Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers

<p>Abstract</p> <p>Background</p> <p>Sesame is an important oil crop, but limited transcriptomic and genomic data are currently available. This information is essential to clarify the fatty acid and lignan biosynthesis molecular mechanism. In addition, a shortage of sesame molecular markers limits the efficiency and accuracy of genetic breeding. High-throughput transcriptomic sequencing is essential to generate a large transcriptome sequence dataset for gene discovery and molecular marker development.</p> <p>Results</p> <p>Sesame transcriptomes from five tissues were sequenced using Illumina paired-end sequencing technology. The cleaned raw reads were assembled into a total of 86,222 unigenes with an average length of 629 bp. Of the unigenes, 46,584 (54.03%) had significant similarity with proteins in the NCBI nonredundant protein database and Swiss-Prot database (E-value < 10^-5). Of these annotated unigenes, 10,805 and 27,588 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In total, 22,003 (25.52%) unigenes were mapped onto 119 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Furthermore, 44,750 unigenes showed homology to 15,460 <it>Arabidopsis </it>genes based on BLASTx analysis against The Arabidopsis Information Resource (TAIR, Version 10) and revealed relatively high gene coverage. In total, 7,702 unigenes were converted into SSR markers (EST-SSR). Dinucleotide SSRs were the dominant repeat motif (67.07%, 5,166), followed by trinucleotide (24.89%, 1,917), tetranucleotide (4.31%, 332), hexanucleotide (2.62%, 202), and pentanucleotide (1.10%, 85) SSRs. AG/CT (46.29%) was the dominant repeat motif, followed by AC/GT (16.07%), AT/AT (10.53%), AAG/CTT (6.23%), and AGG/CCT (3.39%). Fifty EST-SSRs were randomly selected to validate amplification and to determine the degree of polymorphism in the genomic DNA pools. Forty primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 24 sesame accessions.</p> <p>Conclusions</p> <p>This study demonstrates that Illumina paired-end sequencing is a fast and cost-effective approach to gene discovery and molecular marker development in non-model organisms. Our results provide a comprehensive sequence resource for sesame research.</p

Significant inter-annual fluctuation in CO2 and CH4 diffusive fluxes from subtropical aquaculture ponds: implications for climate change and carbon emission evaluations

Aquaculture ponds are potential hotspots for carbon cycling and emission of greenhouse gases (GHGs) like CO and CH , but they are often poorly assessed in the global GHG budget. This study determined the temporal variations of CO and CH concentrations and diffusive fluxes and their environmental drivers in coastal aquaculture ponds in southeastern China over a five-year period (2017-2021). The findings indicated that CH flux from aquaculture ponds fluctuated markedly year-to-year, and CO flux varied between positive and negative between years. The coefficient of inter-annual variation of CO and CH diffusive fluxes was 168% and 127%, respectively, highlighting the importance of long-term observations to improve GHG assessment from aquaculture ponds. In addition to chlorophyll-a and dissolved oxygen as the common environmental drivers, CO was further regulated by total dissolved phosphorus and CH by dissolved organic carbon. Feed conversion ratio correlated positively with both CO and CH concentrations and fluxes, showing that unconsumed feeds fueled microbial GHG production. A linear regression based on binned (averaged) monthly CO diffusive flux data, calculated from CO concentrations, can be used to estimate CH diffusive flux with a fair degree of confidence (r  = 0.66; p < 0.001). This algorithm provides a simple and practical way to assess the total carbon diffusive flux from aquaculture ponds. Overall, this study provides new insights into mitigating the carbon footprint of aquaculture production and assessing the impact of aquaculture ponds on the regional and global scales

Responses of coastal sediment organic and inorganic carbon to habitat modification across a wide latitudinal range in southeastern China

Coastal wetlands are important to the global carbon (C) budget and climate regulation. Plant invasion and aquaculture reclamation have drastically transformed China’s coastal wetlands, but knowledge of the effects on sediment carbon remains limited. We sampled top layer sediments (0–20 cm) in 21 coastal wetlands in southeastern China across the tropical-subtropical climate gradient, that have experienced the same sequence of habitat transformation from native mudflats (MFs) to Spartina alterniflora marshes (SAs) then to aquaculture ponds (APs). We measured the sediment carbon contents and ancillary physicochemical parameters. Landscape change from MFs to SAs increased sediment organic carbon (SOC) but decreased sediment inorganic carbon (SIC) content, whereas conversion of SAs to APs resulted in the opposite changes. Based on stepwise regression analysis, ammonium concentration and particle size distribution were the common factors that affected changes in SOC between habitat types, whereas for SIC it was ammonium and chloride concentrations. Habitat change affected SOC to a larger degree than SIC. Overall, invasion of MFs by SAs increased total carbon storage in the top sediment by 22%, or 6.6 × 106 g C ha−1; conversion of SAs to APs decreased it by 9.7%, or 3.5 × 106 g C ha−1. Our results showed the differential effects of different habitat modification scenarios on the sediment carbon pools and help assess how landscape-scale change affects terrestrial carbon budget and emission in the context of global climate change

Effects of landscape modification on coastal sediment nitrogen availability, microbial functional gene abundances and N2O production potential across the tropical-subtropical gradient

Wetland sediment is an important nitrogen pool and a source of the greenhouse gas nitrous oxide (N O). Modification of coastal wetland landscape due to plant invasion and aquaculture activities may drastically change this N pool and the related dynamics of N O. This study measured the sediment properties, N O production and relevant functional gene abundances in 21 coastal wetlands across five provinces along the tropical-subtropical gradient in China, which all had experienced the same sequence of habitat transformation from native mudflats (MFs) to invasive Spartina alterniflora marshes (SAs) and subsequently to aquaculture ponds (APs). Our results showed that change from MFs to SAs increased the availability of NH -N and NO -N and the abundance of functional genes related to N O production (amoA, nirK, nosZ Ⅰ, and nosZ Ⅱ), whereas conversion of SAs to APs resulted in the opposite changes. Invasion of MFs by S. alterniflora increased N O production potential by 127.9%, whereas converting SAs to APs decreased it by 30.4%. Based on structural equation modelling, nitrogen substrate availability and abundance of ammonia oxidizers were the key factors driving the change in sediment N O production potential in these wetlands. This study revealed the main effect patterns of habitat modification on sediment biogeochemistry and N O production across a broad geographical and climate gradient. These findings will help large-scale mapping and assessing landscape change effects on sediment properties and greenhouse gas emissions along the coast