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Abstract Aegilops tauschii is the donor of the D subgenome of hexaploid wheat and a valuable genetic resource for wheat improvement. Several reference-quality genome sequences have been reported for A. tauschii accession AL8/78. A new genome sequence assembly (Aet v6.0) built from long Pacific Biosciences HiFi reads and employing an optical genome map constructed with a new technology is reported here for this accession. The N50 contig length of 31.81 Mb greatly exceeded that of the previous AL8/78 genome sequence assembly (Aet v5.0). Of 1,254 super-scaffolds, 92, comprising 98% of the total super-scaffold length, were anchored on a high-resolution genetic map, and pseudomolecules were assembled. The number of gaps in the pseudomolecules was reduced from 52,910 in Aet v5.0 to 351 in Aet v6.0. Gene models were transferred from the Aet v5.0 assembly into the Aet v6.0 assembly. A total of 40,447 putative orthologous gene pairs were identified between the Aet v6.0 and Chinese Spring wheat IWGSC RefSer v2.1 D-subgenome pseudomolecules. Orthologous gene pairs were used to compare the structure of the A. tauschii and wheat D-subgenome pseudomolecules. A total of 223 structural differences were identified. They included 44 large differences in sequence orientation and 25 differences in sequence location. A technique for discriminating between assembly errors and real structural variation between closely related genomes is suggested. 

Abstract Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the 3 subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo-assembled transcriptomes. 

Abstract. Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere in a changing climate is critical to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe and synthesize datasets and methodologies to quantify the five major components of the global carbon budget and their uncertainties. Fossil CO2 emissions (EFOS) are based on energy statistics and cement production data, while emissions from land-use change (ELUC) are based on land-use and land-use change data and bookkeeping models. Atmospheric CO2 concentration is measured directly, and its growth rate (GATM) is computed from the annual changes in concentration. The global net uptake of CO2 by the ocean (SOCEAN, called the ocean sink) is estimated with global ocean biogeochemistry models and observation-based fCO2 products (fCO2 is the fugacity of CO2). The global net uptake of CO2 by the land (SLAND, called the land sink) is estimated with dynamic global vegetation models. Additional lines of evidence on land and ocean sinks are provided by atmospheric inversions, atmospheric oxygen measurements, and Earth system models. The sum of all sources and sinks results in the carbon budget imbalance (BIM), a measure of imperfect data and incomplete understanding of the contemporary carbon cycle. All uncertainties are reported as ±1σ. For the year 2023, EFOS increased by 1.3 % relative to 2022, with fossil emissions at 10.1 ± 0.5 GtC yr−1 (10.3 ± 0.5 GtC yr−1 when the cement carbonation sink is not included), and ELUC was 1.0 ± 0.7 GtC yr−1, for a total anthropogenic CO2 emission (including the cement carbonation sink) of 11.1 ± 0.9 GtC yr−1 (40.6 ± 3.2 GtCO2 yr−1). Also, for 2023, GATM was 5.9 ± 0.2 GtC yr−1 (2.79 ± 0.1 ppm yr−1; ppm denotes parts per million), SOCEAN was 2.9 ± 0.4 GtC yr−1, and SLAND was 2.3 ± 1.0 GtC yr−1, with a near-zero BIM (−0.02 GtC yr−1). The global atmospheric CO2 concentration averaged over 2023 reached 419.31 ± 0.1 ppm. Preliminary data for 2024 suggest an increase in EFOS relative to 2023 of +0.8 % (−0.2 % to 1.7 %) globally and an atmospheric CO2 concentration increase by 2.87 ppm, reaching 422.45 ppm, 52 % above the pre-industrial level (around 278 ppm in 1750). Overall, the mean of and trend in the components of the global carbon budget are consistently estimated over the period 1959–2023, with a near-zero overall budget imbalance, although discrepancies of up to around 1 GtC yr−1 persist for the representation of annual to semi-decadal variability in CO2 fluxes. Comparison of estimates from multiple approaches and observations shows the following: (1) a persistent large uncertainty in the estimate of land-use change emissions, (2) low agreement between the different methods on the magnitude of the land CO2 flux in the northern extra-tropics, and (3) a discrepancy between the different methods on the mean ocean sink. This living-data update documents changes in methods and datasets applied to this most recent global carbon budget as well as evolving community understanding of the global carbon cycle. The data presented in this work are available at https://doi.org/10.18160/GCP-2024 (Friedlingstein et al., 2024). 

