LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice

Analyzing lignin biosynthesis pathways in rattan using improved co-expression networks of NACs and MYBs

BACKGROUND

The rattan is a valuable plant resource with multiple applications in tropical forests. Calamus simplicifolius and Daemonorops jenkinsiana are the two most representative rattan species, supplying over 95% of the raw materials for the rattan industry. Hence, the wood properties of both rattans have always attracted researchers' attention.

RESULTS

We re-annotated the genomes, obtained 81 RNA-Seq datasets, and developed an improved pipeline to increase the reliability of co-expression networks of both rattans. Based on the data and pipeline, co-expression relationships were detected in 11 NACs, 49 MYBs, and 86 lignin biosynthesis genes in C. simplicifolius and four NACs, 59 MYBs, and 76 lignin biosynthesis genes in D. jenkinsiana, respectively. Among these co-expression pairs, several genes had a close relationship to the development of wood properties. Additionally, we detected the enzyme gene on the lignin biosynthesis pathway was regulated by either NAC or MYB, while LACCASES was regulated by both NAC and MYB. For D. jenkinsiana, the lignin biosynthesis regulatory network was characterized by positive regulation, and MYB possible negatively regulate non-expressed lignin biosynthesis genes in stem tissues. For C. simplicifolius, NAC may positively regulate highly expressed genes and negatively regulate non-expressed lignin biosynthesis genes in stem tissues. Furthermore, we established core regulatory networks of NAC and MYB for both rattans.

CONCLUSIONS

This work improved the accuracy of rattan gene annotation by integrating an efficient co-expression network analysis pipeline, enhancing gene coverage and accuracy of the constructed network, and facilitating an understanding of co-expression relationships among NAC, MYB, and lignin biosynthesis genes in rattan and other plants.

Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation

Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.

With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa. We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2 Mb and 62.9 Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.

Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.

Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome.

Genome-wide Annotation and Comparative Analysis of Long Terminal Repeat Retrotransposons between Pear Species of P. bretschneideri and P. Communis

Recent sequencing of the Oriental pear (P. bretschneideri Rehd.) genome and the availability of the draft genome sequence of Occidental pear (P. communis L.), has provided a good opportunity to characterize the abundance, distribution, timing, and evolution of long terminal repeat retrotransposons (LTR-RTs) in these two important fruit plants. Here, a total of 7247 LTR-RTs, which can be classified into 148 families, have been identified in the assembled Oriental pear genome. Unlike in other plant genomes, approximately 90% of these elements were found to be randomly distributed along the pear chromosomes. Further analysis revealed that the amplification timeframe of elements varies dramatically in different families, super-families and lineages, and the Copia-like elements have highest activity in the recent 0.5 million years (Mys). The data also showed that two genomes evolved with similar evolutionary rates after their split from the common ancestor ~0.77–1.66 million years ago (Mya). Overall, the data provided here will be a valuable resource for further investigating the impact of transposable elements on gene structure, expression, and epigenetic modification in the pear genomes.

[Identification and analysis methods of plant LTR retrotransposon sequences]

LTR retrotransposons are an important class of eukaryotic transposable elements, which are ubiquitous and highly heterogeneous in plant and play a major role in genome evolution of eukaryote. They are now extensively employed in gene function and genetic diversity analyses. Identification of LTR retrotransposons is the precondition for its application. Therefore, it has important theoretical significance and practical application value in studying identification and analysis methods LTR retrotransposon sequences. Bioinformatic software of the sequence analysis, according to the work principle, can be classified roughly into two types: sequence alignment and sequence identification of conserved domains. Alignment software, such as BLAST and DNAstar, produce the corresponding sequence information through comparison of sequence similarity; however, this kind of software cannot be applied for full length sequences. According to the principle, LTR retro-transposon sequence identification software can be roughly sorted into four types: de novo repeat discovery method, com-parative genomic method, homology-based method, and structure-based method. For example, LTR_Finder based on de novo repeat discovery method can accurately predict and annotate LTR retrotransposons for full length sequences; Repeat-Masker, which is based on homology-based method, can discover LTR retrotransposons by comparing the similarity with known sequences in the database. In this article, different methods of identification and analysis of retrotransposon se-quences were compared and analyzed, and a set of flow of LTR retrotransposons sequence analysis was summarized in order to provide the reference for LTR retrotransposons sequence analysis.

Paleogenomic analysis of the short arm of chromosome 3 reveals the history of the African and Asian progenitors of cultivated rices

Rice is one of the most important crops, feeding more than half of the world population. There are two cultivated species, the African rice Oryza glaberrima and the Asian rice O. sativa. Although the African species is gradually replaced by O. sativa in most of African rice agrosystems, this species represents an important reservoir of genes of agronomical interest. Their exploitation for the development of modern African rice varieties requires a good understanding of the genetic relationships between the two cultivated species. We took advantage of the recent availability of the sequence of the chromosome 3 short arm of O. glaberrima to estimate the date of radiation between O. glaberrima and O. sativa lineages, using all the long terminal repeat (LTR)-retrotransposons as paleogenomic markers. We first demonstrated that in two distinct lineages, LTR-retrotransposons mutate at the same rate. Based on LTR-retrotransposons shared by both species in orthologous position, we then estimated that O. glaberrima and O. sativa progenitors diverged 1.2 Ma. This constitutes one of the first studies using such a large sample of transposable elements to reconstruct the phylogeny of species. Given the number of genome sequencing projects, there is no doubt that such approach will allow to resolve phylogenetic incongruities. The application of this method to other plant genomes will also facilitate further understanding of evolution of LTR-retrotransposons and eventually of the whole genome in divergent plant lineages.