Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Feb 1;27(1):dsaa004.
doi: 10.1093/dnares/dsaa004.

Genome-wide analysis of short interspersed nuclear elements provides insight into gene and genome evolution in citrus

Haijun Meng  1 , Jiancan Feng  1 , Tuanhui Bai  1 , Zaihai Jian  1 , Yanhui Chen  1 , Guoliang Wu  1
Affiliations

Genome-wide analysis of short interspersed nuclear elements provides insight into gene and genome evolution in citrus

Haijun Meng et al. DNA Res. .

Abstract

Short interspersed nuclear elements (SINEs) are non-autonomous retrotransposons that are highly abundant, but not well annotated, in plant genomes. In this study, we identified 41,573 copies of SINEs in seven citrus genomes, including 11,275 full-length copies. The citrus SINEs were distributed among 12 families, with an average full-length rate of 0.27, and were dispersed throughout the chromosomes, preferentially in AT-rich areas. Approximately 18.4% of citrus SINEs were found in close proximity (≤1 kb upstream) to genes, indicating a significant enrichment of SINEs in promoter regions. Citrus SINEs promote gene and genome evolution by offering exons as well as splice sites and start and stop codons, creating novel genes and forming tandem and dispersed repeat structures. Comparative analysis of unique homologous SINE-containing loci (HSCLs) revealed chromosome rearrangements in sweet orange, pummelo, and mandarin, suggesting that unique HSCLs might be valuable for understanding chromosomal abnormalities. This study of SINEs provides us with new perspectives and new avenues by which to understand the evolution of citrus genes and genomes.

Keywords: citrus; evolution; gene association; genome; short interspersed nuclear elements.

PubMed Disclaimer

Figures

Figure 1
Figure 1
The full-length rate of citrus SINEs characterized on the SINE family and genome level. Full-length rates for each family are presented for Clementine mandarin, Satsuma mandarin, Mangshan wild mandarin, pummelo, sweet orange, citron, Ichang papeda, and the average across all seven genomes (average). The dashed line represents the average full-length rate of all citrus SINEs.
Figure 2
Figure 2
Graphical representation of insertion site preferences and dendrogram showing the divergence and grouping of citrus SINE families. (A) Relative nucleotide frequency at five positions upstream of the 5′ TSD (positions −5 to −1) and the first six positions of the 5′ TSD (positions 0–5). (B) The dendrogram is based on the 20 full-length SINE sequences of each citrus SINE family that had the highest similarity to the consensus sequence. The insertion site preferences of the remaining seven SINE families are shown in Supplementary Fig. S3.
Figure 3
Figure 3
Comparison of copy numbers and sequence similarities among citrus SINE families. For three SINE families, histograms were created based on the identity of each full-length SINE copy within the family to the consensus sequence. Different example patterns are shown, namely, (A) a consistent activity over a long period, (B) a recent activity, (C) transposition activity a long time ago, and (D) an aged, rapid amplification. The complete data for the remaining 74 SINE families by genome are shown in Supplementary Fig. S4.
Figure 4
Figure 4
Genomic sequence variations derived from SINE insertion. (A) Alignment of reference sequences of a predicted polygalacturonase gene showing the location of a SINE insertion and PCR primers. The inserted SINEs were mainly derived from CitruS-IIa. Three PCR primers are indicated with green arrowheads. TSDs are indicated with green line, poly(A) tail is indicated with red box. (B) PCR results of two primer pairs using three primers. Lane 1: Clementine mandarin (cultivar ‘Caffin’); lanes 2–8: sweet orange (cultivars ‘Valencia’, ‘Qingjia’, ‘Lunwan’, ‘Xuecheng’, ‘Hamlin’, ‘Newhall’, and ‘Jinchen’, respectively); lanes 9–11: mandarins (cultivars ‘Ponkan’, ‘Guoqing I’, and ‘Bendizao’, respectively); lanes 12–14 : pummelo (cultivars ‘Chandler’, ‘Guanximiyou’, and ‘Gaoban’, respectively); and lane M: DNA ladder. White triangle I indicates PCR products of primer_forward + primer_reverse_outside with a SINE insertion (473 bp). White triangle II indicates PCR products of primer_forward + primer_reverse_inside which suggested a SINE insertion (212 bp). White triangle III indicates PCR products of primer_forward + primer_reverse_outside without a SINE insertion (129 bp). (C) Chromosomal location of the SINE insertion.
Figure 5
Figure 5
Gene association and chromosomal distribution of citrus SINEs. (A) The frequency and position of citrus SINEs relative to the annotated genes for each genome. The average distribution across all seven genomes is shown in ‘the average of citrus’. (B) Chromosomal mapping of all SINEs in pummelo, sweet orange, and Satsuma mandarin. Scale provided in Mbp.
Figure 6
Figure 6
The pattern of SINEs affecting the splicing and translation of annotated genes and creating novel genes in sweet orange. Citrus SINEs were identified that (A) created a new exon and contributed two splice sites, (B and F) provided the first exon donating a start codon and (B) a 5′ splice site, (C and D) donated stop codons, and (E, F) created novel genes.
Figure 7
Figure 7
Chromosomal rearrangements revealed by unique HSCLs. Distribution of syntenic blocks linked to scaffold 1 of Clementine mandarin (A) and chromosome 1 of Satsuma mandarin (B). All 12 SINE families were included. Sweet orange is a descendant of ancient pummelo and an ancestor of Clementine mandarin.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Harris C.J., Scheibe M., Wongpalee S.P., et al.2018, A DNA methylation reader complex that enhances gene transcription, Science, 362, 1182–6. - PMC - PubMed
    1. Naito K., Zhang F., Tsukiyama T., et al.2009, Unexpected consequences of a sudden and massive transposon amplification on rice gene expression, Nature, 461, 1130–4. - PubMed
    1. Wang L., He F., Huang Y., et al.2018, Genome of wild mandarin and domestication history of mandarin, Mol. Plant, 11, 1024–37. - PubMed
    1. Zhang J., Yu C., Krishnaswamy L., Peterson T. 2011, Transposable elements as catalysts for chromosome rearrangements. In: Birchler J.A., ed., Plant Chromosome Engineering: Methods and Protocols, Humana Press: Totowa, NJ, pp. 315–26. - PubMed
    1. Feinberg A.P. 2007, Phenotypic plasticity and the epigenetics of human disease, Nature, 447, 433–40. - PubMed