TEsorter: An accurate and fast method to classify LTR-retrotransposons in plant genomes

Zhang, Rengang; Li, Guangyuan; Wang, Xiaoling; Dainat, Jacques; Wang, Zhaoxuan; Ou, Shujun; Ma, Yongpeng

doi:10.1093/hr/uhac017

Cited by 132 publications

(90 citation statements)

References 10 publications

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“…To do this, LTR‐TRs are de novo detected using the LTR harvest v.1.6.1 (Ellinghaus et al ., 2008) and LTR finder v.1.07 (Xu & Wang, 2007) programs. To reduce false‐positives, TE sorter v.1.3.0 (Zhang et al ., 2022) is used to reconstruct the classification of LTR‐RTs and further refine this classification. The subgenome‐specific k ‐mer sequences are mapped to the LTR‐RT sequences using a substring match procedure to identify the subgenome‐specific LTR‐RTs by Fisher’s exact test.…”

Section: Methodsmentioning

confidence: 99%

SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome‐specific k‐mers

Jia

Wang²,

Wang

et al. 2022

New Phytologist

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Summary With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome‐phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome‐specific sequence (k‐mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome‐specific sequences like wheat, but fails on autopolyploids lacking subgenome‐specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.

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Section: Methodsmentioning

confidence: 99%

SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome‐specific k‐mers

Jia

Wang²,

Wang

et al. 2022

New Phytologist

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“…The species‐specific k ‐mers were identified first, then an LTR‐RT library was constructed through scanning the assembled genome by calling LTR harvest (Ellinghaus et al, 2008) and LTR Finder (Xu and Wang, 2007). The clade level of LTR‐RTs was classified by TEsorter (https://github.com/zhangrengang/TEsorter) (Zhang et al, 2022) and the LTR‐RT protein domains (INT, RH and RT domains) were identified and extracted. LTR‐RT protein sequences were aligned with Mafft (Katoh and Standley, 2013) and then merged into one sequence.…”

Section: Methodsmentioning

confidence: 99%

Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)

Zhang

Qiao

et al. 2022

JIPB

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Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosome‐level genome sequence of the hawthorn cultivar “Qiu Jinxing.” We assembled an 823.41 Mb genome encoding 40 571 genes and further anchored the 779.24 Mb sequence into 17 pseudo‐chromosomes, which account for 94.64% of the assembled genome. Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae (apple tribe) at approximately 35.4 Mya. Notably, genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome. In addition, our results indicated that the Maleae share a unique ancient tetraploidization event; however, no recent independent whole‐genome duplication event was specifically detected in hawthorn. The amplification of non‐specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome. Furthermore, we identified two paleo‐sub‐genomes in extant species of Maleae and found that these two sub‐genomes showed different rearrangement mechanisms. We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleo‐polyploid origin patterns (autopolyploidization or allopolyploidization) of Maleae. Overall, our study provides an improved context for understanding the evolution of Maleae species, and this new high‐quality reference genome provides a useful resource for the horticultural improvement of hawthorn.

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“…In order to examine the evolutionary dynamics of LTR-RTs that determine rice genome size variation, 8,154 intact LTR-RTs from the twelve Oryza genomes, belonging to AA-, BB-, CC-, FF-, and GG genome types, were detected and classified by TEsorter ( Zhang et al, 2022 ; Figure 3 ). Of them, Ale is the lineage with the most abundant and the longest length of intact LTR RTs of the Copia superfamily among AA, BB, and GG genome types, while the Ivana lineage harbored the most intact LTR-RTs in O. officinalis and O. brachyantha ( Figure 3 ).…”

Section: Resultsmentioning

confidence: 99%

“…All intact LTR-RTs generated by LTR_retriever (version 2.8) ( Ou and Jiang, 2018 ) were classified by TEsorter with default parameters ( Zhang et al, 2022 ). The terminal repeat regions and other non-coding regions are the fastest evolving parts of TEs.…”

Section: Methodsmentioning

confidence: 99%

Genome Size Variation and Evolution Driven by Transposable Elements in the Genus Oryza

et al. 2022

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Genome size variation and evolutionary forces behind have been long pursued in flowering plants. The genus Oryza, consisting of approximately 25 wild species and two cultivated rice, harbors eleven extant genome types, six of which are diploid (AA, BB, CC, EE, FF, and GG) and five of which are tetraploid (BBCC, CCDD, HHJJ, HHKK, and KKLL). To obtain the most comprehensive knowledge of genome size variation in the genus Oryza, we performed flow cytometry experiments and estimated genome sizes of 166 accessions belonging to 16 non-AA genome Oryza species. k-mer analyses were followed to verify the experimental results of the two accessions for each species. Our results showed that genome sizes largely varied fourfold in the genus Oryza, ranging from 279 Mb in Oryza brachyantha (FF) to 1,203 Mb in Oryza ridleyi (HHJJ). There was a 2-fold variation (ranging from 570 to 1,203 Mb) in genome size among the tetraploid species, while the diploid species had 3-fold variation, ranging from 279 Mb in Oryza brachyantha (FF) to 905 Mb in Oryza australiensis (EE). The genome sizes of the tetraploid species were not always two times larger than those of the diploid species, and some diploid species even had larger genome sizes than those of tetraploids. Nevertheless, we found that genome sizes of newly formed allotetraploids (BBCC-) were almost equal to totaling genome sizes of their parental progenitors. Our results showed that the species belonging to the same genome types had similar genome sizes, while genome sizes exhibited a gradually decreased trend during the evolutionary process in the clade with AA, BB, CC, and EE genome types. Comparative genomic analyses further showed that the species with different rice genome types may had experienced dissimilar amplification histories of retrotransposons, resulting in remarkably different genome sizes. On the other hand, the closely related rice species may have experienced similar amplification history. We observed that the contents of transposable elements, long terminal repeats (LTR) retrotransposons, and particularly LTR/Gypsy retrotransposons varied largely but were significantly correlated with genome sizes. Therefore, this study demonstrated that LTR retrotransposons act as an active driver of genome size variation in the genus Oryza.

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TEsorter: An accurate and fast method to classify LTR-retrotransposons in plant genomes

Cited by 132 publications

References 10 publications

SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome‐specific k‐mers

SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome‐specific k‐mers

Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)

Genome Size Variation and Evolution Driven by Transposable Elements in the Genus Oryza

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