TY - GEN

T1 - Relevance of integration of cytogenetics data and chromosome-length genome assemblies at the example of various vertebrates' groups

AU - Романенко, Светлана Анатольевна

AU - Беклемишева, Виолетта Робертовна

AU - Перельман, Полина Львовна

AU - Андреюшкова, Дарья Александровна

AU - Марченко, Сергей Александрович

AU - Lemskaya, Natalia A.

AU - Biltueva, Larisa S.

AU - Kliver, Sergei

AU - Трифонов, Владимир Александрович

N1 - Conference code: 14

PY - 2024/8

Y1 - 2024/8

N2 - Motivation and Aim: Сhromosome-length genome assemblies are the gold standard for de novo whole genome sequencing [1–3]. The availability of high-quality vertebrate reference genomes led to significant advances in functional, comparative and population genomics [4, 5]. Problematic steps in constructing a reliable reference genome are the correct orientation of contigs and scaffolds relative to each other and the assembly of superscaffolds into structured chromosomal scaffolds, as well as the sequencing and positioning of genomic regions with repeated sequences or segmental duplications [6–8]. Many of the above problems are overcome by integrating genome sequencing data with cytogenetics data. A combined approach that assembles the genome down to the chromosome level is much more successful in answering fundamental biological questions than genomic or cytogenetic approaches alone [9–11]. Unfortunately, integration of genome sequencing data with cytogenetics data is often not carried out, which leads to inconsistency in chromosome numbering even for species for which standardized karyotypes are available, incorrect orientation of scaffolds, incorrect assessment of chromosome sizes due to failure to take into account heterochromatic blocks, and other problems. The purpose of this work is to draw attention to the importance of understanding and applying a combined approach when performing chromosome-length genome assemblies.

AB - Motivation and Aim: Сhromosome-length genome assemblies are the gold standard for de novo whole genome sequencing [1–3]. The availability of high-quality vertebrate reference genomes led to significant advances in functional, comparative and population genomics [4, 5]. Problematic steps in constructing a reliable reference genome are the correct orientation of contigs and scaffolds relative to each other and the assembly of superscaffolds into structured chromosomal scaffolds, as well as the sequencing and positioning of genomic regions with repeated sequences or segmental duplications [6–8]. Many of the above problems are overcome by integrating genome sequencing data with cytogenetics data. A combined approach that assembles the genome down to the chromosome level is much more successful in answering fundamental biological questions than genomic or cytogenetic approaches alone [9–11]. Unfortunately, integration of genome sequencing data with cytogenetics data is often not carried out, which leads to inconsistency in chromosome numbering even for species for which standardized karyotypes are available, incorrect orientation of scaffolds, incorrect assessment of chromosome sizes due to failure to take into account heterochromatic blocks, and other problems. The purpose of this work is to draw attention to the importance of understanding and applying a combined approach when performing chromosome-length genome assemblies.

M3 - Conference contribution

SN - 978-5-91291-067-8

SP - 25

EP - 28

BT - Bioinformatics of Genome Regulation and Structure Systems Biology (BGRS/SB-2024): The 14th International Multiconference (05-10 August 2024, Novosibirsk, Russia)

PB - Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences

CY - Новосибирск

T2 - Bioinformatics of Genome Regulation and Structure / Systems Biology (BGRS/SB-2024): The 14th International Multiconference

Y2 - 5 August 2024 through 10 August 2024

ER -