NDLI: A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences

Content Provider	Springer Nature : BioMed Central
Author	Nørrevang, Anton Frisgaard Shabala, Sergey Palmgren, Michael
Abstract	Databases of genome sequences are growing exponentially, but, in some cases, assembly is incomplete and genes are poorly annotated. For evolutionary studies, it is important to identify all members of a given gene family in a genome. We developed a method for identifying most, if not all, members of a gene family from raw genomes in which assembly is of low quality, using the P-type ATPase superfamily as an example. The method is based on the translation of an entire genome in all six reading frames and the co-occurrence of two family-specific sequence motifs that are in close proximity to each other. To test the method’s usability, we first used it to identify P-type ATPase members in the high-quality annotated genome of barley (Hordeum vulgare). Subsequently, after successfully identifying plasma membrane H+-ATPase family members (P3A ATPases) in various plant genomes of varying quality, we tested the hypothesis that the number of P3A ATPases correlates with the ability of the plant to tolerate saline conditions. In 19 genomes of glycophytes and halophytes, the total number of P3A ATPase genes was found to vary from 7 to 22, but no significant difference was found between the two groups. The method successfully identified P-type ATPase family members in raw genomes that are poorly assembled.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-023-09859-4.pdf
Ending Page	13
Page Count	13
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-023-09859-4
Journal	BMC Genomics
Issue Number	1
Volume Number	25
Language	English
Publisher	BioMed Central
Publisher Date	2024-01-03
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Fragmented genomes Gene families Halophytes P-type ATPase Plasma membrane H+-ATPase Two-motif
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Unsupervised statistical discovery of spaced motifs in prokaryotic genomes

Evolution of mitochondrial genomes in Baikalian amphipods

Using paired-end sequences to optimise parameters for alignment of sequence reads against related genomes

Identification and analysis of gene families from the duplicated genome of soybean using EST sequences

Mitochondrial genomes of two Sinochloraspecies (Orthoptera): novel genome rearrangements and recognition sequence of replication origin

Inference of transcriptional regulation using gene expression data from the bovine and human genomes

Systematic identification of stem-loop containing sequence families in bacterial genomes

IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes

TREC-IN: gene knock-in genetic tool for genomes cloned in yeast

A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences

Similar Documents

Unsupervised statistical discovery of spaced motifs in prokaryotic genomes

Evolution of mitochondrial genomes in Baikalian amphipods

Using paired-end sequences to optimise parameters for alignment of sequence reads against related genomes

Identification and analysis of gene families from the duplicated genome of soybean using EST sequences

Mitochondrial genomes of two Sinochloraspecies (Orthoptera): novel genome rearrangements and recognition sequence of replication origin

Inference of transcriptional regulation using gene expression data from the bovine and human genomes

Systematic identification of stem-loop containing sequence families in bacterial genomes

IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes

TREC-IN: gene knock-in genetic tool for genomes cloned in yeast

A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences