Maize was domesticated from lowland teosinte (Zea mays ssp. parviglumis), but the contribution of highland teosinte (Zea mays ssp. mexicana, hereafter mexicana) to modern maize is not clear. Here, two genomes for Mo17 (a modern maize inbred) and mexicana are assembled using a meta-assembly strategy after sequencing of 10 lines derived from a maize-teosinte cross. Comparative analyses reveal a high level of diversity between Mo17, B73, and mexicana, including three Mb-size structural rearrangements. The maize spontaneous mutation rate is estimated to be 2.17 × 10−8 ~3.87 × 10−8 per site per generation with a nonrandom distribution across the genome. A higher deleterious mutation rate is observed in the pericentromeric regions, and might be caused by differences in recombination frequency. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Our data offer a rich resource for constructing the pan-genome of Zea mays and genetic improvement of modern maize varieties.

Long intergenic non-coding RNAs (lincRNAs) may play widespread roles in gene regulation and other biological processes, however, a systematic examination of the functions of lincRNAs in the biological responses of rice to phosphate (Pi) starvation has not been performed. Here, we used a computational method to predict the functions of lincRNAs in Pi-starved rice. Overall, 3,170 lincRNA loci were identified using RNA sequencing data from the roots and shoots of control and Pi-starved rice. A competing endogenous RNA (ceRNA) network was constructed for each tissue by considering the competing relationships between lincRNAs and genes, and the correlations between the expression levels of RNAs in ceRNA pairs. Enrichment analyses showed that most of the communities in the networks were related to the biological processes of Pi starvation. The lincRNAs in the two tissues were individually functionally annotated based on the ceRNA networks, and the differentially expressed lincRNAs were biologically meaningful. For example, XLOC_026030 was upregulated from 3 days after Pi starvation, and its functional annotation was ‘cellular response to Pi starvation’. In conclusion, we systematically annotated lincRNAs in rice and identified those involved in the biological response to Pi starvation.

Summary Long intergenic non‐coding RNAs (lincRNAs) play important roles in various biological processes in plants. However, little information is known about the evolutionary characteristics of lincRNAs among closely related plant species. Here, we present a large‐scale comparative study of lincRNA transcription patterns in nine citrus species. By strand‐specific RNA‐sequencing, we identified 18 075 lincRNAs (14 575 lincRNA loci) from 34 tissue samples. The results indicated that the evolution of lincRNA transcription is more rapid than that of mRNAs. In total, 82.8–97.6% of sweet orange (Citrus sinensis) lincRNA genes were shown to have homologous sequences in other citrus genomes. However, only 15.5–28.8% of these genes had transcribed homologous lincRNAs in these citrus species, presenting a strong contrast to the high conservation of mRNA transcription (81.6–84.7%). Moreover, primitive and modern citrus lincRNAs were preferentially expressed in reproductive and vegetative organs, respectively. Evolutionarily conserved lincRNAs showed higher expression levels and lower tissue specificity than species‐specific lincRNAs. Notably, we observed a similar tissue expression pattern of homologous lincRNAs in sweet orange and pummelo (Citrus grandis), suggesting that these lincRNAs may be functionally conserved and selectively maintained. We also identified and validated a lincRNA with the highest expression in fruit that acts as an endogenous target mimic (eTM) of csi‐miR166c, and two lincRNAs that act as a precursor and target of csi‐miR166c, respectively. These lincRNAs together with csi‐miR166c could form an eTM166‐miR166c‐targeted lincRNA regulatory network that possibly affects citrus fruit development.

