Expansions and contractions of the inverted repeat,as well as gene loss and potential pseudogenization shape plastome evolution in Hechtioideae(Bromeliaceae,Poales)

Ivón M.Ramírez-Morillo ¹Laura A.Espinosa-Barrera ²Carolina Granados Mendoza ³Sandra I.Vera-Paz ⁴Daniel D.Díaz Contreras Díaz ⁴Katya J.Romero-Soler⁵

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作者信息

1. Unidad de Recursos Naturales,Centro de Investigación Científica de Yucatán A.C.,Mérida 97205,Yucatán,Mexico
2. Unidad de Recursos Naturales,Centro de Investigación Científica de Yucatán A.C.,Mérida 97205,Yucatán,Mexico;Laboratorio de Agrobiotecnología,Tecnoparque CLQ,Universidad de Colima,Colima 28629,Mexico
3. Departamento de Botánica,Instituto de Biología,Universidad Nacional Autónoma de México,Coyoacán,Mexico City 04510,Mexico
4. Departamento de Botánica,Instituto de Biología,Universidad Nacional Autónoma de México,Coyoacán,Mexico City 04510,Mexico;Posgrado en Ciencias Biológicas,Universidad Nacional Autónoma de México,Coyoacán,Mexico City 04510,Mexico
5. Unidad de Recursos Naturales,Centro de Investigación Científica de Yucatán A.C.,Mérida 97205,Yucatán,Mexico;Departamento de Botánica,Instituto de Biología,Universidad Nacional Autónoma de México,Coyoacán,Mexico City 04510,Mexico
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Abstract

Full plastomes have recently proven to be a valuable data source for resolving recalcitrant phylogenetic relationships in the flowering plant family Bromeliaceae.The study of complete plastomes has additionally led to the discovery of new structural rearrangements and advanced our understanding of bromeliad plastome diversity and evolution.Here,we focus on the study of full plastomes of the bromeliad subfamily Hechtioideae to assess phylogenetic relationships,marker informativeness,and plastome structure and evolution.Using whole-genome sequencing data,we de novo assembled and annotated new plastid genomes of 19 Hechtioideae species plus one representative each from the Pitcairnioideae and Puyoideae subfamilies and compared them with four additional available plastomes from other bromeliad subfamilies.Our phylogenetic analysis using complete plastome sequences not only recovered the three currently recognized genera of Hechtioideae as monophyletic,strongly supporting Mesoamerantha as sister of Bakerantha and Hechtia,but also improved statistical support at different phylogenetic depths within the subfamily.We identified a set of highly informative loci,some of them explored for the first time in Hechtioideae.Structural rearrangements,including expansions and contractions of the inverted repeats,large inversions,and gene loss and potential pseudogenization were detected mainly within the genus Hechtia.Evolutionary trait rate shifts were associated with the size and guanine-cytosine content of the small single copy and inverted repeats.

Key words

Bromeliaceae/Hechtioideae/ndh gene family/phylogenetic informativeness/phylogenomics/plastid genome/structural rearrangements

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基金项目

the"Consejo Nacional de Ciencia y Tecnología"(CONACYT)projects(183281)

the"Consejo Nacional de Ciencia y Tecnología"(CONACYT)projects(283357)

UNAM-DGAPA-PAPIIT project(IA202319)

Investigación Científica Básica,Consejo Nacional de Ciencia y Tecnología(CONACYT)(286249)

CONACYT for fellowship(391947)

Dirección General de Asuntos del Personal Académico(DGAPA-UNAM,)(2022-2023)()

master scholarship from CONACYT(750269)

master scholarship from CONACYT(756019)

master scholarship from CONACYT(respectively)

出版年

2024

植物分类学报

中国科学院植物研究所　中国植物学会

植物分类学报

CSTPCD

影响因子：0.322

ISSN：1674-4918

参考文献量1

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