Abstract. Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere in a changing climate is critical to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe and synthesize data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. Fossil CO2 emissions (EFOS) are based on energy statistics and cement production data, while emissions from land-use change (ELUC), mainly deforestation, are based on land-use and land-use change data and bookkeeping models. Atmospheric CO2 concentration is measured directly, and its growth rate (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) is estimated with global ocean biogeochemistry models and observation-based fCO2 products. The terrestrial CO2 sink (SLAND) is estimated with dynamic global vegetation models. Additional lines of evidence on land and ocean sinks are provided by atmospheric inversions, atmospheric oxygen measurements, and Earth system models. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and incomplete understanding of the contemporary carbon cycle. All uncertainties are reported as ±1σ. For the year 2022, EFOS increased by 0.9 % relative to 2021, with fossil emissions at 9.9±0.5 Gt C yr−1 (10.2±0.5 Gt C yr−1 when the cement carbonation sink is not included), and ELUC was 1.2±0.7 Gt C yr−1, for a total anthropogenic CO2 emission (including the cement carbonation sink) of 11.1±0.8 Gt C yr−1 (40.7±3.2 Gt CO2 yr−1). Also, for 2022, GATM was 4.6±0.2 Gt C yr−1 (2.18±0.1 ppm yr−1; ppm denotes parts per million), SOCEAN was 2.8±0.4 Gt C yr−1, and SLAND was 3.8±0.8 Gt C yr−1, with a BIM of −0.1 Gt C yr−1 (i.e. total estimated sources marginally too low or sinks marginally too high). The global atmospheric CO2 concentration averaged over 2022 reached 417.1±0.1 ppm. Preliminary data for 2023 suggest an increase in EFOS relative to 2022 of +1.1 % (0.0 % to 2.1 %) globally and atmospheric CO2 concentration reaching 419.3 ppm, 51 % above the pre-industrial level (around 278 ppm in 1750). Overall, the mean of and trend in the components of the global carbon budget are consistently estimated over the period 1959–2022, with a near-zero overall budget imbalance, although discrepancies of up to around 1 Gt C yr−1 persist for the representation of annual to semi-decadal variability in CO2 fluxes. Comparison of estimates from multiple approaches and observations shows the following: (1) a persistent large uncertainty in the estimate of land-use changes emissions, (2) a low agreement between the different methods on the magnitude of the land CO2 flux in the northern extra-tropics, and (3) a discrepancy between the different methods on the strength of the ocean sink over the last decade. This living-data update documents changes in methods and data sets applied to this most recent global carbon budget as well as evolving community understanding of the global carbon cycle. The data presented in this work are available at https://doi.org/10.18160/GCP-2023 (Friedlingstein et al., 2023). 

Abstract. Accurate assessment of anthropogenic carbon dioxide (CO2) emissions andtheir redistribution among the atmosphere, ocean, and terrestrial biospherein a changing climate is critical to better understand the global carboncycle, support the development of climate policies, and project futureclimate change. Here we describe and synthesize datasets and methodology toquantify the five major components of the global carbon budget and theiruncertainties. Fossil CO2 emissions (EFOS) are based on energystatistics and cement production data, while emissions from land-use change(ELUC), mainly deforestation, are based on land use and land-use changedata and bookkeeping models. Atmospheric CO2 concentration is measureddirectly, and its growth rate (GATM) is computed from the annualchanges in concentration. The ocean CO2 sink (SOCEAN) is estimatedwith global ocean biogeochemistry models and observation-baseddata products. The terrestrial CO2 sink (SLAND) is estimated withdynamic global vegetation models. The resulting carbon budget imbalance(BIM), the difference between the estimated total emissions and theestimated changes in the atmosphere, ocean, and terrestrial biosphere, is ameasure of imperfect data and understanding of the contemporary carboncycle. All uncertainties are reported as ±1σ. For the firsttime, an approach is shown to reconcile the difference in our ELUCestimate with the one from national greenhouse gas inventories, supportingthe assessment of collective countries' climate progress. For the year 2020, EFOS declined by 5.4 % relative to 2019, withfossil emissions at 9.5 ± 0.5 GtC yr−1 (9.3 ± 0.5 GtC yr−1 when the cement carbonation sink is included), and ELUC was 0.9 ± 0.7 GtC yr−1, for a total anthropogenic CO2 emission of10.2 ± 0.8 GtC yr−1 (37.4 ± 2.9 GtCO2). Also, for2020, GATM was 5.0 ± 0.2 GtC yr−1 (2.4 ± 0.1 ppm yr−1), SOCEAN was 3.0 ± 0.4 GtC yr−1, and SLANDwas 2.9 ± 1 GtC yr−1, with a BIM of −0.8 GtC yr−1. Theglobal atmospheric CO2 concentration averaged over 2020 reached 412.45 ± 0.1 ppm. Preliminary data for 2021 suggest a rebound in EFOSrelative to 2020 of +4.8 % (4.2 % to 5.4 %) globally. Overall, the mean and trend in the components of the global carbon budgetare consistently estimated over the period 1959–2020, but discrepancies ofup to 1 GtC yr−1 persist for the representation of annual tosemi-decadal variability in CO2 fluxes. Comparison of estimates frommultiple approaches and observations shows (1) a persistent largeuncertainty in the estimate of land-use changes emissions, (2) a lowagreement between the different methods on the magnitude of the landCO2 flux in the northern extra-tropics, and (3) a discrepancy betweenthe different methods on the strength of the ocean sink over the lastdecade. This living data update documents changes in the methods and datasets used in this new global carbon budget and the progress in understandingof the global carbon cycle compared with previous publications of this dataset (Friedlingstein et al., 2020, 2019; LeQuéré et al., 2018b, a, 2016, 2015b, a, 2014, 2013). Thedata presented in this work are available at https://doi.org/10.18160/gcp-2021 (Friedlingstein et al., 2021). 

Abstract Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9 Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species.