Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses

Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses

A Chromosome-Scale Reference Assembly of a Tibetan Loach, Triplophysa siluroides

Cobitoidea is one of the two superfamilies in Cypriniformes; however, few genomes have been sequenced for Cobitoidea fishes. Here, we obtained a total of 252.90 Gb of short Illumina reads and 31.60 Gb of long PacBio Sequel reads, representing approximate genome coverage of 256x and 50x, respectively. The final assembled genome is about 583.47 Mb with contig N50 sizes of 2.87 Mb, which accounts for 91.44% of the estimated genome size of 638.07 Mb. Using Hi-C-based chromatin contact maps, 99.31% of the genome assembly was placed into 25 chromosomes, and the N50 is 22.3 Mb. The gene annotation completeness was evaluated by BUSCO, and 2,470 of the 2,586 conserved genes (95.5%) could be found in our assembly. Repetitive elements were calculated to reach 33.08% of the whole genome. Moreover, we identified 25,406 protein-coding genes, of which 92.59% have been functionally annotated. This genome assembly will be a valuable genomic resource to understand the biology of the Tibetan loaches and will also set a stage for comparative analysis of the classification, diversification, and adaptation of fishes in Cobitoidea

Infestation of Platypodine Beetles (Coleoptera: Curculionidae) on Rubber Trees in China

Lai, Shengchang, Wang, Jianguo, Fu, Yueguan, Duan, Bo, Hongchang, A, Zhang, Ling, Tarno, Hagus (2020): Infestation of Platypodine Beetles (Coleoptera: Curculionidae) on Rubber Trees in China. The Coleopterists Bulletin 74 (3): 626-631, DOI: 10.1649/0010-065X-74.3.626, URL: http://dx.doi.org/10.1649/0010-065x-74.3.62

Comparative Genomics of Pathogens Causing Brown Spot Disease of Tobacco: <i>Alternaria longipes</i> and <i>Alternaria alternata</i>

<div><p>The genus <i>Alternaria</i> is a group of infectious/contagious pathogenic fungi that not only invade a wide range of crops but also induce severe allergic reactions in a part of the human population. In this study, two strains <i>Alternaria longipes</i> cx1 and <i>Alternaria alternata</i> cx2 were isolated from different brown spot lesions on infected tobacco leaves. Their complete genomes were sequenced, <i>de novo</i> assembled, and comparatively analyzed. Phylogenetic analysis revealed that <i>A</i>. <i>longipes</i> cx1 and <i>A</i>. <i>alternata</i> cx2 diverged 3.3 million years ago, indicating a recent event of speciation. Seventeen non-ribosomal peptide synthetase (NRPS) genes and 13 polyketide synthase (PKS) genes in <i>A</i>. <i>longipes</i> cx1 and 13 NRPS genes and 12 PKS genes in <i>A</i>. <i>alternata</i> cx2 were identified in these two strains. Some of these genes were predicted to participate in the synthesis of non-host specific toxins (non-HSTs), such as tenuazonic acid (TeA), alternariol (AOH) and alternariol monomethyl ether (AME). By comparative genome analysis, we uncovered that <i>A</i>. <i>longipes</i> cx1 had more genes putatively involved in pathogen-plant interaction, more carbohydrate-degrading enzymes and more secreted proteins than <i>A</i>. <i>alternata</i> cx2. In summary, our results demonstrate the genomic distinction between <i>A</i>. <i>longipes</i> cx1 and <i>A</i>. <i>altenata</i> cx2. They will not only improve the understanding of the phylogenetic relationship among genus <i>Alternaria</i>, but more importantly provide valuable genomic resources for the investigation of plant-pathogen interaction.</p></div

<i>A</i>. <i>longipes</i> cx1 and <i>A</i>. <i>alternata</i> cx2 genome features.

<p><i>A</i>. <i>longipes</i> cx1 and <i>A</i>. <i>alternata</i> cx2 genome features.</p

Three gene families specific to <i>A</i>. <i>longipes</i> cx1 and <i>A</i>. <i>alternata</i> cx2 have different gene copies between these two strains.

<p>Three gene families specific to <i>A</i>. <i>longipes</i> cx1 and <i>A</i>. <i>alternata</i> cx2 have different gene copies between these two strains.</p

Phylogenetic relationship between CX1 and CX2.

<p>(A) Phylogenetic relationship constructed by MEGA5 based on ITS sequences of CX1, CX2, <i>A</i>. <i>longipes</i> EGS30-033, <i>A</i>. <i>alternata</i> SDHeze-9, <i>A</i>. <i>tenuissima</i> CSPF5 and <i>A</i>. <i>brassicicola</i> Ab4UP. (B) Phylogenetic relationship constructed by MEGA5 based on large co-linear sequence among CX1, CX2, <i>A</i>. <i>alternata</i> atcc11680, <i>A</i>. <i>longipes</i> bmp0313 and <i>A</i>. <i>tenuissima</i> bmp0304.</p

Phylogenetic relationship among <i>A</i>. <i>longipes</i> cx1, <i>A</i>. <i>alternata</i> cx2, <i>F</i>. <i>oxysporum</i>, <i>M</i>. <i>oryzae</i>, <i>A</i>. <i>nidulans</i>, <i>L</i>. <i>maculans</i>, <i>P</i>. <i>teres</i>, <i>P</i>. <i>nodorum</i>, <i>A</i>. <i>abrassicicola and A</i>. <i>alternata</i> SRC1lrK1f.

<p>The estimates of divergence time and its interval based on sequence identity are indicated at each node. The red dot on branches means divergence time has been adjusted by fossil evidence.</p

Novel Microporous Metal–Organic Framework Exhibiting High Acetylene and Methane Storage Capacities

A new organic hexacarboxylic acid, 5,5′,5″-(9<i>H</i>-carbazole-3,6,9-triyl)­triisophthalic acid (H₆CTIA), was developed to construct its first microporous metal–organic framework (MOF), Cu₆(CTIA)₂ (ZJU-70). With open metal sites and suitable pore sizes, this MOF exhibits high acetylene and methane storage capacities at room temperature