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turbot (Scophthalmus maximus) is a commercially important flatfish species in aquaculture. It has a drastic sexual dimorphism, with females growing faster than males. In the present study, we sequenced and de novo assembled female and male turbot genomes. The assembled female genome was 568 Mb (scaffold N50, 6.2 Mb, BUSCO 97.4%), and the male genome was 584 Mb (scaffold N50, 5.9 Mb, BUSCO 96.6%). Using two genetic maps, we anchored female scaffolds representing 535 Mb onto 22 chromosomes. Annotation of the female anchored genome identified 87.8 Mb transposon elements and 20,134 genes. We identified 17,936 gene families, of which 369 gene families were flatfish specific. Phylogenetic analysis showed that the turbot, Japanese flounder and Chinese tongue sole form a clade that diverged from other teleosts approximately 78 Mya. This report of female and male turbot draft genomes and annotated genes provides a new resource for identifying sex determination genes, elucidating the evolution of adaptive traits in flatfish and developing genetic techniques to increase the sustainability of turbot aquaculture. Background & Summary Turbot (Scophthalmus maximus) is an economically important flatfish with both eyes on the upper side of the body, and it is commonly found along the Atlantic coast of Europe. Aquaculture of turbot was initiated in Scotland in the 1970s and subsequently expanded into other European countries by the early 1980s 1. In the 1990s, turbot was introduced to China where its farming has since developed rapidly. China is currently the largest producer of turbot in the world 2. Turbot growth is sexually dimorphic, with females eventually attaining sizes up to 50% larger than those of males 3. An all-female stock can potentially increase the production value of turbot aquaculture. The sex determination system of turbot follows the ZW/ZZ model, and this system can be affected by environmental factors 4. Therefore, understanding the genomic architecture of female and male turbot may enable screening for sex determination loci, improve understanding of the interactions between genetic and environmental factors in sex determination, and lead to the acquisition of genomic resources for molecular breeding. Four sex-related QTLs, located on four different linkage groups, have been found in turbot 5. Though the turbot genome has been assembled, the sex-determining mechanism of turbot remains unclear 6. In this study, we sequenced, assembled and annotated the female and male turbot genomes, and conducted a phylogenetic analysis using the genome sequences of eight other closely related species. A 568 Mb female genome sequence and 584 Mb male genome sequence were assembled. The draft turbot genomes represent a valuable resource for isolating the sex determination genes, increasing our understanding of flatfish development and improving the molecular breeding techniques for turbot. Methods Turbot samples and genome sequencing. One female (ZW) and one male (ZZ) adult turbot were selected for whole genome shotgun sequenci...

Agrobacterium tumefaciens strain C58 is a Gram-negative soil bacterium capable of inducing tumors (crown galls) on many dicotyledonous plants. The genome of A. tumefaciens strain C58 was re-annotated based on the Z-curve method. First, all the ‘hypothetical genes’ were re-identified, and 29 originally annotated ‘hypothetical genes’ were recognized to be non-coding open reading frames (ORFs). Theoretical evidence obtained from principal component analysis, clusters of orthologous groups of proteins occupation, and average length distribution showed that these non-coding ORFs were highly unlikely to encode proteins. Results from the reverse transcription-polymerase chain reaction (RT-PCR) experiments on three different growth stages of A. tumefaciens C58 confirmed that 23 (79%) of the identified non-coding ORFs have no transcripts in these growth stages. In addition, using theoretical prediction, 19 potential protein-coding genes were predicted to be new protein-coding genes. Fifteen (79%) of these genes were verified with RT-PCR experiments. The RT-PCR experimental results confirmed the reliability of our theoretical prediction, indicating that false-positive prediction and missing genes always exist in the annotation of A. tumefaciens C58 genome. The improved annotation will serve as a valuable resource for the research of the lifestyle, metabolism, and pathogenicity of A. tumefaciens C58. The re-annotation of A. tumefaciens C58 can be obtained from http://211.69.128.148/Atum/.

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Vibrio harveyi is a major bacterial pathogen that causes fatal vibriosis in Chinese tongue sole (Cynoglossus semilaevis), resulting in massive mortality in the farming industry. However, the molecular mechanisms of C. semilaevis response to V. harveyi infection are poorly understood. Here, we performed transcriptomic analysis of C. semilaevis, comparing resistant and susceptible families in response to V. harveyi challenge (CsRC and CsSC) and control conditions (CsRU and CsSU). RNA libraries were constructed using 12 RNA samples isolated from three biological replicates of the four groups. We performed transcriptome sequencing on an Illumina HiSeq platform, and generating a total of 1,095 million paired-end reads, with the number of clean reads per library ranging from 75.27 M to 99.97 M. Through pairwise comparisons among the four groups, we identified 713 genes exhibiting significant differences at the transcript level. Furthermore, the expression levels were validated by real-time qPCR. Our results provide a valuable resource and new insights into the immune response to V. harveyi infection.