Cotton Genomics and Genetics 2024, Vol.15, No.2, 112-126 http://cropscipublisher.com/index.php/cgg 114 technology. PacBio reads can span several kilobases, providing a more comprehensive view of the genome, including complex regions and structural variants. This technology offers significant advantages in resolving complex genomic regions, including large structural variations and repetitive sequences. This technology is particularly advantageous for de novo genome assembly and the identification of full-length transcripts without the need for assembly (Cui et al., 2020; Athanasopoulou et al., 2021). Despite its benefits, PacBio sequencing can be more expensive and has a higher error rate compared to short-read technologies (Lang et al., 2020). Figure 1 Scientific background of both third-generation sequencing technologies (Adopted from Athanasopoulou et al., 2021) Image caption: (a) PacBio sequencing. The method is based on DNA sequencing by synthesis. The mobile single-stranded DNA is attached to the stable polymerase, which catalyzes the incorporation of dNTPs in a newly synthesized complementary DNA strand. The reaction occurs in specially designed zero-mode waveguides (ZMWs) that enable the observation of the emitted light. Afterwards, the signal is translated into nucleotide sequence, a procedure known as basecalling; (b) Nanopore sequencing. The method relies on the guidance of a single-stranded DNA or RNA molecule to a nanopore, a reader protein that detects alterations in the electrical current, which occurs during the passing through of the DNA/RNA (Adopted from Athanasopoulou et al., 2021)
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