Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis

Costa, Zirlane Portugal; Cauz-Santos, Luiz Augusto; Ragagnin, Geovani Tolfo; Sluys, Marie‐Anne Van; Dornelas, Marcelo Carnier; Bergès, Hélène; Varani, Alessandro de Mello; Vieira, Maria Lúcia Carneiro

doi:10.1007/s11033-019-05047-4

Cited by 8 publications

(16 citation statements)

References 99 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Intriguingly, long interspersed nuclear elements have significantly proliferated in P. organensis, although they are less probable in plants (Wicker et al, 2007). In addition, insertion time analysis suggested that LTR-RTs were recently inserted into the P. organensis genome, a pattern similar to that found in P. edulis (Costa et al, 2019), possibly indicating that full-length LTR-RT elements have recently become active. Note that repetitive sequences are very difficult to assemble and, consequently, can result in highly fragmented assemblies.…”

Section: Discussionmentioning

confidence: 81%

“…Most of the TEs were located in intergenic spaces (∼70%), although some overlapped genes. Long terminal repeat retroelements predominated, consisting mainly of Gypsy elements, with overrepresentation of the RLG_peDel (or Tekay lineage according to Neumann et al [2019]), and single elements of P. edulis were obtained for the first time (Costa et al, 2019). Additionally, Sader, Dias, et al (2019), who used a Gypsy element sequence as a probe for in situ hybridization, found a dispersed and uniform distribution pattern along P. edulis chromosomes, implying that they were abundant and could have significantly influenced the genome size.…”

Section: Introductionmentioning

confidence: 99%

“…Long terminal repeat retroelements predominated, consisting mainly of Gypsy elements, with over‐representation of the RLG_peDel (or Tekay lineage according to Neumann et al. [2019]), and single elements of P. edulis were obtained for the first time (Costa et al., 2019). Additionally, Sader, Dias, et al.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis

et al. 2021

Self Cite

View full text Add to dashboard Cite

The genus Passiflora comprises a large group of plants popularly known as passionfruit, much appreciated for their exotic flowers and edible fruits. The species (∼500) are morphologically variable (e.g., growth habit, size, and color of flowers) and are adapted to distinct tropical ecosystems. In this study, we generated the genome of the wild diploid species Passiflora organensis Gardner by adopting a hybrid assembly approach. Passiflora organensis has a small genome of 259 Mbp and a heterozygosity rate of 81%, consistent with its reproductive system. Most of the genome sequences could be integrated into its chromosomes with cytogenomic markers (satellite DNA) as references. The repeated sequences accounted for 58.55% of the total DNA analyzed, and the Tekay lineage was the prevalent retrotransposon. In total, 25,327 coding genes were predicted. Passiflora organensis retains 5,609 singletons and 15,671 gene families. We focused on the genes potentially involved in the locus determining

show abstract

Section: Discussionmentioning

confidence: 81%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…Mpb, Yotoko et al 2011), Costa et al (2019) corroborated Angela as the most abundant lineage (1.9%) from the Ty1/copia superfamily (3.12%), although -Tekay (8.5%, referred to as Del) from Ty3/gypsy (10.52%) was more abundant in their analysis. In P. organensis, Tekay accounted for most of its repetitive fraction as seen in P. quadrangularis, Angela was not detected, suggesting it might have played a significant role in its reduced genome size.…”

Section: Such Differences In Percentage Of Te Explains Most Of the DImentioning

confidence: 84%

Large vs small genomes inPassiflora: the influence of the mobilome and the satellitome

Sader

Vaio

Cauz-Santos

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a ten-fold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of these genera representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified Long Terminal Repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicate that while large genome evolve by an accumulation of retrotransponsons, small genomes most evolved by diversification of different repeat types, particularly satDNAs.

show abstract

“…It is deemed that the 5′ and 3’ LTRs are the same at transposition time for each LTR-RT. Consequently, based on nucleotide substitutions/divergence among LTR-RT, the 5’ and 3’ LTRs accumulated through ages were applied to estimate the insertion time [ 86 – 88 ]. In the present investigation, the 5′ and 3’ LTR nucleotide substitutions were used to estimate the identified intact LTR-RT insertion time across Cicer species.…”

Section: Resultsmentioning

confidence: 99%

CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species

et al. 2021

View full text Add to dashboard Cite

Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php

show abstract

Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis

Cited by 8 publications

References 99 publications

A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis

A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis

Large vs small genomes inPassiflora: the influence of the mobilome and the satellitome

CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species

Contact Info

Product

Resources

About