Complex branching patterns in a newly recognized species of Compsocradus Berry et Stein (Iridopteridales) from the Middle Devonian of north Xinjiang, China

Specimens, including the largest known axes, of an iridopteridalean plant of late Middle Devonian age are described from northern Xinjiang, China. The plant consists of three orders branching and dichotomous appendages. The first-order axis probably represents the stem. Lateral organs (lower-order branches and appendages) are attached along the primary axis in up to 10 ranks. The insertion pattern can be broken down into cycles in which one lateral is inserted in each rank, and each cycle is divided into two loose whorls; in one loose whorl, laterals occur in about half of the ranks, some adjacent, and in the other loose whorl, laterals occur in the other ranks. These ranks are believed to map the position of xylem ribs of the vascular system, which has not been preserved. The appendages are isodichotomously divided up to five times. Pairs of recurved sporangia terminate the fertile appendages. A collection of small axes (second and third order) of this plant from the same locality, lacking the distinctive branching patterns displayed in our first order axes, was recently given the name Ramophyton givetianum by D. M. Wang. Our enlarged concept of the plant includes several morphological similarities to Compsocradus laevigatus Berry et Stein from Venezuela, particularly relating to the branching pattern. The Xinjiang plant is therefore reassigned to Compsocradus givetianus (Wang DM) Fu, Wang Y, Berry et Xu comb. nov. It further increases knowledge of branching patterns amongst Iridopteridales, important for evaluating relationships to other plant groups

Environmental influences on the stable carbon isotopic composition of Devonian and Early Carboniferous land plants

Systematic analysis of the stable carbon isotopic composition of fossil land plants (δ13Cp) has the potential to offer new insights regarding paleoclimate variation and plant-environment interactions in early terrestrial ecosystems. δ13Cp was measured for 190 fossil plant specimens belonging to 10 genera of Early to Late Devonian age (Archaeopteris, Drepanophycus, Haskinsia, Leclercqia, Pertica, Psilophyton, Rhacophyton, Sawdonia, Tetraxylopteris, and Wattieza) and 2 genera of Early Carboniferous age (Genselia and Rhodeopteridium) collected from sites located mainly in the Appalachian Basin (22–30°S paleolatitude). For the full carbon-isotopic dataset (n=309), δ13Cp ranges from −20.3‰ to −30.5‰ with a mean of −25.5‰, similar to values for modern C3 land plants. In addition to a secular trend, δ13Cp exhibits both intra- and intergeneric variation. Intrageneric variation is expressed as a small (mean 0.45‰) 13C-enrichment of leaves and spines relative to stems that may reflect differential compound-specific compositions. Intergeneric variation is expressed as a much larger (to ~5‰) spread in the mean δ13Cp values of coeval plant genera that was probably controlled by taxon-specific habitat preferences and local environmental humidity. Among Early Devonian taxa, Sawdonia yielded the most 13C-depleted values (−27.1 ± 1.7‰), reflecting lower water-use efficiency that was probably related to growth in wetter habitats, and Leclercqia, Haskinsia, and Psilophyton yielded the most 13C-enriched values (−23.0 ± 1.6‰, −22.3 ± 1.3‰, and −24.8 ± 1.6‰, respectively), reflecting higher water-use efficiency probably related to growth in drier habitats

Environmental influences on the stable carbon isotopic composition of Devonian and Early Carboniferous land plants

