Genetic diversity, population structure, and phylogenetic relationships of a widespread East Asia herb, Cryptotaenia japonica Hassk. (Apiaceae) based on genomic SNP data generated by dd-RAD sequencing DOI Creative Commons

Baocheng Wu,

Jun Wen, Ruisen Lu

и другие.

Frontiers in Genetics, Год журнала: 2024, Номер 15

Опубликована: Авг. 14, 2024

Single-nucleotide polymorphisms (SNPs) represent the most prevalent form of genomic polymorphism and are extensively used in population genetics research. Using dd-RAD sequencing, a high-throughput sequencing method, we investigated genome-level diversity, structure, phylogenetic relationships among three morphological forms widely distributed taxon Cryptotaenia japonica Hassk., which is native to East Asia. Our study aimed assess species status C. according its genetic structure diversity patterns 66 naturally populations, comprising 26 f. , 36 dissecta (Y. Yabe) Hara 4 pinnatisecta S. L. Liou accessions. Based on SNP data generated by conducted principal component, neighbor-joining (NJ) phylogenetic, admixture clustering, differentiation analyses. The findings revealed following: (1) 5,39,946 unlinked, high-quality SNPs, with mean π H O, E F IS values 0.062, 0.066, 0.043 −0.014, respectively, were generated; (2) divergence was unaffected isolation through distance; (3) six main distinct regions corresponding geographic locations exhibiting various levels identified; (4) pairwise ST analysis showed significant ( P < 0.05) 0%–14% populations after sequential Bonferroni correction; (5) migration events (historical gene flow) indicated east‒west directionality. Moreover, contemporary flow using Jost’s D, Nei’s G Nm highlighted middle latitude area Asia as contributor structuring . Overall, our elucidates relatively low across Asia, further enhancing understanding plant lineage diversification Sino-Japanese Floristic Region.

Язык: Английский

Study of the Genetic Mechanisms of Siberian Stone Pine (Pinus sibirica Du Tour) Adaptation to the Climatic and Pest Outbreak Stresses Using Dendrogenomic Approach DOI Open Access

Serafima V. Novikova,

Н. В. Орешкова,

Вадим Шаров

и другие.

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(21), С. 11767 - 11767

Опубликована: Ноя. 1, 2024

A joint analysis of dendrochronological and genomic data was performed to identify genetic mechanisms adaptation assess the adaptive potential Siberian stone pine (

Язык: Английский

Процитировано

1
Genetic diversity, population structure, and phylogenetic relationships of a widespread East Asia herb, Cryptotaenia japonica Hassk. (Apiaceae) based on genomic SNP data generated by dd-RAD sequencing DOI Creative Commons

Baocheng Wu,

Jun Wen, Ruisen Lu

и другие.

Frontiers in Genetics, Год журнала: 2024, Номер 15

Опубликована: Авг. 14, 2024

Single-nucleotide polymorphisms (SNPs) represent the most prevalent form of genomic polymorphism and are extensively used in population genetics research. Using dd-RAD sequencing, a high-throughput sequencing method, we investigated genome-level diversity, structure, phylogenetic relationships among three morphological forms widely distributed taxon Cryptotaenia japonica Hassk., which is native to East Asia. Our study aimed assess species status C. according its genetic structure diversity patterns 66 naturally populations, comprising 26 f. , 36 dissecta (Y. Yabe) Hara 4 pinnatisecta S. L. Liou accessions. Based on SNP data generated by conducted principal component, neighbor-joining (NJ) phylogenetic, admixture clustering, differentiation analyses. The findings revealed following: (1) 5,39,946 unlinked, high-quality SNPs, with mean π H O, E F IS values 0.062, 0.066, 0.043 −0.014, respectively, were generated; (2) divergence was unaffected isolation through distance; (3) six main distinct regions corresponding geographic locations exhibiting various levels identified; (4) pairwise ST analysis showed significant ( P < 0.05) 0%–14% populations after sequential Bonferroni correction; (5) migration events (historical gene flow) indicated east‒west directionality. Moreover, contemporary flow using Jost’s D, Nei’s G Nm highlighted middle latitude area Asia as contributor structuring . Overall, our elucidates relatively low across Asia, further enhancing understanding plant lineage diversification Sino-Japanese Floristic Region.

Язык: Английский

Процитировано

0