Genome-wide transcriptomic analysis identifies candidate genes involved in jasmonic acid-mediated salt tolerance of alfalfa.

Soil salinity imposes a major threat to plant growth and agricultural productivity. Despite being one of the most common fodder crops in saline locations, alfalfa is vulnerable to salt stress. Jasmonic acid (JA) is a phytohormone that influences plant response to abiotic stimuli such as salt stress. However, key genes and pathways by which JA-mediated salt tolerance of alfalfa are little known. A comprehensive transcriptome analysis was performed to elucidate the underlying molecular mechanisms of JA-mediated salt tolerance. The transcripts regulated by salt (S) compared to control (C) and JA+salt (JS) compared to C were investigated. Venn diagram and expression pattern of DEGs indicated that JS further altered a series of genes expression regulated by salt treatment, implying the roles of JA in priming salt tolerance. Enrichment analysis revealed that DEGs exclusively regulated by JS treatment belonged to primary or secondary metabolism, respiratory electron transport chain, and oxidative stress resistance. Alternatively, splicing (AS) was induced by salt alone or JA combined treatment, with skipped exon (SE) events predominately. DEGs undergo exon skipping involving some enriched items mentioned above and transcription factors. Finally, the gene expressions were validated using quantitative polymerase chain reaction (qPCR), which produced results that agreed with the sequencing results. Taken together, these findings suggest that JA modulates the expression of genes related to energy supply and antioxidant capacity at both the transcriptional and post-transcriptional levels, possibly through the involvement of transcription factors and AS events.

In silico genome wide identification and expression analysis of the WUSCHEL-related homeobox gene family in Medicago sativa.

Alfalfa (Medicago sativa) is an important food and feed crop which rich in mineral sources. The WUSCHEL-related homeobox (WOX) gene family plays important roles in plant development and identification of putative gene families, their structure, and potential functions is a primary step for not only understanding the genetic mechanisms behind various biological process but also for genetic improvement. A variety of computational tools, including MAFFT, HMMER, hidden Markov models, Pfam, SMART, MEGA, ProtTest, BLASTn, and BRAD, among others, were used. We identified 34 MsWOX genes based on a systematic analysis of the alfalfa plant genome spread in eight chromosomes. This is an expansion of the gene family which we attribute to observed chromosomal duplications. Sequence alignment analysis revealed 61 conserved proteins containing a homeodomain. Phylogenetic study sung reveal five evolutionary clades with 15 motif distributions. Gene structure analysis reveals various exon, intron, and untranslated structures which are consistent in genes from similar clades. Functional analysis prediction of promoter regions reveals various transcription binding sites containing key growth, development, and stress-responsive transcription factor families such as MYB, ERF, AP2, and NAC which are spread across the genes. Most of the genes are predicted to be in the nucleus. Also, there are duplication events in some genes which explain the expansion of the family. The present research provides a clue on the potential roles of MsWOX family genes that will be useful for further understanding their functional roles in alfalfa plants.

RNA viromes from terrestrial sites across China expand environmental viral diversity.

Environmental RNA viruses are ubiquitous and diverse, and probably have important ecological and biogeochemical impacts. Understanding the global diversity of RNA viruses is limited by sampling biases, dependence on cell culture and PCR for virus discovery, and a focus on viruses pathogenic to humans or economically important animals and plants. To address this knowledge gap, we generated metatranscriptomic sequence data from 32 diverse environments in 16 provinces and regions of China. We identified 6,624 putatively novel virus operational taxonomic units from soil, sediment and faecal samples, greatly expanding known diversity of the RNA virosphere. These newly identified viruses included positive-sense, negative-sense and double-strand RNA viruses from at least 62 families. Sediments and animal faeces were rich sources of viruses. Virome compositions were affected by local environmental factors, including organic content and eukaryote species abundance. Notably, environmental factors had a greater impact on the abundance and diversity of plant, fungal and bacterial viruses than of animal viromes. Our data confirm that RNA viruses are an integral part of both terrestrial and aquatic ecosystems.

A new species of the deep-sea shrimp genus Spongicoloides (Decapoda: Spongicolidae) from the South China Sea.

