PMID- 30717300 OWN - NLM STAT- MEDLINE DCOM- 20191220 LR - 20231006 IS - 2073-4425 (Print) IS - 2073-4425 (Electronic) IS - 2073-4425 (Linking) VI - 10 IP - 2 DP - 2019 Feb 1 TI - Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species. LID - 10.3390/genes10020113 [doi] LID - 113 AB - Repetitive DNA including tandem repeats (TRs) is a significant part of most eukaryotic genomes. TRs include rapidly evolving satellite DNA (satDNA) that can be shared by closely related species, their abundance may be associated with evolutionary divergence, and they have been widely used for chromosome karyotyping using fluorescence in situ hybridization (FISH). The recent progress in the development of whole-genome sequencing and bioinformatics tools enables rapid and cost-effective searches for TRs including satDNA that can be converted into molecular cytogenetic markers. In the case of closely related taxa, the genome sequence of one species (donor) can be used as a base for the development of chromosome markers for related species or genomes (target). Here, we present a pipeline for rapid and high-throughput screening for new satDNA TRs in whole-genome sequencing of the donor genome and the development of chromosome markers based on them that can be applied in the target genome. One of the main peculiarities of the developed pipeline is that preliminary estimation of TR abundance using qPCR and ranking found TRs according to their copy number in the target genome; it facilitates the selection of the most prospective (most abundant) TRs that can be converted into cytogenetic markers. Another feature of our pipeline is the probe preparation for FISH using PCR with primers designed on the aligned TR unit sequences and the genomic DNA of a target species as a template that enables amplification of a whole pool of monomers inherent in the chromosomes of the target species. We demonstrate the efficiency of the developed pipeline by the example of FISH probes developed for A, B, and R subgenome chromosomes of hexaploid triticale (BBAARR) based on a bioinformatics analysis of the D genome of Aegilops tauschii (DD) whole-genome sequence. Our pipeline can be used to develop chromosome markers in closely related species for comparative cytogenetics in evolutionary and breeding studies. FAU - Kroupin, Pavel AU - Kroupin P AUID- ORCID: 0000-0001-6858-3941 AD - Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia. pavelkroupin1985@gmail.com. AD - Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia. pavelkroupin1985@gmail.com. FAU - Kuznetsova, Victoria AU - Kuznetsova V AD - Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia. vika-kuz367@yandex.ru. AD - Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia. vika-kuz367@yandex.ru. FAU - Romanov, Dmitry AU - Romanov D AD - Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia. akabos1987@gmail.com. FAU - Kocheshkova, Alina AU - Kocheshkova A AD - Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia. alina.korotaeva@gmail.com. FAU - Karlov, Gennady AU - Karlov G AUID- ORCID: 0000-0002-9016-103X AD - Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia. karlovg@gmail.com. FAU - Dang, Thi Xuan AU - Dang TX AD - Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia. xuxu.dang91@gmail.com. FAU - Khuat, Thi Mai L AU - Khuat TML AD - Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia. hoamoclantt_36@yahoo.com. FAU - Kirov, Ilya AU - Kirov I AD - Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia. kirovez@gmail.com. FAU - Alexandrov, Oleg AU - Alexandrov O AD - Laboratory of Plant Cell Engineering, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia. olegsandrov@gmail.com. FAU - Polkhovskiy, Alexander AU - Polkhovskiy A AD - Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia. polkhovsky.a.w@gmail.com. FAU - Razumova, Olga AU - Razumova O AD - Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia. razumovao@gmail.com. FAU - Divashuk, Mikhail AU - Divashuk M AUID- ORCID: 0000-0001-6221-3659 AD - Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia. divashuk@gmail.com. AD - Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya str. 49, Moscow 127550, Russia. divashuk@gmail.com. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190201 PL - Switzerland TA - Genes (Basel) JT - Genes JID - 101551097 RN - 0 (DNA, Satellite) RN - 0 (Genetic Markers) SB - IM MH - DNA, Satellite MH - Genetic Markers MH - Genotyping Techniques/*methods MH - In Situ Hybridization, Fluorescence/*methods MH - Poaceae/*genetics MH - Polymerase Chain Reaction/methods MH - Polyploidy MH - Tandem Repeat Sequences PMC - PMC6409974 OTO - NOTNLM OT - DNA repeats OT - bioinformatics search OT - cytogenetic markers OT - fluorescence in situ hybridization OT - rye OT - satellite DNA OT - tandem repeats OT - triticale OT - wheat OT - whole-genome sequencing COIS- The authors declare no conflict of interest. EDAT- 2019/02/06 06:00 MHDA- 2019/02/06 06:01 PMCR- 2019/02/01 CRDT- 2019/02/06 06:00 PHST- 2018/12/30 00:00 [received] PHST- 2019/01/23 00:00 [revised] PHST- 2019/01/28 00:00 [accepted] PHST- 2019/02/06 06:00 [entrez] PHST- 2019/02/06 06:00 [pubmed] PHST- 2019/02/06 06:01 [medline] PHST- 2019/02/01 00:00 [pmc-release] AID - genes10020113 [pii] AID - genes-10-00113 [pii] AID - 10.3390/genes10020113 [doi] PST - epublish SO - Genes (Basel). 2019 Feb 1;10(2):113. doi: 10.3390/genes10020113.