comprehensive analyses regarding the bioinformatics and phylogenetics of novel genomic and transcriptomic sequencing data of 21 Rhodophyta and 19 Ochrophyta marine algal species revealed that brown algalvHPOshave two gene types, vanadium-dependent bromoperoxidase (vBPO) and vanadium-dependent iodoperoxidase (vIPO), with secondary endosymbiotic host origin. The enzyme activity ofS. japonicavBPO and vIPO were verified for the first time and were quite stable in a wide range of temperature and pH values. However, the specific activity and optimal conditions were considerably different between vBPO and vIPO. The transcript expression analysis in differentS. japonicatissues (including rhizoids), generations (sporophytes and gametophytes), sexes (male and female), and stress conditions (hyposaline and hyperthermia) also showed great differences betweenvBPOsandvIPOs. Most of thevBPOswere constitutively expressed with higher expression dose, which may be responsible for basal halogen metabolism. On the contrary,vIPOsmainly showed specific expression, which may be involved in tissue differentiation, generation differentiation, sex differentiation, and stress regulation. Comprehensive analysis of gene family evolution, enzyme biochemical characteristics, and complex transcriptional mechanisms were conducive to the environmental adaptation and sophisticated system evolution of Laminariales. The successful bromination of small-molecule compound substrate by SjavBPO provided high activity and efficient enzymatic tools for artificial synthesis of halogenated compounds.

Here, the complete mitogenome of Petalonia binghamiae (J. Agardh) K. L. Vinogradova was determined and analyzed. The length of the complete P. binghamiae mitogenome was determined to be 37,460 bp. ...

In this study, we sequenced and analyzed the complete mitogenome of Grateloupia filicina (Lamouroux) C. Agardh. The complete G. filicina mitogenome was 29,274-bp long, containing 51 genes, including 24 protein-coding genes, 1 intron, 2 rRNA genes, 24 tRNA genes, and 1 unidentified open reading frame. Twenty-one of the 24 (87.5%) protein-coding genes ended with the stop codon TAA, whereas 3 (12.5%) ended with TAG. All the protein-coding genes in G. filicina used the start codon ATG. Phylogenetic analysis revealed that G. filicina clustered with G. taiwanensis. The complete mitochondrial genome sequence provided here would be useful for understanding the evolution of Grateloupia further.