Systematic analysis of the stable carbon isotopic composition of fossil land plants (δ13Cp) has the potential to offer new insights regarding paleoclimate variation and plant-environment interactions in early terrestrial ecosystems. δ13Cp was measured for 190 fossil plant specimens belonging to 10 genera of Early to Late Devonian age (Archaeopteris, Drepanophycus, Haskinsia, Leclercqia, Pertica, Psilophyton, Rhacophyton, Sawdonia, Tetraxylopteris, and Wattieza) and 2 genera of Early Carboniferous age (Genselia and Rhodeopteridium) collected from sites located mainly in the Appalachian Basin (22–30°S paleolatitude). For the full carbon-isotopic dataset (n = 309), δ13Cp ranges from −20.3‰ to −30.5‰ with a mean of −25.5‰, similar to values for modern C3 land plants. In addition to a secular trend, δ13Cp exhibits both intra- and intergeneric variation. Intrageneric variation is expressed as a small (mean 0.45‰) 13C-enrichment of leaves and spines relative to stems that may reflect differential compound-specific compositions. Intergeneric variation is expressed as a much larger (to ~5‰) spread in the mean δ13Cp values of coeval plant genera that was probably controlled by taxon-specific habitat preferences and local environmental humidity. Among Early Devonian taxa, Sawdonia yielded the most 13C-depleted values (−27.1 ± 1.7‰), reflecting lower water-use efficiency that was probably related to growth in wetter habitats, and Leclercqia, Haskinsia, and Psilophyton yielded the most 13C-enriched values (−23.0 ± 1.6‰, −22.3 ± 1.3‰, and −24.8 ± 1.6‰, respectively), reflecting higher water-use efficiency probably related to growth in drier habitats

Provincial Devonian spores from South China, Saudi Arabia and Australia

A spore assemblage from Maoshan, Luquan County, Yunnan Province, South China includes well known Mid Devonian spores including Archaeozonotriletes variabilis, Cirratriradites monogrammos, Grandispora libyensis, Geminospora lemurata, Cymbosporites magnificus and Ancyrospora spp. which constrain the age to Givetian (late Mid Devonian). There are also elements that occur in the Givetian of South China and Australia such as Archaeoperisaccus indistinctus (senior synonym of A. rhacodes) that also occur very rarely in Saudi Arabia. The Maoshan assemblage moreover contains species of Rotaspora. In the Adavale Basin of Australia and Saudi Arabia there is a similar plexus of provincial species of Rotaspora but of Emsian age. In addition, there is the morphologically distinct spore Tribojasporites, a genus that was only known previously from the Emsian of Australia. The converse also occurs with spores such as Dictyotriletes biornatus, only previously known from the late Pragian to mid Emsian of Saudi Arabia, found as rare specimens in Maoshan. This demonstrates that the Maoshan spore assemblage contains spores that are restricted to the northern margin of Gondwana but with younger ranges and represent relict populations that survived in isolation on the South China terrane. Blooms of the hydrodictyacean chlorococcalean alga Musivum gradzinskii previously known only from Poland and Saudi Arabia are also present at Maoshan

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

[EN] The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a `SyntenyViewer¿ to view genome synteny between different cucurbit species and an `RNA-Seq¿ module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.USDA National Institute of Food and Agriculture Specialty Crop Research Initiative [2015-51181-24285]; US-Israel Binational Agricultural Research and Development Fund [IS-3333-02, IS-3877-06CR and IS-4223-09C]; USDA Agricultural Research Service, and by SNC Laboratoire ASL, de Ruiter Seeds B.V., Enza Zaden B.V., Gautier Semences S.A., Nunhems B.V., Rijk Zwaan B.V., Sakata Seed Inc, Semillas Fito S.A., Seminis Vegetable Seeds Inc, Syngenta Seeds B.V., Takii and Company Ltd, Vilmorin and Cie S.A. and Zeraim Gedera Ltd, all of them as part of the support to the International Cucurbit Genomics Initiative (ICuGI). Funding for open access charge: USDA National Institute of Food and Agriculture.Zheng, Y.; Wu, S.; Bai, Y.; Sun, H.; Jiao, C.; Guo, S.; Zhao, K.... (2018). Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research. 47(D1):D1128-D1136. https://doi.org/10.1093/nar/gky944SD1128D113647D

A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F8 population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ∼800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits

The Middle Devonian lycopsid Haskinsia Grierson et Banks from the Ruppert Coast, Marie Byrd Land, West Antarctica

New observations on leaves of herbaceous lycopsid specimens previously attributed to Drepanophycus schopfii Mildenhall from Marie Byrd Land, West Antarctica, indicate that they belong to Haskinsia colophylla Grierson et Banks. Haskinsia was a wide spread lycopsid during the Middle Devonian