PMID- 33561960
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20240331
IS  - 2075-4450 (Print)
IS  - 2075-4450 (Electronic)
IS  - 2075-4450 (Linking)
VI  - 12
IP  - 2
DP  - 2021 Feb 6
TI  - A Gene-Based Method for Cytogenetic Mapping of Repeat-Rich Mosquito Genomes.
LID - 10.3390/insects12020138 [doi]
LID - 138
AB  - Long-read sequencing technologies have opened up new avenues of research on the 
      mosquito genome biology, enabling scientists to better understand the remarkable 
      abilities of vectors for transmitting pathogens. Although new genome mapping 
      technologies such as Hi-C scaffolding and optical mapping may significantly 
      improve the quality of genomes, only cytogenetic mapping, with the help of 
      fluorescence in situ hybridization (FISH), connects genomic scaffolds to a 
      particular chromosome and chromosome band. This mapping approach is important for 
      creating and validating chromosome-scale genome assemblies for mosquitoes with 
      repeat-rich genomes, which can potentially be misassembled. In this study, we 
      describe a new gene-based physical mapping approach that was optimized using the 
      newly assembled Aedes albopictus genome, which is enriched with transposable 
      elements. To avoid amplification of the repetitive DNA, 15 protein-coding gene 
      transcripts were used for the probe design. Instead of using genomic DNA, 
      complementary DNA was utilized as a template for development of the PCR-amplified 
      probes for FISH. All probes were successfully amplified and mapped to specific 
      chromosome bands. The genome-unique probes allowed to perform unambiguous mapping 
      of genomic scaffolds to chromosome regions. The method described in detail here 
      can be used for physical genome mapping in other insects.
FAU - Masri, Reem A
AU  - Masri RA
AUID- ORCID: 0000-0002-9077-9008
AD  - Department of Entomology and the Fralin Life Sciences Institute, Virginia 
      Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
FAU - Karagodin, Dmitriy A
AU  - Karagodin DA
AUID- ORCID: 0000-0002-2064-3738
AD  - Laboratory of Evolutionary Genomics of Insects, The Federal Research Center 
      Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of 
      Sciences, 630090 Novosibirsk, Russia.
FAU - Sharma, Atashi
AU  - Sharma A
AD  - Department of Biochemistry and the Fralin Life Sciences Institute, Virginia 
      Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
FAU - Sharakhova, Maria V
AU  - Sharakhova MV
AUID- ORCID: 0000-0002-5790-3548
AD  - Department of Entomology and the Fralin Life Sciences Institute, Virginia 
      Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
AD  - Laboratory of Evolutionary Genomics of Insects, The Federal Research Center 
      Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of 
      Sciences, 630090 Novosibirsk, Russia.
LA  - eng
GR  - R21 AI135258/AI/NIAID NIH HHS/United States
GR  - R21AI135258/NH/NIH HHS/United States
GR  - numero sign 19-14-00130/Russian Science Foundation/
PT  - Journal Article
DEP - 20210206
PL  - Switzerland
TA  - Insects
JT  - Insects
JID - 101574235
PMC - PMC7916018
OTO - NOTNLM
OT  - DNA hybridization
OT  - genome
OT  - physical mapping
COIS- The authors declare no competing interest.
EDAT- 2021/02/11 06:00
MHDA- 2021/02/11 06:01
PMCR- 2021/02/06
CRDT- 2021/02/10 01:00
PHST- 2020/12/08 00:00 [received]
PHST- 2021/01/19 00:00 [revised]
PHST- 2021/02/01 00:00 [accepted]
PHST- 2021/02/10 01:00 [entrez]
PHST- 2021/02/11 06:00 [pubmed]
PHST- 2021/02/11 06:01 [medline]
PHST- 2021/02/06 00:00 [pmc-release]
AID - insects12020138 [pii]
AID - insects-12-00138 [pii]
AID - 10.3390/insects12020138 [doi]
PST - epublish
SO  - Insects. 2021 Feb 6;12(2):138. doi: 10.3390/insects12020138.