Repetitive Sequences in the Potato and Related Genomes

Grover, Atul; Sharma, Prakash C.

doi:10.1007/978-3-319-66135-3_9

Cited by 2 publications

(2 citation statements)

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“…Long terminal repeat (LTR) sequences are non-coding regions evolving more rapidly than other components of LTR-RTs [58]. They contain start and stop signals of transcription [53,57,59], polyadenylation signals, and enhancers [60] that are critical to the replication process [10].…”

Section: Structure Diversity Dynamics and Function Of Retrotranmentioning

confidence: 99%

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Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning

Orozco-Arias

Isaza

Guyot

2019

IJMS

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Transposable elements (TEs) are genomic units able to move within the genome of virtually all organisms. Due to their natural repetitive numbers and their high structural diversity, the identification and classification of TEs remain a challenge in sequenced genomes. Although TEs were initially regarded as “junk DNA”, it has been demonstrated that they play key roles in chromosome structures, gene expression, and regulation, as well as adaptation and evolution. A highly reliable annotation of these elements is, therefore, crucial to better understand genome functions and their evolution. To date, much bioinformatics software has been developed to address TE detection and classification processes, but many problematic aspects remain, such as the reliability, precision, and speed of the analyses. Machine learning and deep learning are algorithms that can make automatic predictions and decisions in a wide variety of scientific applications. They have been tested in bioinformatics and, more specifically for TEs, classification with encouraging results. In this review, we will discuss important aspects of TEs, such as their structure, importance in the evolution and architecture of the host, and their current classifications and nomenclatures. We will also address current methods and their limitations in identifying and classifying TEs.

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Section: Structure Diversity Dynamics and Function Of Retrotranmentioning

confidence: 99%

“…Non-LTR retrotransposons often contain a poly-A tail at the 3′end as a result of the transcription cycle [58,77]. SINEs are also terminated by an A-rich tail but, unlike LINEs, they have a sequence similarity to the host genes.…”

Section: Structure Diversity Dynamics and Function Of Retrotranmentioning

confidence: 99%