The common bean (Phaseolus vulgaris) is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of P. vulgaris, its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Among the 31 PCGs, four genes (mttB, nad1, nad4L, and rps10) use ACG as initiation codons, which are altered to standard initiation codons by RNA editing. In addition, the termination codon CGA in the ccmF_C gene is converted to UGA. Selective pressure analysis indicates that the ccmB, ccmF_C, rps1, rps10, and rps14 genes were under evolutionary positive selection. The proportions of five amino acids (Phe, Leu, Pro, Arg, and Ser) in the whole amino acid profile of the proteins in each mitogenome can be used to distinguish angiosperms from gymnosperms. Phylogenetic analyses show that P. vulgaris is evolutionarily closer to the Glycininae than other leguminous plants. The results of the present study not only provide an important opportunity to conduct further genomic breeding studies in the common bean, they also provide valuable information for future evolutionary and molecular studies of leguminous plants.

Colonies are the basic geometric building blocks of coral reefs. However, the forming regulations of both colonies and reefs are still not understood adequately. Therefore, in this study, we reconstructed 25 samples using high‐resolution micro‐computed tomography to investigate coral growth patterns and parameters. Our skeleton and canal reconstructions revealed the characteristics of different coral species, and we further visualized the growth axes and growth rings to understand the coral growth directions. We drew a skeleton grayscale map and calculated the coral skeleton void ratios to ascertain the skeletal diversity, devising a method to quantify coral growth. On the basis of the three‐dimensional (3D) reconstructions and growth parameters, we investigated the growth strategies of different coral species. This research increases the breadth of knowledge on how reef‐building corals grow their colonies, providing information on reef‐forming regulations. The data in this paper contain a large amount of coral growth information, which can be used in further research on reef‐forming patterns under different conditions. The method used in this study can also be applied to animals with porous skeletons.

Coral reefs are formed by living polyps, and understanding the dynamic processes behind the reefs is crucial for marine ecosystem restoration. However, these processes are still unclear because the growth and budding patterns of living polyps are poorly known. Here, we investigate the growth pattern of a widely distributed reef-building coral Pocillopora damicornis from Xisha Islands using high-resolution computed tomography. We examine the corallites in a single corallum of the species in detail, to interpret the budding, growth, and distribution pattern of the polyps, to reconstruct the growth pattern of this important reef-building species. Our results reveal a three-stage growth pattern of P. damicornis, based on different growth bundles that are secreted by polyps along the dichotomous growth axes of the corallites. Our work on the three-dimensional reconstruction of calice and inter-septal space structure of P. damicornis sheds lights on its reef-building processes by reconstructing the budding patterns.

Background: Amphioxus is a model organism for vertebrate evolutionary research. The significant contrast between morphological phenotypic similarity and high-level genetic polymorphism among amphioxus populations has aroused scientists' attention. Here we resequenced 21 amphioxus genomes to over 100X depth and mapped them to a haploid reference. Results: More than 11.5 million common SNPs were detected in the amphioxus population, which mainly affect genes enriched in ion transport, signal transduction and cell adhesion, while protein structure analysis via AlphaFold2 revealed that these SNPs fail to bring effective structural variants. Conclusions: Our work provides explanation for “amphioxus polymorphism paradox” in a micro view, and generates an enhanced genomic dataset for amphioxus research.