A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences
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A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences. / Nørrevang, Anton Frisgaard; Shabala, Sergey; Palmgren, Michael.
In: BMC Genomics, Vol. 25, 26, 2024.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences
AU - Nørrevang, Anton Frisgaard
AU - Shabala, Sergey
AU - Palmgren, Michael
N1 - Publisher Copyright: © 2023, The Author(s).
PY - 2024
Y1 - 2024
N2 - 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.
AB - 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.
KW - Fragmented genomes
KW - Gene families
KW - Halophytes
KW - P-type ATPase
KW - Plasma membrane H-ATPase
KW - Two-motif
U2 - 10.1186/s12864-023-09859-4
DO - 10.1186/s12864-023-09859-4
M3 - Journal article
C2 - 38172704
AN - SCOPUS:85181238864
VL - 25
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
M1 - 26
ER -
ID: 380151820