Spongicoloides zhoui sp. nov. (Crustacea: Decapoda: Spongicolidae), a species of deep-sea hexactinellid sponge-associated shrimp, is described based on specimens collected from the Zhenbei Seamount in the South China Sea. The new species is morphologically most similar to the Western Pacific congeneric species Spongicoloides iheyaensis Saito, Tsuchida Yamamoto, 2006 in that the ischium of the third pereiopod is unarmed and the fixed finger of the third pereiopod is armed with small teeth on the distoventral margin. However, S. zhoui sp. nov. can be distinguished from S. iheyaensis in that its female antennal basicerite has three large spines on the distolateral margin. Molecular analyses based on nuclear histone H3, and mitochondrial cytochrome c oxidase subunit I (COI), 12S ribosomal RNA (rRNA), and 16S rRNA gene fragments confirmed the placement of S. zhoui sp. nov. within a clade of Spongicoloides/Spongiocaris species, and their sequence divergences were large enough to justify the recognition of this new species.

Chromosome-level genome of Poropuntius huangchuchieni provides a diploid progenitor-like reference genome for the allotetraploid Cyprinus carpio.

The diploid Poropuntius huangchuchieni in the cyprinid family, which is widely distributed in the Mekong and Red River basins, is one of the most closely related diploid progenitor-like species of allotetraploid common carp, which was generated by merging of two diploid genomes during evolution. Therefore, the P. huangchuchieni genome is essential for polyploid evolution studies in Cyprinidae. Here, we report a high-quality chromosome-level genome assembly of P. huangchuchieni by integrating Oxford Nanopore and Hi-C technologies. The assembled genome size was 1,021.38 Mb, 895.66 Mb of which was anchored onto 25 chromosomes with a N50 of 32.93 Mb. The genome contained 486.28 Mb repetitive elements and 24,099 protein-coding genes. Approximately 95.9% of the complete BUSCOs were detected, suggesting a high completeness of the genome. Evolutionary analysis revealed that P. huangchuchieni diverged from Cyprinus carpio at approximately 12 Mya. Genome comparison between P. huangchuchieni and the B subgenome of C. carpio provided insights into chromosomal rearrangements during the allotetraploid speciation. With the complete gene set, 17,474 orthologous genes were identified between P. huangchuchieni and C. carpio, providing a broad view of the gene component in the allotetraploid genome, which is critical for future genetic analyses. The high-quality genomic data set created for P. huangchuchieni provides a diploid progenitor-like reference for the evolution and adaptation of allotetraploid carps.

Complete mitochondrial genome and the phylogenetic position of a new species, Johnius taiwanensis (Perciformes: Sciaenidae) from Chinese waters.

In this study, the complete mitogenome of a new species, Johnius taiwanensis (Chao et al. 2019) was obtained. Its mitogenome is 18,451 bp in length, consisting of 37 genes with the typical gene order and direction of transcription in vertebrates. Gene rearrangement was found in J. taiwanensis. The overall nucleotide composition is: 24.2% A; 18.0% C; 21.1% G, and 36.7% T. Sizes of the 22 tRNA genes range from 66 to 75 bp. Two start codons (ATG and GTG) and three stop codons (TAG, AGA and TAA/TA/T) were detected in 13 protein-coding genes. In the Bayesian tree based on the complete mitogenomes of 26 species (including J. taiwanensis) from the family Sciaenidae, all nodes were strongly supported. The result shows that J. taiwanensis was placed as sister to the Trewavas croaker J. trewavasae of the same genus. The mechanism of gene rearrangement in the genus Johnius merits further investigation.

Complete mitochondrial genome and the phylogenetic position of the blackmouth croaker Atrobucca nibe (Perciformes: Sciaenidae).

In this study, the complete mitogenome of the blackmouth croaker Atrobucca nibe was obtained. Its mitogenome is 16,842 bp in length, consisting of 37 genes with the typical gene order and direction of transcription in vertebrates. The overall nucleotide composition is: 27.2% A; 31.2% C; 16.4% G and 25.2% T. Sizes of the 22 tRNA genes range from 66 to 74 bp. One start codons (ATG) and three stop codons (TAG, AGA, and TAA/TA/T) were detected in 13 protein-coding genes. In the Bayesian tree based on the complete mitogenomes of 20 species (including A. nibe) from the family Sciaenidae, all nodes were strongly supported. The result suggested that A. nibe was subsequent to the group with genera Otolithes, Chrysochir, Megalonibea, Pennahia, Nibea, Dendrophysa, and Johnius.

Complete mitochondrial genome and the phylogenetic position of the Caroun croaker Johnius carouna (perciformes: Sciaenidae).

In this study, the complete mitogenome of the Caroun croaker Johnius carouna was obtained. Its mitogenome is 18,752 bp in length, consisting of 37 genes with the typical gene order and direction of transcription in vertebrates. Gene rearrangement was found in J. carouna, same as another two Johnius species available in GenBank, J. distinctus (MF083699) and J. grypotus (KC491206). The overall nucleotide composition is: 24.2% A; 18.0% C; 21.4% G, and 36.4% T. Sizes of the 23 tRNA genes range from 67 to 75 bp. One start codons (ATG) and three stop codons (TAG, AGG, and TAA/TA/T) were detected in 13 protein-coding genes. In the Bayesian tree based on the complete mitogenomes of 21 species (including J. carouna) from the family Sciaenidae, all nodes were strongly supported. The result shows that J. carouna was placed as sister to the silver croaker J. grypotus of the same genus. The mechanism of gene rearrangement in the genus Johnius merits further investigation.

Complete mitochondrial genome and the phylogenetic position of the brown-spotted grouper Epinephelus chlorostigma (Perciformes: Epinephelidae).

The complete mitogenome of the brown-spotted grouper Epinephelus chlorostigma was determined in this study. It is 16,894 bp in length, containing 37 genes with the typical order and transcriptional direction in the vertebrates. The overall nucleotide composition is: 28.7% A; 28.0% C; 16.3% G and 27.0% T. The lengths of 22 transfer RNA (tRNA) genes range from 67 (tRNA-Cys) to 76 (tRNA-Leu1) bp. Two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) were found in the protein-coding genes. The nodes of phylogenetic tree were strongly supported based on the complete mitogenomes of available groupers. The phylogenetic results suggested E. chlorostigma is the closest to E. areolatus within the genus Epinephelus.

Complete mitochondrial genome of the hardnose shark Carcharhinus macloti (Carcharhiniformes: Carcharhinidae).

The complete mitochondrial genome of Carcharhinus macloti was determined in this study. It is 16,701 bp in length and contains 37 genes with the typical gene order and transcriptional orientation in vertebrates. A total of 29 bp overlaps and 29 bp short intergenic spaces located in 22 gene junctions. The overall base composition is 31.6% A, 26.2% C, 13.0% G and 29.2% T. Two start codons (ATG and GTG) and three stop codons (AGG, TAG and TAA/T) were found in 13 protein-coding genes. The length of 22 tRNA genes ranged from 66 bp (tRNA-Ser2) to 75 bp (tRNA-Leu1). The tRNA-Ser2 (GCU) lacks the dihydrouridine arm by a simple loop and can not be folded into the typical cloverleaf structure. The control region is 1066 bp in length with high A+T content (68.2%).

Complete mitochondrial genome of the humpback grouper Cromileptes altivelis.

The complete mitochondrial genome (16,497 bp) of the humpback grouper Cromileptes altivelis is first presented in this study. The gene arrangement and translate orientation of C. altivelis is identical to most vertebrates, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a putative control region. The overall nucleotide composition of the H-strand is 29.80% A, 26.23% T, 15.67% G and 29.02% C. The origin of the light-strand replication was identified between the tRNA-Asn and tRNA-Cys genes, while the termination associated sequence (TAS) and conserved sequence blocks (CSB1-3) were identified in the control region.

[Biological process of phosphorus turnover in surface water body of Xiamen Harbor. II: Grazing pressure of copepod on phytoplankton].

To understand the roles of copepod in the biogeochemical cycling of phosphorus, gut fluorescence method was applied to examine in situ the grazing rate of copepod on the phytoplankton in Xiamen Time Station (XMTS) in May, August and November 2005 and March 2006. In the meanwhile, the abundance and species composition of copepod were investigated, and the grazing pressure of copepod on the phytoplankton was estimated. The results showed that the annual average grazing rate of copepod was 55.53 microg x m(-3) x d(-1), being the highest (108.98 microg x m(-3) x d(-1)) in autumn and the lowest (7.18 microg x m(-3) x d(-1)) in summer. Based on the estimation from our experimental data, the daily grazing rate of copepod populations on the phytoplankton in Xiamen Harbor was, on annual average, about 1.81% of the phytoplankton's standing stock, with the values in spring, summer, autumn, and winter being 3.22%, 0.06%, 3.52% and 0.46%, respectively.